CoChat
Sign Up
Cited by 111Gut microbiota and healthMicrobial Community Ecology and PhysiologyOral microbiology and periodontitis research

Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana

Open access
Hansen, Matthew E. B., Rubel, Meagan A., Bailey, Aubrey G., Ranciaro, Alessia, Thompson, Simon R., Campbell, Michael C., Beggs, William, Dave, Jaanki R. +7 more·2019·Genome Biology
DOI 10.1186/s13059-018-1616-9PMC PMC6341659
Open this paper in CoChat — free accountOpen PDF

Abstract

BACKGROUND: Gut microbiota from individuals in rural, non-industrialized societies differ from those in individuals from industrialized societies. Here, we use 16S rRNA sequencing to survey the gut bacteria of seven non-industrialized populations from Tanzania and Botswana. These include populations practicing traditional hunter-gatherer, pastoralist, and agropastoralist subsistence lifestyles and a comparative urban cohort from the greater Philadelphia region. RESULTS: We find that bacterial diversity per individual and within-population phylogenetic dissimilarity differs between Botswanan and Tanzanian populations, with Tanzania generally having higher diversity per individual and lower dissimilarity between individuals. Among subsistence groups, the gut bacteria of hunter-gatherers are phylogenetically distinct from both agropastoralists and pastoralists, but that of agropastoralists and pastoralists were not significantly different from each other. Nearly half of the Bantu-speaking agropastoralists from Botswana have gut bacteria that are very similar to the Philadelphian cohort. Based on imputed metagenomic content, US samples have a relative enrichment of genes found in pathways for degradation of several common industrial pollutants. Within two African populations, we find evidence that bacterial composition correlates with the genetic relatedness between individuals. CONCLUSIONS: Across the cohort, similarity in bacterial presence/absence compositions between people increases with both geographic proximity and genetic relatedness, while abundance weighted bacterial composition varies more significantly with geographic proximity than with genetic relatedness.

AI snapshot

Written from the paper’s full text.

TL;DR

In a 16S rRNA survey of gut bacteria from 126 people in rural Tanzania, rural Botswana, and Philadelphia, bacterial diversity and composition differed more by country/region than by subsistence practice, and a subset of Botswanan Bantu agropastoralists had microbiota similar to the US cohort. Similarity in bacterial presence/absence increased with geographic proximity and host genetic relatedness, while abundance-weighted composition tracked geography more than relatedness.

Key findings

  • Tanzanian populations generally had higher within-individual bacterial diversity and lower within-population phylogenetic dissimilarity than Botswanan populations; the Sandawe had the highest Shannon diversity and the US cohort the lowest. Hunter-gatherers were phylogenetically distinct from both agropastoralists and pastoralists, while agropastoralists and pastoralists were not significantly different from each other.
  • Prevotellaceae was the most abundant bacterial family in 70.2% of Africans, whereas Bacteroidaceae was most abundant in 50% of US samples. Twenty-three Africans had Prevotellaceae abundances within one standard deviation of the US mean (12.4%); 19 were from Botswana and 12 were Bantu. Nearly half of Bantu-speaking agropastoralists from Botswana had gut bacteria very similar to the Philadelphia cohort, and 12 low-Prevotellaceae Bantu were not statistically different from US samples by weighted UniFrac (PERMANOVA p = 0.12).
  • Imputed metagenomes showed 146 KEGG pathways significantly differentially enriched between US and African cohorts and 148 between Botswana and Tanzania; US samples had relative enrichment of pathways for degradation of industrial pollutants, and DDT degradation was enriched in Botswanan but not Tanzanian or US samples.
  • Within-population bacterial composition correlated with host genetic relatedness in the Hadza (both unweighted and weighted UniFrac) and Maasai (unweighted UniFrac). Across the cohort, unweighted UniFrac similarity increased with both geographic proximity and genetic relatedness, while weighted UniFrac varied significantly only with geographic separation.

Methods

  • Stool samples from 126 participants were analyzed by 16S rRNA V1–V2 sequencing: 60 from Tanzania, 54 from Botswana, and 12 from Philadelphia; 114 African adults were recruited, and US samples came from prior studies. Samples were processed with the same laboratory and computational pipelines.
  • Reads were clustered into operational taxonomic units at 97% identity using QIIME/Swarm, taxonomically assigned with Greengenes, and analyzed with UniFrac, PERMANOVA (50,000 permutations), PCoA, ANCOM, and PICRUSt. qPCR quantified 16S rRNA gene copies and screened for *Entamoeba histolytica*.
  • A subset of 97 African individuals was genotyped on the Illumina Omni5M Exome array; genetic relatedness was estimated using identity-by-descent and a genetic relationship matrix, and linear models tested UniFrac distances as functions of geographic distance and host relatedness.

