The DOI matches its Crossref record; 76 of the 76 references it cites were found in a registry or an index; none of the 47 sources its claims cite is checked for support yet.
The human tumor microbiome is composed of tumor type–specific intracellular bacteria
Open accessAbstract
Profiling tumor bacteria: Bacteria are well-known residents in human tumors, but whether their presence is advantageous to the tumors or to the bacteria themselves has been unclear. As an initial step toward addressing this question, Nejman et al. produced an exhaustive catalog of the bacteria present in more than 1500 human tumors representing seven different tumor types (see the Perspective by Atreya and Turnbaugh). They found that the bacteria within tumors were localized within both cancer cells and immune cells and that the bacterial composition varied according to tumor type. Certain biologically plausible associations were identified. For example, breast cancer subtypes characterized by increased oxidative stress were enriched in bacteria that produce mycothiol, which can detoxify reactive oxygen species. Science , this issue p. 973 ; see also p. 938
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“Pathological examination of tumor cores indicated that LPS and bacterial 16S rRNA were localized mainly in cancer cells and immune cells”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
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“Levels of bacterial DNA in all tumor types were significantly higher than those found in both DNA extraction and paraffin controls (Fig. 1B; P value <10−10 for each tumor type, Wilcoxon rank sum test).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Bacterial DNA, RNA, and lipopolysaccharide are present in many human solid tumors
plainn = 1,010 ·- Asserted: passes — The authors put it forward as true.
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“Combined LPS fluorescence staining and transmission electron microscopy (TEM) imaging of the same cells clearly demonstrated the intracellular localization of bacteria in all four tumors”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
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In the paper
“We found that different cancer types vary in the proportion of tumors that are positive for bacterial DNA, ranging from only 14.3% in melanoma to >60% in breast, pancreatic, and bone tumors.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Bacterial DNA, RNA, and lipopolysaccharide are present in many human solid tumors
plaincorrelationaln = 1,010- Asserted: passes — The authors put it forward as true.
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“LTA-positive bacteria were almost exclusively found in macrophages, as detected by hematoxylin and eosin (H&E) staining and verified by immunofluorescence (IF) for CD68”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
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“Although the intensity of bacterial LPS and LTA staining was very strong in CD45+/CD68+ cells, bacterial 16S rRNA was only rarely found in macrophages by FISH”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
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“typical bacterial rods or cocci were only rarely detected (in 3 of 426 cores).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
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“LTA was rarely detected in cancer cells or in CD45+/CD68− immune cells”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
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In the paper
“Bacterial DNA was also detected in solid tumors that have no direct connection with the external environment, such as ovarian cancer, glioblastoma multiforme (GBM), and bone cancer.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Bacterial DNA, RNA, and lipopolysaccharide are present in many human solid tumors
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“In many cases, the bacteria were found in close proximity to the nuclear membrane.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“CD45-positive leukocytes generally exhibited a stronger cytoplasmic bacterial staining by 16S rRNA staining than that exhibited by cancer cells”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“degradation of hydroxyprolines by bacteria (MetaCyc PWY-5159) was enriched in bone tumors (effect size 14.6%, P value <0.01, proportion test).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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- Rests on an assumption: Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We also observed a distinct microbiome across subtypes of the same tumor type.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Overall, we detected 9190 bacterial species across the different tumor or normal tissue types”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Comparison of the beta-diversity between all pairs of samples within a given tumor type and across different tumor types revealed that the microbiomes of tumors of the same type tend to be more similar to each other than they are to the microbiomes of other tumor types”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
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In the paper
“We detected intracellular labeling in all four tumors”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“MetaCyc pathways responsible for the degradation of chemicals in cigarette smoke, such as toluene, acrylonitrile, and aminobenzoates (TOLUENE-DEG-2-OH-PWY, P344-PWY, and PWY-6077), were significantly enriched in bacteria found in lung tumors compared with other tumor types (effect size 8.4, 8, and 7.2%, P value <0.001 for all, proportion test).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Unsupervised clustering analysis of 287 predicted metabolic MetaCyc pathways that showed the greatest variability between the tumor types revealed that certain microbiome metabolic pathways were relatively specific to certain tumor types”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Unsupervised clustering of the most prevalent intratumor bacterial species (n = 137 species) demonstrated that many of these species are enriched in certain tumor types”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
boostedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“We also detected taxa of the Actinobacteria phylum, including the Corynebacteriaceae and Micrococcaceae families, mostly in nongastrointestinal tumors”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
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In the paper
“Fusobacterium nucleatum, previously reported to be enriched in colorectal tumors, was also a hit in our breast and pancreatic tumor cohorts”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Overall, these results show that live bacteria from three main phyla—Proteobacteria, Firmicutes, and Actinobacteria—can be found in breast tumors.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plainn = 5- Asserted: passes — The authors put it forward as true.
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In the paper
“Our results demonstrate that intratumor bacteria span a wide spectrum of the bacterial kingdom.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
boosted- Asserted: passes — The authors put it forward as true.
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In the paper
“we found many bacteria that are significantly enriched in breast tumors compared with their NAT”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“A tumor-type distinctive microbiome composition was also apparent at the species level.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“applying the same steps of tissue dissociation and culturing protocol to five full sets of negative control plates (350 plates) using only phosphate-buffered saline (PBS) yielded only five colonies in total.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plainn = 5- Asserted: passes — The authors put it forward as true.
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In the paper
“In contrast, we did not find a higher bacterial load in lung and ovarian tumors compared with their tumor-adjacent normal tissues”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Tumor-adjacent normal breast tissue had an intermediate bacterial load and richness, between those of the breast tumor and normal samples”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Consistent with previous reports, bacteria belonging to the Firmicutes and Bacteroidetes phyla were the most abundant species in colorectal tumors (Fig. 4B) (10).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
What the sources say
- Not checked yetcites [10] Gao Z, Guo B, Gao R, Zhu Q, Qin H, Microbiota disbiosis is associated with colorectal cancer. Front. Microbiol 6, 20 (2015). doi: 10.3389/fmicb.2015.00020pmid:25699023 25699023 PMC4313696 source
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In the paper
“when comparing different subtypes of breast cancer according to their estrogen receptor (ER), progesterone receptor (PR), and HER2 status, we found multiple bacterial taxa whose prevalence was different between the subtypes”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Rests on an assumption: Breast cancer subtype assignment by ER, PR, and HER2 status is accurate.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We found that breast tumors had a richer and more diverse microbiome than all other tumor types tested (P value <10−15 for each tumor type, Wilcoxon rank sum test”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“The distribution of order-level phylotypes revealed marked changes between the bacterial composition of the different tumor types”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“enzymes related to anaerobic respiration were enriched in bacteria from breast cancer versus NAT.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Although we did not find significant changes in the load of bacteria between responders and nonresponders to ICI”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plainn = 48- Asserted: passes — The authors put it forward as true.
