The DOI matches its Crossref record; 54 of the 55 references it cites were found in a registry or an index.
Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption
Open accessAbstract
A mechanistic understanding of the purported health benefits conferred by consumption of probiotic bacteria has been limited by our knowledge of the resident gut microbiota and its interaction with the host. Here, we detail the impact of a single-organism probiotic, Lactobacillus rhamnosus GG ATCC 53103 (LGG), on the structure and functional dynamics (gene expression) of the gut microbiota in a study of 12 healthy individuals, 65 to 80 years old. The analysis revealed that while the overall community composition was stable as assessed by 16S rRNA profiling, the transcriptional response of the gut microbiota was modulated by probiotic treatment. Comparison of transcriptional profiles based on taxonomic composition yielded three distinct transcriptome groups that displayed considerable differences in functional dynamics. The transcriptional profile of LGG in vivo was remarkably concordant across study subjects despite the considerable interindividual nature of the gut microbiota. However, we identified genes involved in flagellar motility, chemotaxis, and adhesion from Bifidobacterium and the dominant butyrate producers Roseburia and Eubacterium whose expression was increased during probiotic consumption, suggesting that LGG may promote interactions between key constituents of the microbiota and the host epithelium. These results provide evidence for the discrete functional effects imparted by a specific single-organism probiotic and challenge the prevailing notion that probiotics substantially modify the resident microbiota within nondiseased individuals in an appreciable fashion. IMPORTANCE Probiotic bacteria have been used for over a century to promote digestive health. Many individuals report that probiotics alleviate a number of digestive issues, yet little evidence links how probiotic microbes influence human health. Here, we show how the resident microbes that inhabit the healthy human gut respond to a probiotic. The well-studied probiotic Lactobacillus rhamnosus GG ATCC 53103 (LGG) was administered in a clinical trial, and a suite of measurements of the resident microbes were taken to evaluate potential changes over the course of probiotic consumption. We found that LGG transiently enriches for functions to potentially promote anti-inflammatory pathways in the resident microbes.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
In the citing paper
“data showing butyrate (associated with Bifidobacterium [72]) treatment to protect against age-related muscle atrophy [73] supports the idea that pre- and/or probiotic supplementation, which is shown to increase the abundance of Bifidobacterium and butyrate producers in older individuals [74, 75], may prophylactically moderate aging muscle loss.”
From Gut Microbiota Contribute to Age-Related Changes in Skeletal Muscle Size, Composition, and Function: Biological Basis for a Gut-Muscle Axis (2018) · cites this paper as [74]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
HTSeq—a Python framework to work with high-throughput sequencing data
Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464
Metagenomic biomarker discovery and explanation
Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011) · Genome Biology · doi:10.1186/gb-2011-12-6-r60 · Cited by 16,192
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
UCHIME improves sensitivity and speed of chimera detection
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr381 · Cited by 15,114
Diet rapidly and reproducibly alters the human gut microbiome
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100
Fitting Linear Mixed-Effects Models Using lme4Preprint
Bates, D. M., Maechler, M., Bolker, B. M., & Walker, S. (2014) · arXiv (Cornell University) · doi:10.3929/ethz-b-000105397 · Cited by 9,435
A scaling normalization method for differential expression analysis of RNA-seq data
Robinson, M. D., & Oshlack, A. (2010) · Genome Biology · doi:10.1186/gb-2010-11-3-r25 · Cited by 7,876
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., & Glöckner, F. O. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm864 · Cited by 6,682