Limitations

  • The paper states that individual- and population-level dietary information was not available; PICRUSt imputation may not capture gene content in diverged strains, so shotgun sequencing is needed to verify functional differences; the US cohort is the only urban/industrialized population; larger sample sizes are needed to identify factors causing sex differences; and the BMI–diversity correlation cannot be separated from other environmental or cultural covariates.
  • The paper also notes that cross-study microbiome comparisons are difficult because of different amplicons, protocols, reagents, and primers, and that seasonal variation may affect taxa such as Prevotellaceae.
  • Evident from the text: 16S V1–V2 amplicon data limit taxonomic resolution, with 1,044 unassigned OTUs removed and African samples having more unassigned OTUs; several populations are small (e.g., Herero n = 8, US n = 12), and the design is cross-sectional, limiting causal inference.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1186/s13059-018-1616-9

Cites

93 of 93 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 74 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    Within two African populations, bacterial composition correlates with the genetic relatedness between individuals.

    “Within two African populations, we find evidence that bacterial composition correlates with the genetic relatedness between individuals.”
    Quote in the paperSubstantial claim
  • Findingown data

    The gut bacteria of agropastoralists and pastoralists are not significantly different from each other.

    “Among subsistence groups, the gut bacteria of hunter-gatherers are phylogenetically distinct from both agropastoralists and pastoralists, but that of agropastoralists and pastoralists were not significantly different from each other.”
    Quote in the paperSubstantial claim
  • Findingown data

    Bacterial diversity per individual differs between Botswanan and Tanzanian populations, with Tanzania generally having higher diversity per individual.

    “We find that bacterial diversity per individual and within-population phylogenetic dissimilarity differs between Botswanan and Tanzanian populations, with Tanzania generally having higher diversity per individual and lower dissimilarity between individuals.”
    Quote in the paperSubstantial claim
  • Findingown data

    Nearly half of the Bantu-speaking agropastoralists from Botswana have gut bacteria that are very similar to the Philadelphian cohort.

    “Nearly half of the Bantu-speaking agropastoralists from Botswana have gut bacteria that are very similar to the Philadelphian cohort.”
    Quote in the paperNot a substantial claim
  • Findingown data

    Based on imputed metagenomic content, US samples have a relative enrichment of genes found in pathways for degradation of several common industrial pollutants.

    “Based on imputed metagenomic content, US samples have a relative enrichment of genes found in pathways for degradation of several common industrial pollutants.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: PICRUSt imputation accurately estimates metagenomic content.
  • May combine two claims. 34
  • Classified as probably not a substantial claim. 28

  • May combine two claims.

    Findingown data

    Within-population phylogenetic dissimilarity differs between Botswanan and Tanzanian populations, with Tanzania generally having lower dissimilarity between individuals.

    “We find that bacterial diversity per individual and within-population phylogenetic dissimilarity differs between Botswanan and Tanzanian populations, with Tanzania generally having higher diversity per individual and lower dissimilarity between individuals.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Among subsistence groups, the gut bacteria of hunter-gatherers are phylogenetically distinct from both agropastoralists and pastoralists.

    “Among subsistence groups, the gut bacteria of hunter-gatherers are phylogenetically distinct from both agropastoralists and pastoralists, but that of agropastoralists and pastoralists were not significantly different from each other.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    The Hadza in this study were sampled mid-October through early November, which is the late dry season and the beginning of the wet season, when there is an average rainfall of 57 mm.

    “The Hadza in our study were sampled mid-October through early November, which is the late dry season and the beginning of the wet season, when there is an average rainfall of 57 mm [50].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [50] The World Bank Group. Climate Change Knowledge Portal. [cited 2018 Apr 12]. Available from: http://sdwebx.worldbank.org/climateportal/index.cfm?page=country_historical_climate&ThisCCode=TZA .

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    For unweighted UniFrac bacterial distances, the best fit coefficients of geographic distance and genetic relatedness residuals are both significantly non-zero (T test p < 0.002).

    “For unweighted UniFrac bacterial distances, the best fit coefficients of Dij and G’ij are both significantly non-zero (T test p values < 0.002, Additional file 2: Table S1U)”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The African populations in this cohort are slightly more phylogenetically diverse based on unweighted UniFrac distances (83% of distance between USA and Africa) and are comparable in terms of weighted UniFrac distances (68% of distance between USA and Africa).

    “The African populations in our cohort are slightly more phylogenetically diverse based on unweighted UniFrac distances (83% of distance between USA and Africa) and are comparable in terms of weighted UniFrac distances (68% of distance between USA and Africa).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Within the Bantu, there is heterogeneity in bacterial abundance profiles, where roughly half the population has gut bacteria similar to the other African groups, and the other half has gut bacteria more similar to the US cohort.

    “It is clear from Fig. 2 that there is heterogeneity in bacterial abundance profiles within the Bantu, where roughly half the population has gut bacteria similar to the other African groups, and the other half has gut bacteria more similar to the US cohort.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Bacteroides is significantly variable across the African populations, with generally higher abundances in Botswanans than in Tanzanians.

    “and is significantly variable across the African populations, with generally higher abundances in Botswanans than in Tanzanians.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    None of the populations in this study live in an urban setting; sites are ~60 km or more walking distance from the nearest town.