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- Rests on an assumption: The classification of melanoma patients as responders or nonresponders to immune checkpoint inhibitors is accurate.
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In the paper
“Using multiple visualization methods and culturomics, we were able to validate the presence of bacteria in the tumors and demonstrate their intracellular localization in both cancer and immune cells.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Discussion
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In the paper
“Extending our analysis to the functional level demonstrated that, despite a very large variation in taxa levels, certain tumor environments are enriched for common, relevant bacterial functional traits.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Discussion
boostedcorrelationaln = 1,526- Asserted: passes — The authors put it forward as true.
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In the paper
“The exploration of multiple tumor types with a single platform allowed us to compare different tumor types and uncover cancer type–specific microbial signatures.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Discussion
plaincorrelationaln = 1,526- Asserted: passes — The authors put it forward as true.
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In the paper
“We also found eight MetaCyc pathways related to the biosynthesis of metabolites that can be used by plants—for example, for the biosynthesis of glycine, a key intermediate in plant photorespiration”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
- Rests on an assumption: Patients' smoking status was accurately recorded.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The most significantly enriched pathways in bacteria within ER+ breast tumors were arsenate detoxification and mycothiol biosynthesis.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
- Rests on an assumption: Breast cancer subtype assignment by ER, PR, and HER2 status is accurate.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We found that 17 of the 49 MetaCyc pathways that were significantly enriched in tumors of current smokers were pathways that degrade chemicals found in cigarette smoke, such as nicotine, anthranilate, toluene, and phenol”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
- Rests on an assumption: Patients' smoking status was accurately recorded.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“which can explain the high similarity we found between the tumor microbiome and its NAT microbiome.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Discussion
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“However, none of these bacteria reached significance after correction for multiple-hypothesis testing”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plainn = 100- Asserted: passes — The authors put it forward as true.
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- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Patients' smoking status was accurately recorded.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“multiple MetaCyc pathways were enriched in bacteria from 270 ER+ breast tumors compared with 49 ER− breast tumors”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
- Rests on an assumption: Breast cancer subtype assignment by ER, PR, and HER2 status is accurate.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We were able to demonstrate that a very large number of heterogeneous bacteria contribute to the degradation functions of cigarette smoke metabolites and the biosynthesis of plant metabolites”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
boosteddirectn = 100- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
- Rests on an assumption: Patients' smoking status was accurately recorded.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our data do not establish whether intratumor bacteria play a causal role in the development of cancer or whether their presence simply reflects infections of established tumors (60, 61).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Discussion
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we did find multiple taxa that were differentially more (n = 18) or less (n = 28) abundant in the melanomas of responders compared with nonresponders”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plaincorrelationaln = 29- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: The classification of melanoma patients as responders or nonresponders to immune checkpoint inhibitors is accurate.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Using multiple visualization methods and culturomics, we were able to validate the presence of bacteria in the tumors and demonstrate their intracellular localization in both cancer and immune cells.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Discussion
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We found that most of the enriched taxa in the lung tumors of smokers belong to the Proteobacteria phylum.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plaincorrelationaln = 100- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Patients' smoking status was accurately recorded.
In the paper
“but these bacteria have not been characterized in a comprehensive manner (20)”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Abstract
What the sources say
- Not checked yetcites [20] Goodman B, Gardner H, The microbiome and cancer. J. Pathol 244, 667– 676 (2018).doi: 10.1002/path.5047pmid:29377130 29377130 source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“Because the tumor microbiome has a relatively low biomass, contamination of the tumor samples with bacteria or bacterial DNA can be problematic (30, 31).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Bacterial DNA, RNA, and lipopolysaccharide are present in many human solid tumors
What the sources say
- Not checked yetcites [30] Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW, Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014). doi: 10.1186/s12915-014-0087-zpmid:25387460 25387460 PMC4228153 source
- Not checked yetcites [31] Eisenhofer R, Minich JJ, Marotz C, Cooper A, Knight R, Weyrich LS, Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations. Trends Microbiol. 27, 105– 117 (2019). doi: 10.1016/j.tim.2018.11.003pmid:30497919 30497919 source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“filter 1 removed 167 bacterial species that were detected in >7.5% of our DNA extraction and NTC negative control samples or in the paraffin controls.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“This may reflect a retrograde bacterial migration from the duodenum, to which the pancreatic duct opens, as we have previously reported (16).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
What the sources say
- Not checked yetcites [16] Geller LT, Barzily-Rokni M, Danino T, Jonas OH, Shental N, Nejman D, Gavert N, Zwang Y, Cooper ZA, Shee K, Thaiss CA, Reuben A, Livny J, Avraham R, Frederick DT, Ligorio M, Chatman K, Johnston SE, Mosher CM, Brandis A, Fuks G, Gurbatri C, Gopalakrishnan V, Kim M, Hurd MW, Katz M, Fleming J, Maitra A, Smith DA, Skalak M, Bu J, Michaud M, Trauger SA, Barshack I, Golan T, Sandbank J, Flaherty KT, Mandinova A, Garrett WS, Thayer SP, Ferrone CR, Huttenhower C, Bhatia SN, Gevers D, Wargo JA, Golub TR, Straussman R, Potential role of intratumor bacteria in mediating tumor resistance to the chemothera source