Diversity, stability and resilience of the human gut microbiota
Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012) · Nature · doi:10.1038/nature11550 · Cited by 5,533
McCarthy, D. J., Chen, Y., & Smyth, G. K. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks042 · Cited by 5,195
McDonald, D. T., Price, M. N., Goodrich, J. K., Nawrocki, E. P., DeSantis, T. Z., Probst, A. J., Andersen, G. L., Knight, R. D., & Hugenholtz, P. (2011) · The ISME Journal · doi:10.1038/ismej.2011.139 · Cited by 5,144
The KEGG resource for deciphering the genome
Kanehisa, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh063 · Cited by 5,120
PyNAST: a flexible tool for aligning sequences to a template alignment
Caporaso, J. G., Bittinger, K. L., Bushman, F. D., DeSantis, T. Z., Andersen, G. L., & Knight, R. D. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp636 · Cited by 3,449
Gut microbiota composition correlates with diet and health in the elderly
Claesson, M. J., Jeffery, I. B., Conde, S., Power, S. E., O’Connor, E. M., Cusack, S., Harris, H. M. B., Coakley, M., Lakshminarayanan, B., O’Sullivan, O., et al. (2012) · Nature · doi:10.1038/nature11319 · Cited by 3,314
Peng, Y., Leung, H. C. M., Yiu, S., & Chin, F. Y. L. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts174 · Cited by 2,998
Ab initio gene identification in metagenomic sequences
Zhu, W., Lomsadze, A., & Borodovsky, M. Y. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq275 · Cited by 1,818
Composition, variability, and temporal stability of the intestinal microbiota of the elderly
Claesson, M. J., Cusack, S., O'Sullivan, O., Greene-Diniz, R., de Weerd, H., Flannery, E., Marchesi, J. R., Falush, D., Dinan, T., Fitzgerald, G., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000097107 · Cited by 1,754
Through Ageing, and Beyond: Gut Microbiota and Inflammatory Status in Seniors and Centenarians
Biagi, E., Nylund, L., Candela, M., Ostan, R., Bucci, L., Pini, E., Nikkïla, J., Monti, D., Satokari, R., Franceschi, C., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010667 · Cited by 1,483
The Application of Ecological Theory Toward an Understanding of the Human Microbiome
Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J. M., & Relman, D. A. (2012) · Science · doi:10.1126/science.1224203 · Cited by 1,437
Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens
Lebeer, S., Vanderleyden, J., & De Keersmaecker, S. C. J. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2297 · Cited by 1,062
Genomic variation landscape of the human gut microbiome
Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., et al. (2013) · Nature · doi:10.1038/nature11711 · Cited by 907
Rfam 11.0: 10 years of RNA families
Burge, S., Daub, J., Eberhardt, R. Y., Tate, J. G., Barquist, L., Nawrocki, E. P., Eddy, S. R., Gardner, P. P., & Bateman, A. G. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1005 · Cited by 806
RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses
Zhang, T., Breitbart, M., Lee, W. H., Run, J., Wei, C. L., Soh, S. W., Hibberd, M. L., Liu, E. T., Rohwer, F. L., & Ruan, Y. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0040003 · Cited by 799
Kankainen, M., Paulin, L., Tynkkynen, S., von Ossowski, I., Reunanen, J., Partanen, P., Satokari, R., Vesterlund, S., Hendrickx, A. P. A., Lebeer, S., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0908876106 · Cited by 740
Intestinal microbiota in human health and disease: the impact of probiotics
Gerritsen, J., Smidt, H., Rijkers, G. T., & de Vos, W. M. (2011) · Genes & Nutrition · doi:10.1007/s12263-011-0229-7 · Cited by 724
Beneficial metabolic effects of a probiotic via butyrate-induced GLP-1 hormone secretion
Yadav, H., Lee, J.-H., Lloyd, J., Walter, P., & Rane, S. G. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.452516 · Cited by 709
Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa
Bron, P. A., van Baarlen, P., & Kleerebezem, M. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2690 · Cited by 690
McNulty, N. P., Yatsunenko, T., Hsiao, A., Faith, J. J., Muegge, B. D., Goodman, A. L., Henrissat, B., Oozeer, R., Cools-Portier, S., Gobert, G., et al. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3002701 · Cited by 559