    “None of the populations in our study live in an urban setting; sites are ~ 60 km or more walking distance from the nearest town”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The Hadza are outliers in unweighted UniFrac PCoA, indicating that their bacteria, in terms of presence/absence, are phylogenetically the most dissimilar to other African populations.

    “the Hadza are outliers in unweighted UniFrac PCoA, indicating that their bacteria, in terms of presence/absence, are phylogenetically the most dissimilar to other African populations”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The US and Botswana Bantu agropastoralists have the two lowest measures of taxonomic diversity within hosts and two of the highest measures of inter-individual diversity in this cohort.

    “The US and Botswana Bantu agropastoralists also have the two lowest measures of taxonomic diversity within hosts and two of the highest measures of inter-individual diversity in this cohort.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    The gut bacteria of urban-industrialized populations often have high abundances of Bacteroides, while the gut bacteria from traditional hunter-gatherer or agropastoral societies have higher abundances of Prevotella.

    “The gut bacteria of urban-industrialized populations often have high abundances of Bacteroides, while the gut bacteria from traditional hunter-gatherer or agropastoral societies have higher abundances of Prevotella [22–28].”
    Quote in the paperSubstantial claim0 of 7 sources checked
    • cites [22] De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A. 2010;107:14691–6. source

      Not checked in the free run.

    • cites [23] Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486:222–7. source

      Not checked in the free run.

    • cites [24] Schnorr SL, Candela M, Rampelli S, Centanni M, Consolandi C, Basaglia G, et al. Gut microbiome of the Hadza hunter-gatherers. Nat Commun. 2014;5:3654. source

      Not checked in the free run.

    • cites [25] Obregon-Tito AJ, Tito RY, Metcalf J, Sankaranarayanan K, Clemente JC, Ursell LK, et al. Subsistence strategies in traditional societies distinguish gut microbiomes. Nat Commun. 2015;6:6505. source

      Not checked in the free run.

    • cites [26] Clemente JC, Ursell LK, Parfrey LW, Knight R. The impact of the gut microbiota on human health: an integrative view. Cell. 2012;148:1258–70. source

      Not checked in the free run.

    • cites [27] Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, et al. Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Rep. 2016;14:2142–53. source

      Not checked in the free run.

    • cites [28] Martínez I, Stegen JC, Maldonado-Gómez MX, Eren AM, Siba PM, Greenhill AR, et al. The gut microbiota of rural Papua New Guineans: composition, diversity patterns, and ecological processes. Cell Rep. 2015;11:527–38. source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    Across the cohort, similarity in bacterial presence/absence compositions between people increases with both geographic proximity and genetic relatedness.

    “Across the cohort, similarity in bacterial presence/absence compositions between people increases with both geographic proximity and genetic relatedness, while abundance weighted bacterial composition varies more significantly with geographic proximity than with genetic relatedness.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    The unweighted UniFrac distances between the BaAka and the neighboring Bantu is nearly 74% of the mean distance between the US and the African cohort, while for weighted UniFrac this ratio is nearly 70%.

    “The unweighted UniFrac distances between the BaAka and the neighboring Bantu is nearly 74% of the mean distance between the US and the African cohort, while for weighted UniFrac this ratio is nearly 70%.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [27] Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, et al. Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Rep. 2016;14:2142–53. source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisecitation

    Bacteroides has been used to distinguish between developing (low Bacteroides abundance) and industrialized (high Bacteroides abundance) populations.

    “Bacteroides has been used to distinguish between developing (low Bacteroides abundance) and industrialized (high Bacteroides abundance) populations [22–28, 30]”
    Quote in the paperSubstantial claim0 of 8 sources checked
    • cites [22] De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A. 2010;107:14691–6. source

      Not checked in the free run.

    • cites [23] Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486:222–7. source

      Not checked in the free run.

    • cites [24] Schnorr SL, Candela M, Rampelli S, Centanni M, Consolandi C, Basaglia G, et al. Gut microbiome of the Hadza hunter-gatherers. Nat Commun. 2014;5:3654. source

      Not checked in the free run.

    • cites [25] Obregon-Tito AJ, Tito RY, Metcalf J, Sankaranarayanan K, Clemente JC, Ursell LK, et al. Subsistence strategies in traditional societies distinguish gut microbiomes. Nat Commun. 2015;6:6505. source

      Not checked in the free run.

    • cites [26] Clemente JC, Ursell LK, Parfrey LW, Knight R. The impact of the gut microbiota on human health: an integrative view. Cell. 2012;148:1258–70. source

      Not checked in the free run.

    • cites [27] Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, et al. Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Rep. 2016;14:2142–53. source

      Not checked in the free run.

    • cites [28] Martínez I, Stegen JC, Maldonado-Gómez MX, Eren AM, Siba PM, Greenhill AR, et al. The gut microbiota of rural Papua New Guineans: composition, diversity patterns, and ecological processes. Cell Rep. 2015;11:527–38. source

      Not checked in the free run.