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“which supports the hypothesis that the tumors harbor live intracellular bacteria”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our TEM images also suggest that many of the intracellular bacteria lack a cell wall”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“which indicates that there was no homogeneous population of species conferring this functionality across samples.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
hedgedn = 100- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Patients' smoking status was accurately recorded.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Overall, our analysis of MetaCyc pathways suggests a connection between the functions of bacteria present in the tumor and their tumor microenvironment.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
In the paper
“Mycothiol is used by bacteria to detoxify reactive oxygen species (56).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
What the sources say
- Not checked yetcites [56] Reyes AM, Pedre B, De Armas MI, Tossounian M-A, Radi R, Messens J, Trujillo M, Chemistry and Redox Biology of Mycothiol. Antioxid. Redox Signal 28, 487– 504 (2018).doi: 10.1089/ars.2017.7074pmid:28372502 28372502 source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- It may state two separate claims as one. 20
- Probably not a substantial claim. 22
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Bacterial LPS and 16S rRNA were frequently detected in all tumor types (Fig. 1C) and demonstrated a similar spatial distribution”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Bacterial DNA, RNA, and lipopolysaccharide are present in many human solid tumors
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In cancer cells, bacterial 16S rRNA was detected mostly in the cytoplasm, whereas LPS staining was associated with both the cytoplasm and the nucleus”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“LTA was detected mainly in melanomas and was largely absent in other tumor types.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Bacterial DNA, RNA, and lipopolysaccharide are present in many human solid tumors
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Fifteen isolated species (40.5%) were detected in our breast tumor cohort but did not pass all filters.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plainn = 5- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“An average of 16.4 bacterial species were detected in any single breast tumor sample, whereas the average was <9 in all other tumor types (P value <10−17 for each tumor type, Wilcoxon rank sum test”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Although species belonging to the Proteobacteria and Firmicutes phyla accounted for most of the detected bacterial sequences in all cancer types, the Proteobacteria to Firmicutes (P/F) ratio appears to vary between tumor types”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“>1000 colonies were grown per tumor from four of the tumors, and 37 colonies were grown from one tumor.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plainn = 5- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“although the overall microbial composition of the different tumor types was relatively similar to their NAT microbiome (Fig. 4F), we also detected bacteria with a different prevalence in tumors and in their NAT”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We also found that bacterial load and richness were higher in the breast tumor samples than those found in normal breast samples from healthy subjects.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Whole-genome sequencing of 474 representative colonies from all five tumors demonstrated that they represented 37 different bacterial species, 11 of which (29.7%) are bacteria that were previously detected as hits in our breast tumor cohort”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
boostedn = 5- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“In contrast, Proteobacteria dominated the microbiome of pancreatic cancer, similarly to the normal duodenal microbiome makeup (16, 17, 48, 49).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Different tumor types have distinct microbial compositions
What the sources say
- Not checked yetcites [16] Geller LT, Barzily-Rokni M, Danino T, Jonas OH, Shental N, Nejman D, Gavert N, Zwang Y, Cooper ZA, Shee K, Thaiss CA, Reuben A, Livny J, Avraham R, Frederick DT, Ligorio M, Chatman K, Johnston SE, Mosher CM, Brandis A, Fuks G, Gurbatri C, Gopalakrishnan V, Kim M, Hurd MW, Katz M, Fleming J, Maitra A, Smith DA, Skalak M, Bu J, Michaud M, Trauger SA, Barshack I, Golan T, Sandbank J, Flaherty KT, Mandinova A, Garrett WS, Thayer SP, Ferrone CR, Huttenhower C, Bhatia SN, Gevers D, Wargo JA, Golub TR, Straussman R, Potential role of intratumor bacteria in mediating tumor resistance to the chemothera source
- Not checked yetcites [17] Pushalkar S, Hundeyin M, Daley D, Zambirinis CP, Kurz E, Mishra A, Mohan N, Aykut B, Usyk M, Torres LE, Werba G, Zhang K, Guo Y, Li Q, Akkad N, Lall S, Wadowski B, Gutierrez J, Kochen Rossi JA, Herzog JW, Diskin B, Torres-Hernandez A, Leinwand J, Wang W, Taunk PS, Savadkar S, Janal M, Saxena A, Li X, Cohen D, Sartor RB, Saxena D, Miller G, The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression. Cancer Discov. 8, 403– 416 (2018).doi: 10.1158/2159-8290.CD-17-1134pmid:29567829 29567829 PMC6225783 source
- Not checked yetcites [48] Ou G, Hedberg M, Hörstedt P, Baranov V, Forsberg G, Drobni M, Sandström O, Nyunt Wai S, Johansson I, Hammarström M-L, Hernell O, Hammarström S, Proximal small intestinal microbiota and identification of rod-shaped bacteria associated with childhood celiac disease. Am. J. Gastroenterol 104, 3058– 3067 (2009). doi: 10.1038/ajg.2009.524pmid:19755974 19755974 source
- Not checked yetcites [49] Nistal E, Caminero A, Herrán AR, Arias L, Vivas S, de Morales JMR, Calleja S, de Miera LES, Arroyo P, Casqueiro J, Differences of small intestinal bacteria populations in adults and children with/without celiac disease: Effect of age, gluten diet, and disease. Inflamm. Bowel Dis 18, 649– 656(2012). doi: 10.1002/ibd.21830pmid:21826768 21826768 source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Bacteria expressing these functions are found mainly in the Proteobacteria, Actinobacteria, and Cyanobacteria phyla, and they are depleted from the Firmicutes phylum”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plaincorrelationaln = 100- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Rests on an assumption: Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
- Rests on an assumption: Patients' smoking status was accurately recorded.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Taxa that were more abundant in tumors of responders included Clostridium, whereas Gardnerella vaginalis was more abundant in tumors of nonresponders.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plaincorrelationaln = 29- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Rests on an assumption: The classification of melanoma patients as responders or nonresponders to immune checkpoint inhibitors is accurate.
None of the sources cited for this claim have been checked yet.