An update on the use and investigation of probiotics in health and disease
Sanders, M. E., Guarner, F., Guerrant, R., Holt, P. R., Quigley, E. M., Sartor, R. B., Sherman, P. M., & Mayer, E. A. (2013) · Gut · doi:10.1136/gutjnl-2012-302504 · Cited by 503 · cited 1×
“The majority of randomized clinical trials (RCTs) to evaluate the in vivo health benefits of probiotic species have focused on a variety of clinical indicators from the human host; to date, few studies have focused on the impact of probiotic consumption on the resident gastrointestinal microbiota on a community-wide s…”
BackgroundMetatranscriptomic Approach to Analyze the Functional Human Gut Microbiota
Gosalbes, M. J., Durbán, A., Pignatelli, M., Abellan, J. J., Jiménez‐Hernández, N., Pérez‐Cobas, A. E., Latorre, A., & Moyá, A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017447 · Cited by 395
Regulation of intestinal homeostasis and immunity with probiotic lactobacilli
van Baarlen, P., Wells, J. M., & Kleerebezem, M. (2013) · Trends in Immunology · doi:10.1016/j.it.2013.01.005 · Cited by 378
Tackling soil diversity with the assembly of large, complex metagenomes
Howe, A. C., Jansson, J. K., Malfatti, S., Tringe, S. G., Tiedje, J. M., & Brown, C. T. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1402564111 · Cited by 322
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
Giannoukos, G., Ciulla, D., Huang, K. H., Haas, B. J., Izard, J., Levin, J. Z., Livny, J., Earl, A. M., Gevers, D., Ward, D. V., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-3-r23 · Cited by 269
von Schillde, M., Hörmannsperger, G., Weiher, M., Alpert, C.-A., Hahne, H., Bäuerl, C., Huynegem, K. V., Steidler, L., Hrnčíř, T., Pérez‐Martínez, G., et al. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.02.006 · Cited by 244
A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing DataPreprint
Brown, C. T., Howe, A., Zhang, Q., Pyrkosz, A. B., & Brom, T. H. (2012) · arXiv (Cornell University) · doi:10.48550/arxiv.1203.4802 · Cited by 233
Dedkova, E. N., & Blatter, L. A. (2014) · Frontiers in Physiology · doi:10.3389/fphys.2014.00260 · Cited by 227
The Human Microbiome: From Symbiosis to Pathogenesis
Eloe‐Fadrosh, E. A., & Rasko, D. A. (2013) · Annual Review of Medicine · doi:10.1146/annurev-med-010312-133513 · Cited by 227
Self-citationIsolation of DNA from bacterial samples of the human gastrointestinal tract
Zoetendal, E. G., Heilig, H. G. H. J., Klaassens, E. S., Booijink, C. C., Kleerebezem, M., Smidt, H., & de Vos, W. M. (2006) · Nature Protocols · doi:10.1038/nprot.2006.142 · Cited by 224
Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia
Zaikova, E., Walsh, D. A., Stilwell, C. P., Mohn, W. W., Tortell, P. D., & Hallam, S. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.02058.x · Cited by 211
Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA.
Ellenberger, T. E., Kwon, H. J., Bennik, M. H. J., & Demple, B. (2000) · Nature Structural Biology · doi:10.1038/75213 · Cited by 200
Expression patterns reveal niche diversification in a marine microbial assemblage
Gifford, S., Sharma, S., Booth, M. G., & Moran, M. A. (2012) · The ISME Journal · doi:10.1038/ismej.2012.96 · Cited by 200
Lahti, L., Salonen, A., Kekkonen, R. A., Salojärvi, J., Jalanka, J., Palva, A., Orešič, M., & de Vos, W. M. (2013) · PeerJ · doi:10.7717/peerj.32 · Cited by 198
Segawa, S., Fujiya, M., Konishi, H., Ueno, N., Kobayashi, N., Shigyo, T., & Kohgo, Y. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023278 · Cited by 186
Douillard, F. ⁄. O. P., Ribbera, A., rvinen, H. M. J. ⁄., Kant, R., ⁄, T. E. P., Randazzo, C. L., Paulin, L. G., Laine, P., Caggia, C., von Ossowski, I., et al. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.03467-12 · Cited by 127
Eloe‐Fadrosh, E. A., McArthur, M. A., Seekatz, A. M., Drábek, E. F., Rasko, D. A., Sztein, M. B., & Fraser, C. M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062026 · Cited by 106
Self-citationIsolation of RNA from bacterial samples of the human gastrointestinal tract
Zoetendal, E. G., Booijink, C. C., Klaassens, E. S., Heilig, H. G. H. J., Kleerebezem, M., Smidt, H., & de Vos, W. M. (2006) · Nature Protocols · doi:10.1038/nprot.2006.143 · Cited by 105