    • cites [30] Morton ER, Lynch J, Froment A, Lafosse S, Heyer E, Przeworski M, et al. Variation in rural African gut microbiota is strongly correlated with colonization by Entamoeba and subsistence. PLoS Genet. 2015;11:e1005658. source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Premisecitation

    Prior studies of the Hadza and the Hutterites indicate that seasonally volatile gut bacterial taxa correlate with seasonally available food.

    “Prior studies of the Hadza (Smits et al. 2017) [31] and the Hutterites from the USA [49] indicate that seasonally volatile gut bacterial taxa correlate with seasonally available food.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [31] Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS, Reid G, et al. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science. 2017;357:802–6. source

      Not checked in the free run.

    • cites [49] Davenport ER, Mizrahi-Man O, Michelini K, Barreiro LB, Ober C, Gilad Y. Seasonal Variation in Human Gut Microbiome Composition. PLOS ONE. 2014;9:e90731. source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The compositional similarity between the Bantu and US is noteworthy and may be reflective of individual nutritive changes in the Bantu from Botswana and a shift from traditional to industrialized diets.

    “Given the dissimilarity of food types between industrialized and traditional populations, the compositional similarity between the Bantu and US is noteworthy and may be reflective of individual nutritive changes in the Bantu from Botswana and a shift from traditional to industrialized diets.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    Smits et al. (2017) identified four bacterial families and one bacterial phylum that primarily associate with traditional or industrialized populations.

    “which identified four bacterial families and one bacterial phylum that primarily associate with traditional (Prevotellaceae, Spirochaetaceae, Succinivibrionaceae) or industrialized (Bacteroidaceae, Verrucomicrobia) populations”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Smits et al. (2017) source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Three of these five taxa (Succinivirbionaceae, Spirochaetaceae, and Prevotellaceae) were highly variable with season.

    “Additionally, three of these five taxa (Succinivirbionaceae, Spirochaetaceae, and Prevotellaceae) were highly variable with season.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Smits et al. (2017) source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    Bacterial similarity is greater with closer geographic proximity and closer relatedness.

    “indicating that bacterial similarity is greater with closer geographic proximity and closer relatedness”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Studies have found evidence for heritability of relative bacterial abundances or specific taxa.

    “with studies finding evidence for heritability of relative bacterial abundances or specific taxa [15, 63–68]”
    Quote in the paperNot a substantial claim0 of 7 sources checked
    • cites [15] Wang J, Thingholm LB, Skiecevičienė J, Rausch P, Kummen M, Hov JR, et al. Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota. Nat Genet. 2016;48:1396–406. source

      Not checked in the free run.

    • cites [63] Etienne RS. A new sampling formula for neutral biodiversity. Ecol Lett. 2005;8:253–60. source

      Not checked in the free run.

    • cites [64] Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, et al. Human genetics shape the gut microbiome. Cell. 2014;159:789–99. source

      Not checked in the free run.

    • cites [65] Goodrich JK, Davenport ER, Beaumont M, Jackson MA, Knight R, Ober C, et al. Genetic determinants of the gut microbiome in UK twins. Cell Host Microbe. 2016;19:731–43. source

      Not checked in the free run.

    • cites [66] Xie H, Guo R, Zhong H, Feng Q, Lan Z, Qin B, et al. Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome. Cell Syst. 2016;3:572–584.e3. source

      Not checked in the free run.

    • cites [67] Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, et al. The effect of host genetics on the gut microbiome. Nat Genet. 2016;48:1407–12. source

      Not checked in the free run.

    • cites [68] Turpin W, Espin-Garcia O, Xu W, Silverberg MS, Kevans D, Smith MI, et al. Association of host genome with intestinal microbial composition in a large healthy cohort. Nat Genet. 2016;48:1413–7. source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Treponema within family Spirochetaceae is a common constituent of hunter-gatherer gut microbiomes and a catabolizer of fibrous plant materials (cellulose and xylans) that form a large component of Hadza diets.

    “in particular, the genus Treponema within family Spirochetaceae, which is a common constituent of hunter-gatherer gut microbiomes [24–27, 30] and a catabolizer of fibrous plant materials (cellulose and xylans) that form a large component of Hadza diets [24]”
    Quote in the paperNot a substantial claim0 of 5 sources checked
    • cites [24] Schnorr SL, Candela M, Rampelli S, Centanni M, Consolandi C, Basaglia G, et al. Gut microbiome of the Hadza hunter-gatherers. Nat Commun. 2014;5:3654. source

      Not checked in the free run.

    • cites [25] Obregon-Tito AJ, Tito RY, Metcalf J, Sankaranarayanan K, Clemente JC, Ursell LK, et al. Subsistence strategies in traditional societies distinguish gut microbiomes. Nat Commun. 2015;6:6505. source

      Not checked in the free run.

    • cites [26] Clemente JC, Ursell LK, Parfrey LW, Knight R. The impact of the gut microbiota on human health: an integrative view. Cell. 2012;148:1258–70. source

      Not checked in the free run.

    • cites [27] Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, et al. Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Rep. 2016;14:2142–53. source

      Not checked in the free run.