In the paper
“Intratumor bacteria have been reported in many tumor types (2-19)”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Abstract
What the sources say
- Not checked yetcites [2] Xuan C, Shamonki JM, Chung A, Dinome ML, Chung M, Sieling PA, Lee DJ, Microbial dysbiosis is associated with human breast cancer. PLOS ONE 9, e83744 (2014).doi: 10.1371/journal.pone.0083744pmid:24421902 24421902 PMC3885448 source
- Not checked yetcites [3] Thompson KJ, Ingle JN, Tang X, Chia N, Jeraldo PR, Walther-Antonio MR, Kandimalla KK, Johnson S, Yao JZ, Harrington SC, Suman VJ, Wang L, Weinshilboum RL, Boughey JC, Kocher J-P, Nelson H, Goetz MP, Kalari KR, A comprehensive analysis of breast cancer microbiota and host gene expression. PLOS ONE 12, e0188873 (2017). doi: 10.1371/journal.pone.0188873pmid:29190829 29190829 PMC5708741 source
- Not checked yetcites [4] Banerjee S, Tian T, Wei Z, Shih N, Feldman MD, Peck KN, DeMichele AM, Alwine JC, Robertson ES, Distinct Microbial Signatures Associated With Different Breast Cancer Types. Front. Microbiol 9, 951 (2018). doi: 10.3389/fmicb.2018.00951pmid:29867857 29867857 PMC5962706 source
- Not checked yetcites [5] Costantini L, Magno S, Albanese D, Donati C, Molinari R, Filippone A, Masetti R, Merendino N, Characterization of human breast tissue microbiota from core needle biopsies through the analysis of multi hypervariable 16S-rRNA gene regions. Sci. Rep 8, 16893 (2018). doi: 10.1038/s41598-018-35329-z pmid:30442969 30442969 PMC6237987 source
- Not checked yetcites [6] Greathouse KL, White JR, Vargas AJ, Bliskovsky VV, Beck JA, von Muhlinen N, Polley EC, Bowman ED, Khan MA, Robles AI, Cooks T, Ryan BM, Padgett N, Dzutsev AH, Trinchieri G, Pineda MA, Bilke S, Meltzer PS, Hokenstad AN, Stickrod TM, Walther-Antonio MR, Earl JP, Mell JC, Krol JE, Balashov SV, Bhat AS, Ehrlich GD, Valm A, Deming C, Conlan S, Oh J, Segre JA, Harris CC, Interaction between the microbiome and TP53 in human lung cancer. Genome Biol. 19, 123 (2018).doi: 10.1186/s13059-018-1501-6 pmid:30143034 30143034 PMC6109311 source
- Not checked yetcites [7] Peters BA, Hayes RB, Goparaju C, Reid C, Pass HI, Ahn J, The Microbiome in Lung Cancer Tissue and Recurrence-Free Survival. Cancer Epidemiol. Biomark. Prev 28, 731– 740 (2019). doi: 10.1158/1055-9965.EPI-18-0966 pmid:30733306 PMC6449216 30733306 source
- Not checked yetcites [8] Apostolou P, Tsantsaridou A, Papasotiriou I, Toloudi M, Chatziioannou M, Giamouzis G, Bacterial and fungal microflora in surgically removed lung cancer samples. J. Cardiothorac. Surg 6, 137 (2011).doi: 10.1186/1749-8090-6-137 pmid:21999143 21999143 PMC3212932 source
- Not checked yetcites [9] Banerjee S, Tian T, Wei Z, Shih N, Feldman MD, Alwine JC, Coukos G, Robertson ES, The ovarian cancer oncobiome. Oncotarget 8, 36225– 36245 (2017). doi: 10.18632/oncotarget.16717 pmid:28410234 28410234 PMC5482651 source
- Not checked yetcites [10] Gao Z, Guo B, Gao R, Zhu Q, Qin H, Microbiota disbiosis is associated with colorectal cancer. Front. Microbiol 6, 20 (2015). doi: 10.3389/fmicb.2015.00020pmid:25699023 25699023 PMC4313696 source
- Not checked yetcites [11] Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, Holt RA, Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res. 22, 299– 306 (2012). doi: 10.1101/gr.126516.111pmid:22009989 22009989 PMC3266037 source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“This observation, combined with the fact that no cell wall polymer LTA was detected in cancer cells—despite the detection of many Gram-positive bacteria in human tumors by 16S rDNA sequencing—suggests that bacteria in tumor cells may have altered their envelope, perhaps leading to a cell wall–deficient state, akin to L-forms (41).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
What the sources say
- Not checked yetcites [41] Klieneberger-Nobel E, Origin, development and significance of L-forms in bacterial cultures. J. Gen. Microbiol 3, 434– 443 (1949). doi: 10.1099/00221287-3-3-434pmid:18147756 18147756 source
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“it is also important to use mechanical tissue shearing in the DNA isolation protocol to ensure the complete recovery of DNA from within the cell wall of Gram-positive bacteria—a step not included in most standard DNA isolation protocols (6, 7).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Bacterial DNA, RNA, and lipopolysaccharide are present in many human solid tumors
What the sources say
- Not checked yetcites [6] Greathouse KL, White JR, Vargas AJ, Bliskovsky VV, Beck JA, von Muhlinen N, Polley EC, Bowman ED, Khan MA, Robles AI, Cooks T, Ryan BM, Padgett N, Dzutsev AH, Trinchieri G, Pineda MA, Bilke S, Meltzer PS, Hokenstad AN, Stickrod TM, Walther-Antonio MR, Earl JP, Mell JC, Krol JE, Balashov SV, Bhat AS, Ehrlich GD, Valm A, Deming C, Conlan S, Oh J, Segre JA, Harris CC, Interaction between the microbiome and TP53 in human lung cancer. Genome Biol. 19, 123 (2018).doi: 10.1186/s13059-018-1501-6 pmid:30143034 30143034 PMC6109311 source
- Not checked yetcites [7] Peters BA, Hayes RB, Goparaju C, Reid C, Pass HI, Ahn J, The Microbiome in Lung Cancer Tissue and Recurrence-Free Survival. Cancer Epidemiol. Biomark. Prev 28, 731– 740 (2019). doi: 10.1158/1055-9965.EPI-18-0966 pmid:30733306 PMC6449216 30733306 source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“we introduced 643 negative controls that were processed with the samples, including 437 DNA extraction controls and 206 polymerase chain reaction (PCR) no-template controls (NTCs).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Bacterial DNA, RNA, and lipopolysaccharide are present in many human solid tumors
plainn = 643- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
In the paper
“It has been previously demonstrated that the processing of bacterial LPS by macrophages is very slow; therefore, LPS can be found in these cells months after the bacteria were ingested and processed (38).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
What the sources say
- Not checked yetcites [38] Forestier C, Moreno E, Pizarro-Cerda J, Gorvel JP, Lysosomal accumulation and recycling of lipopolysaccharide to the cell surface of murine macrophages, an in vitro and in vivo study. J. Immunol 162, 6784– 6791 (1999). pmid:10352299 10352299 source
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“we also included 168 paraffin-only samples taken from the margins of the paraffin blocks (without tissue) that were used in the study”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Bacterial DNA, RNA, and lipopolysaccharide are present in many human solid tumors
plainn = 168- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“The gut microbiome has been shown to have multiple effects on tumor biology, such as the transformation process, tumor progression, and the response to anticancer therapies including immunotherapy (21-29).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Abstract
What the sources say
- Not checked yetcites [21] Wong SH, Zhao L, Zhang X, Nakatsu G, Han J, Xu W, Xiao X, Kwong TNY, Tsoi H, Wu WKK, Zeng B, Chan FKL, Sung JJY, Wei H, Yu J, Gavage of Fecal Samples From Patients With Colorectal Cancer Promotes Intestinal Carcinogenesis in Germ-Free and Conventional Mice. Gastroenterology 153, 1621– 1633.e6 (2017). doi: 10.1053/j.gastro.2017.08.022pmid:28823860 28823860 source