Community Health Care: Therapeutic Opportunities in the Human Microbiome
Sonnenburg, J. L., & Fischbach, M. A. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3001626 · Cited by 102
Hibberd, P. L., Kleimola, L., Fiorino, A., Botelho, C. A., Haverkamp, M. R., Andreyeva, I., Poutsiaka, D. D., Fraser, C. M., Solano-Aguilar, G. I., & Snydman, D. R. (2014) · PLoS ONE · doi:10.1371/journal.pone.0113456 · Cited by 53
Self-citationNeville, B., Sheridan, P., Harris, H., Coughlan, S., Flint, H., Duncan, S., Jeffery, I., Claesson, M., Ross, R. P., Scott, K., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068919 · Cited by 50
FISH analysis of Lactobacillus biofilms in the gastrointestinal tract of different hosts
Lebeer, S., Verhoeven, T. L. A., Claes, I. J. J., Hertogh, G., Vermeire, S., Buyse, J., Immerseel, F. V., Vanderleyden, J., & Keersmaecker, S. C. J. D. (2010) · Letters in Applied Microbiology · doi:10.1111/j.1472-765x.2010.02994.x · Cited by 49
Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG
Crabtree, J., Agrawal, S., Mahurkar, A., Myers, G. S. A., Rasko, D. A., & White, O. R. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu505 · Cited by 36
Self-citation
Flagged first, then by citations
1 of the 55 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Influence of diet on the gut microbiome and implications for human health
Singh, R. K., Chang, H.-W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., Abrouk, M., Farahnik, B., Nakamura, M., Zhu, T. H., et al. (2017) · Journal of Translational Medicine · doi:10.1186/s12967-017-1175-y · Cited by 2,599
Rivière, A., Selak, M., Lantin, D., Leroy, F., & Vuyst, L. D. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00979 · Cited by 1,810
Zmora, N., Zilberman-Schapira, G., Suez, J., Mor, U., Dori-Bachash, M., Bashiardes, S., Kotler, E., Zur, M., Regev-Lehavi, D., Brik, R. B.-Z., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.041 · Cited by 1,695
The central nervous system and the gut microbiome
Sharon, G., Sampson, T. R., Geschwind, D. H., & Mazmanian, S. K. (2016) · Cell · doi:10.1016/j.cell.2016.10.027 · Cited by 1,513
The pros, cons, and many unknowns of probiotics
Suez, J., Zmora, N., Segal, E., & Elinav, E. (2019) · Nature Medicine · doi:10.1038/s41591-019-0439-x · Cited by 1,398
Metadata
- Authors
- Eloe-Fadrosh, E. A., Brady, A., Crabtree, J., Drabek, E. F., Ma, B., Mahurkar, A., Ravel, J., Haverkamp, M., Fiorino, A.-M., Botelho, C., Andreyeva, I., Hibberd, P. L., & Fraser, C. M.
- Affiliations
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- University of Maryland, Baltimore (US)
- Massachusetts General Hospital (US)
- Corresponding author
- Fraser, Claire M.
- ORCID
- Venue
- mBio
- Publisher
- American Society for Microbiology
- Published
- 2015-05
- Volume
- 6
- Issue
- 2
- ISSN
- 2150-7511 (ISSN-L)
- 2161-2129
- PMC
- PMC4453556
- OpenAlex
- W2156573030
- Cited by
- 160
- References
- 55
- Citations by year
- 2026: 3 · 2025: 11 · 2024: 8 · 2023: 11 · 2022: 14 · 2021: 21 · 2020: 11 · 2019: 19 · 2018: 20 · 2017: 19 · 2016: 19 · 2015: 4
- FWCI
- 27.59
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- mBio (publishedVersion, cc-by-nc-sa)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-sa)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Science Foundation (0959894)
- National Institutes of Health
- National Center for Complementary and Alternative Medicine
- National Center for Complementary and Integrative Health (K24AT003683, U01AT002952, U01AT002133, U01AT002388)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Keywords
- probiotics, Lactobacillus rhamnosus GG, gut microbiota, older adults, Bifidobacterium, Roseburia, Eubacterium, flagellar motility, chemotaxis, adhesion, host-microbe interactions, anti-inflammatory pathways, interindividual variability, 16S rRNA gene profiling
- MeSH terms
- Gastrointestinal Microbiome, Aged, Aged, 80 and over, DNA, Bacterial, DNA, Ribosomal, Female, Humans, Male, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Cluster Analysis, Sequence Analysis, DNA, Probiotics, Gene Expression Profiling, Gastrointestinal Tract, Lacticaseibacillus rhamnosus, Microbial Interactions
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