    • cites [30] Morton ER, Lynch J, Froment A, Lafosse S, Heyer E, Przeworski M, et al. Variation in rural African gut microbiota is strongly correlated with colonization by Entamoeba and subsistence. PLoS Genet. 2015;11:e1005658. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The Sandawe settled into villages and adopted small-scale agropastoral practices in the mid-1800s.

    “The Sandawe settled into villages and adopted small-scale agropastoral practices in the mid-1800s [54].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [54] Newman JL. The Ecological Basis for Subsistence Change among the Sandawe of Tanzania. Washington D.C.: National Academy of Sciences; 1970.

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Botswana is more economically developed than Tanzania, reflected in higher yearly per capita gross national income ($15.5k in Botswana to $1.75k in Tanzania), and a higher percentage of Botswanans (57%) than Tanzanians (30%) live in urban areas.

    “Botswana is more economically developed than Tanzania, reflected in higher yearly per capita gross national income ($15.5 k in Botswana to $1.75 k in Tanzania), and a higher percentage of Botswanans (57%) than Tanzanians (30%) live in urban areas [52, 53].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [52] Regional Office for Africa, Africa Health Organization, World Health Organization. United Republic of Tanzania: Factsheets of Health Statistics 2016. 2016. Available from: http://www.aho.afro.who.int/profiles_information/images/c/c8/Tanzania-Statistical_Factsheet.pdf

      Not checked in the free run.

    • cites [53] Regional Office for Africa, Africa Health Organization, World Health Organization. Botswana: Factsheets of Health Statistics 2016. 2016. Available from: http://www.aho.afro.who.int/profiles_information/images/0/05/Botswana-Statistical_Factsheet.pdf

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    The high Shannon diversity values in the Sandawe are consistent with the "Intermediate Disturbance Hypothesis" which proposes diversity of bacteria is maximized under conditions of fluctuating environments.

    “The high Shannon diversity values in the Sandawe are consistent with the “Intermediate Disturbance Hypothesis” which proposes diversity of bacteria is maximized under conditions of fluctuating environments (e.g., diet in this case) [55, 56].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [55] Kadmon R, Benjamini Y. Effects of productivity and disturbance on species richness: a neutral model. Am Nat. 2006;167:939–46. source

      Not checked in the free run.

    • cites [56] Jiang L, Patel SN. Community assembly in the presence of disturbance: a microcosm experiment. Ecology. 2008;89:1931–40. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Other studies estimate that host genetics explain only a minor percentage of microbiome variation.

    “and alternately, estimating that host genetics explain only a minor percentage of microbiome variation [69].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [69] Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature. 2018;555:210–5. source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    The negative correlation between α and β-diversity exists among a set of non-Western populations practicing largely traditional subsistence lifestyles, demonstrating that the correlation is not entirely a Western versus non-Western phenomenon.

    “first, the negative correlation between α and β-diversity exists among a set of non-Western populations practicing largely traditional subsistence lifestyles, demonstrating that the correlation is not entirely a Western versus non-Western phenomenon”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductreasoning

    All fecal and blood samples were extracted, sequenced, and analyzed using the same laboratory and computational pipelines, thereby reducing the impact of batch effects in the cross-population comparisons.

    “All fecal and blood samples were extracted, sequenced, and analyzed using the same laboratory and computational pipelines, thereby reducing the impact of batch effects in the cross-population comparisons.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Maasai diets primarily consist of meat, milk, and blood, which are lactose rich and high in fat and cholesterol, though they supplement that diet with maize traded from neighboring groups.

    “Maasai diets primarily consist of meat, milk, and blood, which are lactose rich and high in fat and cholesterol, though they supplement that diet with maize traded from neighboring groups [75].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [75] Århem K. Maasai Food Symbolism: The Cultural Connotations of Milk, Meat, and Blood in the Pastoral Maasai Diet. Anthropos. 1989;84:1–23.

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Botswana, but not Tanzania, is one of nine countries worldwide that uses indoor residence spraying of traditional structures for control of malaria-carrying mosquitos.

    “Interestingly, Botswana, but not Tanzania, is one of nine countries worldwide that uses indoor residence spraying of traditional structures for control of malaria-carrying mosquitos [70, 71].”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [70] Chihanga S, Haque U, Chanda E, Mosweunyane T, Moakofhi K, Jibril HB, et al. Malaria elimination in Botswana, 2012–2014: achievements and challenges. Parasit Vectors. 2016;9:99. source

      Not checked in the free run.

    • cites [71] World Health Organization, Global Malaria Programme. World malaria report 2017. 2017. source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The factors causing a shift towards western microbiome compositions remain unknown but appear to have a regional component that is not entirely due to differences in agricultural, pastoral, or hunting-gathering subsistence modes.

    “The factors causing a shift towards western microbiome compositions remain unknown but appear to have a regional component that is not entirely due to differences in agricultural, pastoral, or hunting-gathering subsistence modes.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The traditional diet of San hunter-gatherers is composed of foraged meat, vegetables, fruits, and nuts, the latter of which contributed the largest percentage of dietary protein and calories.