- Not checked yetcites [22] Kostic AD, Chun E, Robertson L, Glickman JN, Gallini CA, Michaud M, Clancy TE, Chung DC, Lochhead P, Hold GL, El-Omar EM, Brenner D, Fuchs CS, Meyerson M, Garrett WS, Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe 14, 207– 215 (2013). doi: 10.1016/j.chom.2013.07.007pmid:23954159 23954159 PMC3772512 source
- Not checked yetcites [23] Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC, Karpinets TV, Prieto PA, Vicente D, Hoffman K, Wei SC, Cogdill AP, Zhao L, Hudgens CW, Hutchinson DS, Manzo T, Petaccia de Macedo M, Cotechini T, Kumar T, Chen WS, Reddy SM, Szczepaniak Sloane R, Galloway-Pena J, Jiang H, Chen PL, Shpall EJ, Rezvani K, Alousi AM, Chemaly RF, Shelburne S, Vence LM, Okhuysen PC, Jensen VB, Swennes AG, McAllister F, Marcelo Riquelme Sanchez E, Zhang Y, Le Chatelier E, Zitvogel L, Pons N, Austin-Breneman JL, Haydu LE, Burton EM, Gardner JM, Sirmans E, Hu J, Lazar AJ, Tsujikawa T, Diab A, Tawbi H, Glitza I source
- Not checked yetcites [24] Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y, Alegre M-L, Luke JJ, Gajewski TF, The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Science 359, 104– 108(2018). doi: 10.1126/science.aao3290pmid:29302014 29302014 PMC6707353 source
- Not checked yetcites [25] Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daillère R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP, Fidelle M, Flament C, Poirier-Colame V, Opolon P, Klein C, Iribarren K, Mondragón L, Jacquelot N, Qu B, Ferrere G, Clémenson C, Mezquita L, Masip JR, Naltet C, Brosseau S, Kaderbhai C, Richard C, Rizvi H, Levenez F, Galleron N, Quinquis B, Pons N, Ryffel B, Minard-Colin V, Gonin P, Soria J-C, Deutsch E, Loriot Y, Ghiringhelli F, Zalcman G, Goldwasser F, Escudier B, Hellmann MD, Eggermont A, Raoult D, Albiges L, Kroemer G, Zitvogel L, Gut microbiome influences efficacy of PD-1-ba source
- Not checked yetcites [26] Viaud S, Saccheri F, Mignot G, Yamazaki T, Daillère R, Hannani D, Enot DP, Pfirschke C, Engblom C, Pittet MJ, Schlitzer A, Ginhoux F, Apetoh L, Chachaty E, Woerther P-L, Eberl G, Bérard M, Ecobichon C, Clermont D, Bizet C, Gaboriau-Routhiau V, Cerf-Bensussan N, Opolon P, Yessaad N, Vivier E, Ryffel B, Elson CO, Doré J, Kroemer G, Lepage P, Boneca IG, Ghiringhelli F, Zitvogel L, The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide. Science 342, 971– 976 (2013).doi: 10.1126/science.1240537pmid:24264990 24264990 PMC4048947 source
- Not checked yetcites [27] Iida N, Dzutsev A, Stewart CA, Smith L, Bouladoux N, Weingarten RA, Molina DA, Salcedo R, Back T, Cramer S, Dai R-M, Kiu H, Cardone M, Naik S, Patri AK, Wang E, Marincola FM, Frank KM, Belkaid Y, Trinchieri G, Goldszmid RS, Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment. Science 342, 967 970 (2013). doi: 10.1126/science.1240527pmid:24264989 24264989 PMC6709532 source
- Not checked yetcites [28] Helmink BA, Khan MAW, Hermann A, Gopalakrishnan V, Wargo JA, The microbiome, cancer, and cancer therapy. Nat. Med 25, 377– 388 (2019). doi: 10.1038/s41591-019-0377-7pmid:30842679 30842679 source
- Not checked yetcites [29] Rutkowski MR, Stephen TL, Svoronos N, Allegrezza MJ, Tesone AJ, Perales-Puchalt A, Brencicova E, Escovar-Fadul X, Nguyen JM, Cadungog MG, Zhang R, Salatino M, Tchou J, Rabinovich GA, Conejo-Garcia JR, Microbially driven TLR5-dependent signaling governs distal malignant progression through tumor-promoting inflammation. Cancer Cell 27, 27– 40 (2015). doi: 10.1016/j.ccell.2014.11.009pmid:25533336 25533336 PMC4293269 source
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“To control for nonspecific staining, IHC-negative controls (no primary antibody) and FISH-negative controls (nonspecific complement probe) were also applied to the samples”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Bacterial DNA, RNA, and lipopolysaccharide are present in many human solid tumors
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Moreover, it can be applied to partially degraded DNA originating from formalin-fixed paraffin-embedded tumors.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“we applied a strict set of six filters to control for potential sources of contamination.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
In the paper
“Although D-alanine is used by bacteria to generate peptidoglycan, an essential component of the bacterial cell wall, it is not used by mammalian cells (fig. S14) (47).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
What the sources say
- Not checked yetcites [47] Siegrist MS, Whiteside S, Jewett JC, Aditham A, Cava F, Bertozzi CR, (D)-Amino acid chemical reporters reveal peptidoglycan dynamics of an intracellular pathogen. ACS Chem. Biol 8, 500– 505 (2013).doi: 10.1021/cb3004995pmid:23240806 23240806 PMC3601600 source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“By amplifying 68% of the bacterial 16S rRNA gene using short amplicons, this method increases the coverage and resolution of the detection of bacterial species compared with the widely used V4 or V3-V4 amplification”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Bone collagen is a main source of hydroxyproline, and many bone pathologies, like bone tumors, have been shown to result in elevated hydroxyproline levels (53).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
What the sources say
- Not checked yetcites [53] Nakagawa M, Sugiura Y, Oshima T, Kajino G, Hirako H, Urinary hydroxyproline excretion in orthopedic disease, with special reference to systemic bone disease and bone tumor (secondary report). Nagoya J. Med. Sci 29, 345– 367 (1967). pmid:6066099 6066099
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Cell wall–deficient bacteria are known to be found exclusively inside cells, where their morphology transforms into less-defined structures of highly variable sizes and shapes (42, 43).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
What the sources say
- Not checked yetcites [42] Errington J, L-form bacteria, cell walls and the origins of life. Open Biol. 3, 120143 (2013).doi: 10.1098/rsob.120143pmid:23303308 23303308 PMC3603455 source
- Not checked yetcites [43] Errington J, Cell wall-deficient, L-form bacteria in the 21st century: A personal perspective. Biochem. Soc. Trans 45, 287– 295 (2017). doi: 10.1042/BST20160435pmid:28408469 28408469 PMC5390494 source
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Thirty-nine samples and 10 controls that had fewer than 1000 normalized reads were discarded from further analysis”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > The microbiome of breast tumors is richer and more diverse than that of other tumor types
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Because ER+ breast tumors are known to have increased oxidative stress compared with ER− tumors (57)”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
What the sources say
- Not checked yetcites [57] Karihtala P, Kauppila S, Soini Y, Arja-Jukkola-Vuorinen, Oxidative stress and counteracting mechanisms in hormone receptor positive, triple-negative and basal-like breast carcinomas. BMC Cancer 11, 262 (2011).doi: 10.1186/1471-2407-11-262 pmid:21693047 21693047 PMC3141776 source
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we hypothesize that bacteria with the ability to synthesize mycothiol can better survive in the ER+ tumor microenvironment.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
plainconditional- Asserted: fails — The authors may not put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The authors may not put it forward as true.