    “The traditional diet of San hunter-gatherers is composed of foraged meat, vegetables, fruits, and nuts, the latter of which contributed the largest percentage of dietary protein and calories [76–80].”
    Quote in the paperNot a substantial claim0 of 5 sources checked
    • cites [76] Silberbauer G. Report to the government of Bechuanaland on the bushmen survey. Gaborone: Bechuanaland Government Printer; 1965.

      Not checked in the free run.

    • cites [77] Silberbauer G. The G/wi Bushmen. In: Bicchieri M, editor. Hunt Gatherers Today. New York: Holt, Rinehart and Winston; 1972. p. 271–326.

      Not checked in the free run.

    • cites [78] Lee R. The !Kung san: men, women, and work in a foraging society. New York: Cambridge University Press; 1979.

      Not checked in the free run.

    • cites [79] Tanaka J. The san, hunter-gatherers of the Kalahari. Tokyo: University of Tokyo Press; 1980.

      Not checked in the free run.

    • cites [80] Valiente-Noailles C. The Kua: life and soul of the central Kalahari bushmen. A.A. Balkema: Rotterdam; 1993.

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    Written informed consent was obtained from all participants, and ethics/research approval and permits were obtained from the listed institutions prior to sample collection.

    “Written informed consent was obtained from all participants, and ethics/research approval and permits were obtained from the following institutions prior to the start of sample collection”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    The US population may reasonably be expected to contain more industrial pollutants in the general environment than in the environment of any of the populations sampled in Africa.

    “which we may reasonably expect to contain more industrial pollutants in the general environment than in the environment of any of the populations we sampled in Africa.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The Sandawe have admixed with neighboring populations of diverse ancestries who migrated into Tanzania within the past 5000 years.

    “The Sandawe have admixed with neighboring populations of diverse ancestries who migrated into Tanzania within the past 5000 years [73].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [73] Tishkoff SA, Reed FA, Friedlaender FR, Ehret C, Ranciaro A, Froment A, et al. The genetic structure and history of Africans and African Americans. Science. 2009;324:1035–44. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S4 (based). May combine two claims.

    Interpretationnone given

    The sampled African populations live far from industrial centers and arguably have less contact with plastics and industrial by-products compared to the US individuals.

    “The sampled African populations live far from industrial centers and arguably have less contact with plastics and industrial by-products compared to the US individuals”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The Sandawe also adopted the agropastoral subsistence practices of neighboring Bantu-speaking Turu, which comprises the bulk of their caloric intake, though they continue to supplement a small portion of their diet with hunting and gathering.

    “The Sandawe also adopted the agropastoral subsistence practices of neighboring Bantu-speaking Turu, which comprises the bulk of their caloric intake, though they continue to supplement a small portion of their diet with hunting and gathering [54, 74].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [54] Newman JL. The Ecological Basis for Subsistence Change among the Sandawe of Tanzania. Washington D.C.: National Academy of Sciences; 1970.

      Not checked in the free run.

    • cites [74] Yatsuka H. Hunter-gatherers and their neighbors in Asia, Africa, and South America. Senri Ethnol Stud. 2016;94:81–105.

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    These results suggest potential metagenomic adaptation to increased exposure to industrial compounds in western populations, and to DDT in Botswanans.

    “These results suggest potential metagenomic adaptation to increased exposure to industrial compounds in western populations, and to DDT in Botswanans.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductnone given

    Reads were removed during quality filtering if they did not match the Golay error-corrected barcode with fewer than two mismatches, if read pairs could not be joined with an overlapping sequence of less than 35 bp, if they had a homopolymer sequence greater than 6 bp, or if they had more than two ambiguous base calls (N's).

    “During the quality-filtering process, reads were removed from the analysis if they did not match Golay error-corrected barcode with less than two mismatches, if the read pairs could not be joined with an overlapping sequence of less than 35 bp, if they had a homopolymer sequence (repeated base call) greater than 6 bp, and if they had more than two ambiguous base calls (N’s).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    All individuals in the study have BMI measurements, allowing testing for correlations between α-diversity and BMI.

    “All of the individuals in our study have BMI measurements, which allowed testing for correlations between α-diversity and BMI.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductcitation

    All OTUs were tested for correlation between proportional abundance and post-PCR amplicon concentration, and OTUs with a significant negative correlation were considered contaminants and removed.

    “As an additional quality control step, all OTUs were tested for correlations between the proportional abundance of the OTU and the post-PCR amplicon concentration of a sample using the method developed by Jervis-Brady et al. [90] as implemented in the contam_test program for R (https://github.com/eclarke/eclectic).”
    • Also stated in: § Biological sample processing and quantification · plain
      “Correlation significance is assessed using Pearson’s rho, and OTUs with a significant negative correlation are considered contaminants and removed.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [90] Jervis-Bardy J, Leong LEX, Marri S, Smith RJ, Choo JM, Smith-Vaughan HC, et al. Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data. Microbiome. 2015;3:19. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    97 of the 114 African individuals were genotyped on the Illumina Omni5M Exome array.