- Rests on an assumption: Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
- Rests on an assumption: Breast cancer subtype assignment by ER, PR, and HER2 status is accurate.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Intratumor bacteria may also arise from the NAT, which can explain the high similarity we found between the tumor microbiome and its NAT microbiome.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Discussion
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“We took multiple measures to minimize and control for contamination (supplementary note)”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Discussion
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“As tumors develop, their disorganized, leaky vasculature may allow circulating bacteria to enter, and the immunosuppressed environment may provide a refuge for them (61, 62).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Discussion
What the sources say
- Not checked yetcites [61] Cummins J, Tangney M, Bacteria and tumours: Causative agents or opportunistic inhabitants? Infect. Agent. Cancer 8, 11 (2013). doi: 10.1186/1750-9378-8-11 pmid:23537317 23537317 PMC3668256 source
- Not checked yetcites [62] Baban CK, Cronin M, O’Hanlon D, O’Sullivan GC, Tangney M, Bacteria as vectors for gene therapy of cancer. Bioeng. Bugs 1, 385– 394 (2010). doi: 10.4161/bbug.1.6.13146 pmid:21468205 21468205 PMC3056088 source
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Arsenic is a Group 1 carcinogen that can increase the risk of breast cancer (54) and has been shown to induce expression of the estrogen receptor in human breast cancer (55).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
What the sources say
- Not checked yetcites [54] Khanjani N, Jafarnejad A-B, Tavakkoli L, Arsenic and breast cancer: A systematic review of epidemiologic studies. Rev. Environ. Health 32, 267– 277 (2017). doi: 10.1515/reveh-2016-0068 pmid:28284039 28284039 source
- Not checked yetcites [55] Du J, Zhou N, Liu H, Jiang F, Wang Y, Hu C, Qi H, Zhong C, Wang X, Li Z, Arsenic induces functional re-expression of estrogen receptor α by demethylation of DNA in estrogen receptor-negative human breast cancer. PLOS ONE 7, e35957 (2012). doi: 10.1371/journal.pone.0035957pmid:22558281 22558281 PMC3338760 source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“As tumors develop, their disorganized, leaky vasculature may allow circulating bacteria to enter, and the immunosuppressed environment may provide a refuge for them (61, 62).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Discussion
What the sources say
- Not checked yetcites [61] Cummins J, Tangney M, Bacteria and tumours: Causative agents or opportunistic inhabitants? Infect. Agent. Cancer 8, 11 (2013). doi: 10.1186/1750-9378-8-11 pmid:23537317 23537317 PMC3668256 source
- Not checked yetcites [62] Baban CK, Cronin M, O’Hanlon D, O’Sullivan GC, Tangney M, Bacteria as vectors for gene therapy of cancer. Bioeng. Bugs 1, 385– 394 (2010). doi: 10.4161/bbug.1.6.13146 pmid:21468205 21468205 PMC3056088 source
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“This is consistent with a recent publication that demonstrated that reexamination of whole-genome and whole-transcriptome sequencing data from The Cancer Genome Atlas (TCGA) for microbial sequences identified associations between different cancer types and specific microbiota (19).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Discussion
What the sources say
- Not checked yetcites [19] Poore GD, Kopylova E, Zhu Q, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf J, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Knight R, Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature 579, 567– 574 (2020). doi: 10.1038/s41586-020-2095-1pmid:32214244 32214244 PMC7500457 source
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“This observation is somewhat analogous to the relative stability of the human gut microbiome functions compared with its microbial taxa (58, 59).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Discussion
What the sources say
- Not checked yetcites [58] Human Microbiome Project Consortium, Structure, function and diversity of the healthy human microbiome. Nature 486, 207– 214 (2012). doi: 10.1038/nature11234 pmid:22699609 22699609 PMC3564958 source
- Not checked yetcites [59] Eng A, Borenstein E, Taxa-function robustness in microbial communities. Microbiome 6, 45 (2018).doi: 10.1186/s40168-018-0425-4pmid:29499759 29499759 PMC5833107 source
hedgedcorrelationaln = 1,526- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The enrichment for bacteria with the predicted capability to degrade cigarette smoke metabolites in lung tumors may suggest that high levels of these metabolites create a preferred niche for bacteria that can use these metabolites.”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Metabolic functions encoded by intratumor bacteria are associated with clinical features of certain tumor subtypes
hedgedconditionaln = 43- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
- Rests on an assumption: Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
The paper relies on this without support.
Predicted MetaCyc pathways from 16S sequences accurately represent the functional capabilities of intratumor bacteria.
“we used the PICRUSt2 tool (50-52) to map the 16S sequences to the genes and pathways that these bacterial species may harbor”
The paper relies on this without support.
Patients' smoking status was accurately recorded.
“we compared the bacterial functions found in non–small cell lung cancers (NSCLCs) of 100 current smokers with those in NSCLCs of 43 people who had never smoked (never-smokers).”
The paper relies on this without support.
The classification of melanoma patients as responders or nonresponders to immune checkpoint inhibitors is accurate.
“we compared metastatic melanomas from patients who responded to immune checkpoint inhibitors (ICI) (n = 29) with those from patients who did not respond (n = 48).”
The paper relies on this without support.
Breast cancer subtype assignment by ER, PR, and HER2 status is accurate.
“when comparing different subtypes of breast cancer according to their estrogen receptor (ER), progesterone receptor (PR), and HER2 status”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Theoretically, more than one bacterial cell can infect a single cancer cell,38,103 but the total number of unique species per tumor, bacterial or fungal, drops (<50) when decontamination strategies are applied.”
From Melanoma and microbiota: Current understanding and future directions (2024) · cites this paper as [14]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“A growing body of evidence has demonstrated the presence of intratumoral microbes, with studies using either metagenomics or culturomics suggesting the presence of intracellular,14,38,102,103 cancer type-specific,14,104–106 spatially heterogeneous,14,103,107 metabolically active,14,38,49,108,109 pro-metastatic,102,103,110,111 and immunoreactive38,60,112–115 communities of tumor-resident bacteria,”
From Melanoma and microbiota: Current understanding and future directions (2024) · cites this paper as [14]
Experimental — accuracy not yet measuredIn the citing paper
“many of these breast cancer GOMS components (V. parvula, B. uniformis and E. clostridioformis, among others) had previously been identified in an analysis of the breast cancer microbiome comprising >9,000 species after filtering for artefactual contaminants69.”
From Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy (2023) · cites this paper as [69]
In the citing paper
“While the overall bacterial load was similar in responders and non-responders, multiple bacterial taxa had significantly different representation, notably Veillonellaceae and Gammaproteobacteria were associated with resistance, as already identified in GOMS.”
From Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy (2023) · cites this paper as [69]
In the citing paper
“While the overall bacterial load was similar in responders and non-responders, multiple bacterial taxa had significantly different representation, notably Veillonellaceae and Gammaproteobacteria were associated with resistance, as already identified in GOMS.”
From Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy (2023) · cites this paper as [69]
In the citing paper
“First, correlations have been drawn across cancer indications and geographical sites between the taxonomic composition of the gut (and to some degree tumor) microbiota, and ICI responses in patients with melanoma and other cancers.”
From Melanoma and microbiota: Current understanding and future directions (2024) · cites this paper as [14]
In the citing paper
“Quantitative PCR has estimated that among seven cancer types, approximately 0.68% (95% CI: 0.75, 1.46%) of the tumor cellular content is bacterial, with melanoma-specific density estimates at ~33 bacteria/mm2 or ~6.3×106 bacteria/cm3 on average (using bootstrapped values).”
From Melanoma and microbiota: Current understanding and future directions (2024) · cites this paper as [14]
In the citing paper
“It has become increasingly apparent that tumors distant from the gut harbor their own microbiota (Nejman et al., 2020).”
From Microbiota triggers STING-type I IFN-dependent monocyte reprogramming of the tumor microenvironment (2021) · cites this paper as Nejman et al., 2020
In the citing paper
“Emerging evidence also suggests the existence and functional activity of intratumoral bacteria, with overlapping immunohistochemistry, immunofluorescence, electron microscopy, and sequencing data on them in ~10 cancer types.”
From The microbiome and human cancer (2021) · cites this paper as [12]
In the citing paper
“There are also associations between intratumor microbiota and immunogenicity, including differential melanoma immunotherapy response and triple-negative breast cancer associations, but their underlying mechanisms remain uncharacterized (12).”
From The microbiome and human cancer (2021) · cites this paper as [12]
In the citing paper
“Histologic imaging revealed heterogeneous microbial spatial distributions (Fig. 3B)”
From The microbiome and human cancer (2021) · cites this paper as [12]
In the citing paper
“They included 811 experimental controls, covering DNA extraction, PCR amplification, and paraffin embedding, removing 94.3% of bacteria as contaminants.”
From The microbiome and human cancer (2021) · cites this paper as [12]
In the citing paper
“Applying their pipeline to a melanoma immunotherapy cohort suggested microbiome differences between responders and non-responders, but not yet a mechanism.”
From The microbiome and human cancer (2021) · cites this paper as [12]
In the citing paper
“Nejman et al. (12) and Poore et al. (13) suggest distinct intratumoral microbiomes among >30 cancer types (Fig. 3), proposing their applicability to blood-based diagnostics”
From The microbiome and human cancer (2021) · cites this paper as [12]
In the citing paper
“It was only recently suggested that cancer types outside of the aerodigestive tract, such as breast or brain cancer, may also harbor microbiota with unique compositions.”
From The microbiome and human cancer (2021) · cites this paper as [12]
In the citing paper
“However, it is noteworthy that extra-intestinal cancers can develop within tissues that harbor their own microbiome and may play a role in the exacerbation of neoplasia (12, 18, 25, 46).”
From The microbiome and human cancer (2021) · cites this paper as [12]
In the citing paper
“and their frequent intracellular localization in cancer and immune cells (Fig. 3C).”
From The microbiome and human cancer (2021) · cites this paper as [12]
In the citing paper
“Examining the residual 528 bacterial species revealed significant differences in composition, diversity, and inferred metabolic functionality between cancer types.”
From The microbiome and human cancer (2021) · cites this paper as [12]
In the citing paper
“providing imaging evidence of these microbes’ intratumoral spatial distribution and intracellular localization in seven cancer types, although imaging evidence remains lacking for most cancer types.”
From The microbiome and human cancer (2021) · cites this paper as [12]
In the citing paper
“Because bacteria were cultured from only five human breast tumors, the widespread viability of intratumoral bacteria from this study was unclear, particularly in cancers with reportedly fewer bacteria.”
From The microbiome and human cancer (2021) · cites this paper as [12]
In the citing paper
“whether translocated bacteria impact on tumor immunity or ICI from directly within the tumor remained unknown”
From Dietary tryptophan metabolite released by intratumoral Lactobacillus reuteri facilitates immune checkpoint inhibitor treatment (2023) · cites this paper as [26]
In the citing paper
“Analyses of human samples suggest differences in the composition of the tumor microbiota between responders and non-responders for a cohort of melanoma patients undergoing immunotherapy”
From Hallmarks of response, resistance, and toxicity to immune checkpoint blockade (2021) · cites this paper as Nejman et al., 2020
In the citing paper
“Two recent studies demonstrate a high prevalence of microbes within a broad range of tumors, including those not physically associated with the aerodigestive tract and its commensal organisms”
From Hallmarks of response, resistance, and toxicity to immune checkpoint blockade (2021) · cites this paper as Nejman et al., 2020
In the citing paper
“these microbes can be localized within the cancer cells themselves or within tumor-associated immune cells”
From Hallmarks of response, resistance, and toxicity to immune checkpoint blockade (2021) · cites this paper as Nejman et al., 2020
In the citing paper
“intratumoral microbes--yet another component of the tumor microenvironment that was heretofore underappreciated--has been shown to have significant impact on the anti-tumor immune responses and responses to ICB”
From Hallmarks of response, resistance, and toxicity to immune checkpoint blockade (2021) · cites this paper as Nejman et al., 2020
In the citing paper
“these microbes may be tumor-type specific, suggesting distinct functions that may complement the tumor”
From Hallmarks of response, resistance, and toxicity to immune checkpoint blockade (2021) · cites this paper as Nejman et al., 2020
In the citing paper
“The gut and tumor microbiome have been associated with anti-tumor responses and, in some cases, response to immune checkpoint blockade”
From Hallmarks of response, resistance, and toxicity to immune checkpoint blockade (2021) · cites this paper as Nejman et al., 2020
In the citing paper
“Furthermore, mounting evidence suggests the presence of intratumoral microbiota [410].”