    “97 of the 114 African individuals were genotyped on the Illumina Omni5M Exome array that includes a small number of indels and ~ 4.5 million SNPs (see Additional file 2: Table S1A).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Herero pastoralists have diets based on beef, milk, and milk products with supplements of goats, chickens, garden produce, foraged plants and animals, and bulk grains (especially ground corn).

    “Herero pastoralists have diets based on beef, milk, and milk products with supplements of goats, chickens, garden produce, foraged plants and animals, and bulk grains (especially ground corn) [82].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [82] Pennington RL. Economic stratification and health among the Herero of Botswana. In: Leonard WR, Crawford MH, editors. Hum Biol Pastor Popul. Cambridge: Cambridge University Press; 2002.

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    OTUs mapping to chloroplast or mitochondrial sequences were removed.

    “OTUs mapping to chloroplast or mitochondrial sequences were removed.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    The Nearest Sequenced Taxon Index (NSTI) has a mean of 0.140 and standard deviation of 0.037 across all samples, with 10th and 90th percentiles of 0.095 and 0.186.

    “The Nearest Sequenced Taxon Index (NSTI), which measures the phylogenetic distance between observed OTU sequences and the reference, has a mean and standard deviation of 0.140 and 0.037 across all samples, with 10th and 90th percentiles 0.095 and 0.186 (Additional file 2: Table S1AB).”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    ANCOM accounts for the simplex nature of compositional data and therefore does not suffer from spurious negative correlations imposed by the sum-to-one constraint on relative abundances.

    “The ANCOM method accounts for the simplex nature of compositional data, and so does not suffer from spurious negative correlations imposed by the fact that (relative) abundances across all bacteria must sum to one within a given bacterial community.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [40] Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis. 2015;26:27663. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    Primers, probes, and protocols for the qPCR, including methods for generating a recombinant plasmid standard curve, were taken from Mejia et al. (2013).

    “Primers, probes, and protocols for the qPCR, including methods for generating a recombinant plasmid containing target E. histolytica sequence to make a standard curve, were taken from Mejia et al. (2013) [95].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [95] Mejia R, Vicuña Y, Broncano N, Sandoval C, Vaca M, Chico M, et al. A novel, multi-parallel, real-time polymerase chain reaction approach for eight gastrointestinal parasites provides improved diagnostic capabilities to resource-limited at-risk populations. Am J Trop Med Hyg. 2013;88:1041–7. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisereasoning

    ANCOM is a sensitive test for taxa that vary significantly and in an unusual way compared to the other taxa.

    “As such, this is a sensitive test for taxa that vary significantly and in an unusual way compared to the other taxa.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [40] Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis. 2015;26:27663. source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductown data

    Variants were pruned to approximate linkage equilibrium (r2LD < 0.1), leaving 158,891 SNPs for genetic relatedness estimation.

    “We retained the segregating autosomal biallelic single nucleotide polymorphisms (SNPs) over the 97 individuals, and variants were pruned to be in approximate linkage equilibrium, r2LD < 0.1, using plink [93](plink --indep-pairwise 200 kb 20 0.1), leaving 158,891 SNPs for genetic relatedness estimation.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [93] Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015;4:7. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S1 (asserted), S3 (load-bearing). May combine two claims.

    Interpretationreasoning

    The correlation could only be explained by OTU annotation biases that impact certain pathways more than others and have the same mapping biases between Tanzania and Botswana as between the USA and Africa.

    “The above correlation could only be explained by OTU annotation biases that (A) happen to impact certain pathways more than others and (B) have the same mapping biases between Tanzania and Botswana as between the USA and Africa.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: The bacterial strains in each sample have the same gene content as the database strains used for PICRUSt analysis.
49 of 49

  • The paper relies on this without support.

    The range of gut microbiome compositions among African populations with diverse subsistence practices remains largely unknown.

    “Although there have been several studies of microbiome diversity within African populations [22–24, 27, 29–31], the range of gut microbiome compositions among African populations with diverse subsistence practices remains largely unknown.”

  • The paper relies on this without support.

    PICRUSt imputation accurately estimates metagenomic content.

    “We infer that the regional differences in bacterial abundances may lead to regional differences in functional pathway abundances, depending upon the accuracy of gene content imputation.”

  • The authors state this as an assumption.

    Estimation of the identity-by-descent fraction assumes a panmictic population.

    “Estimation of the identity-by-descent fraction assumes a panmictic population and is, therefore, reasonably suited for use as a within-population relatedness metric.”

  • The authors state this as an assumption.

    The bacterial strains in each sample have the same gene content as the database strains used for PICRUSt analysis.

    “PICRUSt relies on the assumption that the bacterial strains in each sample have the same gene content as database strains used for the analysis, which can be inaccurate when strains vary substantially in gene content.”
4 of 4

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 higher biodiversity observed in non-Westernized settings is consistent with more heterogeneous dietary and environmental exposures allowing a broader range of accessory gene content to persist than in industrialized populations.

    “This characteristic is consistent with the higher biodiversity observed in non-Westernized settings, where more heterogeneous dietary and environmental exposures may allow a broader range of accessory gene content to persist than is usually observed in genomes from industrialized populations [73-75] .”

    From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [74]

    The Results (page not provided) report that the US cohort had the least bacterial diversity, and the Discussion proposes that varied lifestyles and diets could increase gut bacterial diversity. The paper does not establish that heterogeneous exposures preserve a broader range of accessory gene content; its Discussion cautions that imputed gene content requires direct verification. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

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.

  • Bantu qPCR sample count differs between Results and Methods

    Minor

    The Results say eight Bantu were among the 52 Africans tested, whereas the Methods say nine Bantu samples were included in that analysis.

  • Hadza Prevotellaceae comparison is 7.25-fold, not nearly tenfold

    Minor

    The stated abundances of approximately 58% and 8% give a ratio of 7.25, substantially below the reported nearly tenfold comparison.

    Reported 10 · recomputed 7.25

  • Overall maximum age conflicts with Botswana maximum

    Minor

    Table 1 lists a maximum age of 92 for both the Botswanan Bantu and the Botswana subtotal, but gives 90 as the maximum for the full cohort.

3 of 3

Cites

Flagged first, then by citations

2 of the 95 references couldn’t be matched to a known paper.

Research works printed but not linked: 7

  1. Yatsuka H. Hunter-gatherers and their neighbors in Asia, Africa, and South America. Senri Ethnol Stud. 2016;94:81–105.
  2. Silberbauer G. Report to the government of Bechuanaland on the bushmen survey. Gaborone: Bechuanaland Government Printer; 1965.
  3. Silberbauer G. The G/wi Bushmen. In: Bicchieri M, editor. Hunt Gatherers Today. New York: Holt, Rinehart and Winston; 1972. p. 271–326.
  4. Tanaka J. The san, hunter-gatherers of the Kalahari. Tokyo: University of Tokyo Press; 1980.
  5. Pennington RL. Economic stratification and health among the Herero of Botswana. In: Leonard WR, Crawford MH, editors. Hum Biol Pastor Popul. Cambridge: Cambridge University Press; 2002.
  6. Hansen MEB, Rubel MA, Bailey AG, Ranciaro A, Thompson SR, Campbell MC, Beggs W, Dave JR, Mokone GG, Mpoloka SW, Nyambo T, Abnet C, Chanock SJ, Bushman FD, Tishkoff SA. Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana. Bioproject, Accession PRJNA395034. 2017. https://www.ncbi.nlm.nih.gov/bioproject/395034 .
  7. Tishkoff SA. Genetics of pigmentation in Eastern and Southern African populations study. dbGAP, Accession phs001396.v1.p1. 2017. https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001396.v1.p1 .

Cited by

Sorted by citations

Related

Authors
Hansen, M. E. B., Rubel, M. A., Bailey, A. G., Ranciaro, A., Thompson, S. R., Campbell, M. C., Beggs, W., Dave, J. R., Mokone, G. G., Mpoloka, S. W., Nyambo, T., Abnet, C., Chanock, S. J., Bushman, F. D., & Tishkoff, S. A.
Affiliations
  • University of Pennsylvania (US)
  • Queen Mary University of London (GB)
  • Howard University (US)
  • Geisinger College of Health Sciences (US)
  • University of Botswana (BW)
  • Muhimbili University of Health and Allied Sciences (TZ)
  • National Cancer Institute (US)
Corresponding author
Tishkoff, Sarah A.
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2019-01-22
Volume
20
Issue
1
Pages
16-16
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-018-1616-9
PMC
PMC6341659
OpenAlex
W2917203974
Semantic Scholar
5d2e60e7e34252019e85b7940dcd5cff9db85af4
Cited by
110
References
95
Citations by year
2026: 7 · 2025: 11 · 2024: 14 · 2023: 8 · 2022: 12 · 2021: 34 · 2020: 16 · 2019: 8
FWCI
5.79
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • IRIS Research product catalog (Sapienza University of Rome) (submittedVersion)
Funders
  • Lewis and Clark Fund
  • University of Pennsylvania
  • National Institutes of Health (5T32AI007532-18, DP1 ES022577-04, 1R01DK104339-01, 1R01GM113657-01, T32ES019851-02)
  • National Science Foundation (BCS-1540432, BCS-1317217)
  • Center of Excellence in Environmental Toxicology
  • Wenner-Gren Foundation (9299)
  • Leakey Foundation
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
Keywords
gut microbiota, population structure, hunter-gatherers, pastoralists, agro-pastoralists, subsistence lifestyle, rural population, bacterial diversity, phylogenetic dissimilarity, Bantu peoples, industrial pollutants, genetic relatedness, geographic proximity, urban comparison, Tanzania, Botswana
MeSH terms
Eubacteriales, Clostridiales, Gastrointestinal Microbiome, Adolescent, Adult, Aged, Aged, 80 and over, Agriculture, Animals, Bacteroidaceae, Botswana, Cattle, Female, Humans, Male, Middle Aged, Rural Population, Tanzania, Philadelphia, Cohort Studies, Population Groups, Metagenome, Young Adult, Diet, Paleolithic

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.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-09.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-09.

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