From Tumor microenvironment signaling and therapeutics in cancer progression (2023) · cites this paper as [410]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
“LTA was rarely detected in cancer cells or in CD45+/CD68− immune cells (Fig. 2).”
§ The human tumor microbiome is composed of tumor type-specific intracellular bacteria > Intratumor bacteria are mostly intracellular and are present in both cancer and immune cells
“no cell wall polymer LTA was detected in cancer cells”
Citations
Cites
1 retracted
RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach
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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
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Cited by
Sorted by citations
Hallmarks of Cancer: New Dimensions
Hanahan, D. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-1059 · Cited by 9,887
“For example, in a survey of 1,526 tumors encompassing seven human cancer types (bone, brain, breast, lung, melanoma, ovary, and pancreas), each type was characterized by a distinctive microbiome that was largely localized inside cancer cells and immune cells, and within each tumor type, variations in the tumor microbi…”
BackgroundHallmarks of response, resistance, and toxicity to immune checkpoint blockade
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BackgroundMethodInfluentialSelf-citationAntimicrobial peptides: mechanism of action, activity and clinical potential
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Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer
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Metadata
- Authors
- Nejman, D., Livyatan, I., Fuks, G., Gavert, N., Zwang, Y., Geller, L. T., Rotter-Maskowitz, A., Weiser, R., Mallel, G., Gigi, E., Meltser, A., Douglas, G. M., Kamer, I., Gopalakrishnan, V., Dadosh, T., Levin-Zaidman, S., Avnet, S., Atlan, T., Cooper, Z. A., Arora, R., Cogdill, A. P., Khan, M. A. W., Ologun, G., Bussi, Y., Weinberger, A., Lotan-Pompan, M., Golani, O., Perry, G., Rokah, M., Bahar-Shany, K., Rozeman, E. A., Blank, C. U., Ronai, A., Shaoul, R., Amit, A., Dorfman, T., Kremer, R., Cohen, Z. R., Harnof, S., Siegal, T., Yehuda-Shnaidman, E., Gal-Yam, E. N., Shapira, H., Baldini, N., Langille, M. G. I., Ben-Nun, A., Kaufman, B., Nissan, A., Golan, T., Dadiani, M., Levanon, K., Bar, J., Yust-Katz, S., Barshack, I., Peeper, D. S., Raz, D. J., Segal, E., Wargo, J. A., Sandbank, J., Shental, N., & Straussman, R.
- Affiliations
- Weizmann Institute of Science (IL)
- Tel Aviv University (IL)
- Dalhousie University (CA)
- Sheba Medical Center (IL)
- The University of Texas MD Anderson Cancer Center (US)
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel.
- Istituto Ortopedico Rizzoli (IT)
- Jerusalem College of Technology (IL)
- AstraZeneca (United States) (US)
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
- Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel.
- The Netherlands Cancer Institute (NL)
- Rambam Health Care Campus (IL)
- Technion – Israel Institute of Technology (IL)
- Rabin Medical Center (IL)
- Institute of Pathology, Megalab, Maccabi Healthcare Services, Rehovot, Israel.
- Breast Oncology Institute, Sheba Medical Center, Ramat Gan, Israel.
- Maccabi Healthcare Services (IL)
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
- City Of Hope National Medical Center (US)
- Open University of Israel (IL)
- Corresponding author
- Nejman, Deborah
- Livyatan, Ilana
- Fuks, Garold
- Shental, Noam
- Straussman, Ravid
- ORCID
- Nejman, Deborah
- Livyatan, Ilana
- Fuks, Garold
- Gavert, Nancy
- Zwang, Yaara
- Geller, Leore T.
- Rotter-Maskowitz, Aviva
- Weiser, Roi
- Mallel, Giuseppe
- Meltser, Arnon
- Douglas, Gavin M.
- Kamer, Iris
- Gopalakrishnan, Vancheswaran
- Levin-Zaidman, Smadar
- Avnet, Sofia
- Atlan, Tehila
- Cooper, Zachary A.
- Arora, Reetakshi
- Cogdill, Alexandria P.
- Khan, Md Abdul Wadud
- Ologun, Gabriel
- Bussi, Yuval
- Weinberger, Adina
- Lotan-Pompan, Maya
- Golani, Ofra
- Perry, Gili
- Rokah, Merav
- Rozeman, Elisa A.
- Blank, Christian U.
- Shaoul, Ron
- Amit, Amnon
- Cohen, Zvi R.
- Harnof, Sagi
- Siegal, Tali
- Baldini, Nicola
- Langille, Morgan G. I.
- Kaufman, Bella
- Nissan, Aviram
- Golan, Talia
- Dadiani, Maya
- Levanon, Keren
- Bar, Jair
- Yust-Katz, Shlomit
- Barshack, Iris
- Peeper, Daniel S.
- Raz, Dan J.
- Segal, Eran
- Wargo, Jennifer A.
- Sandbank, Judith
- Shental, Noam
- Straussman, Ravid
- Venue
- Science
- Published
- 2020-05-29
- Volume
- 368
- Issue
- 6494
- Pages
- 973-980
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC7757858
- OpenAlex
- W3030942202
- Cited by
- 2,464
- References
- 73
- Citations by year
- 2026: 425 · 2025: 524 · 2024: 466 · 2023: 415 · 2022: 335 · 2021: 234 · 2020: 63
- FWCI
- 85.73
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Archivio istituzionale della ricerca (Alma Mater Studiorum Università di Bologna) (submittedVersion, other-oa)
- Funders
- National Institutes of Health (1R01CA219896-01A1)
- American Association for Cancer Research (SU2C-AACR-IRG-19-17)
- Israel Cancer Research Fund
- H2020 European Research Council (818086)
- United States-Israel Binational Science Foundation (2013332)
- Israel Ministry of Science, Technology & Space (3-11174)
- Israel Science Foundation (2044/17)
- Rising Tide Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biotechnology › Bacterial Cancer Therapy
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Keywords
- tumor microbiome, intratumoral bacteria, intracellular bacteria, breast cancer, lung cancer, ovarian cancer, pancreatic cancer, melanoma, bone tumors, brain tumors, tumor subtypes, smoking, immunotherapy response, tumor immune cells
- MeSH terms
- Bacteria, Breast, Colon, Female, Humans, Immunotherapy, Lung, Macrophages, Male, Neoplasms, Ovary, RNA, Ribosomal, 16S, Microbiota
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