Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa
Open accessAbstract
Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world's population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n = 118) or urban Soweto (n = 51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple "western-nonwestern" axis and contains undescribed microbial diversity.
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Previous studies in adults described differential microbiota patterns in non-westernized populations, including Prevotella spp. as a marker for non-westernized microbiomes.
“Previous studies in adults have described differential microbiota patterns in non-westernized populations, highlighting, for example, Prevotella spp. as a marker for non-westernized microbiomes.26,57”
From Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population (2023) · cites this paper as [57]
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662 · see citing works
Wickham, H. (2016) · Use R! · doi:10.1007/978-3-319-24277-4 · Cited by 33,612 · see citing works
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M. V., Kulikov, A. S., Lesin, V. M., Nikolenko, S., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 25,691 · see citing works
Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L., François, R., Grolemund, G., Hayes, A., Henry, L., Hester, J., et al. (2019) · Journal of Open Source Software · doi:10.21105/joss.01686 · Cited by 22,138 · see citing works
Prokka: rapid prokaryotic genome annotation
Seemann, T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu153 · Cited by 18,512 · see citing works
Modern Applied Statistics with S
Venables, W., & Ripley, B. (2010) · Statisctics and computing/Statistics and computing · doi:10.1007/978-0-387-21706-2 · Cited by 16,188 · see citing works
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894 · see citing works
Minimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807 · see citing works
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496 · see citing works
Lim, S. S., Vos, T., Flaxman, A. D., Danaei, G., Shibuya, K., Adair-Rohani, H., AlMazroa, M. A., Amann, M., Anderson, H. R., Andrews, K. G., et al. (2012) · The Lancet · doi:10.1016/s0140-6736(12)61766-8 · Cited by 11,805 · see citing works
Self-citationStructure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624 · see citing works
QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172 · see citing works
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
Letunic, I., & Bork, P. (2021) · Nucleic Acids Res. · doi:10.1093/nar/gkab301 · Cited by 9,899 · see citing works
Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J. R., Young, S., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0112963 · Cited by 8,994 · see citing works
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823 · see citing works
Human gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815 · see citing works
De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005963107 · Cited by 5,579 · see citing works
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz848 · Cited by 5,176 · see citing works
Kraken: ultrafast metagenomic sequence classification using exact alignments
Wood, D. E., & Salzberg, S. L. (2014) · Genome Biology · doi:10.1186/gb-2014-15-3-r46 · Cited by 4,521 · see citing works
Ribosomal Database Project: data and tools for high throughput rRNA analysis
Cole, J. R., Wang, Q., Fish, J. A., Chai, B., McGarrell, D. M., Sun, Y., Brown, C. T., Porras‐Alfaro, A., Kuske, C. R., & Tiedje, J. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1244 · Cited by 4,322 · see citing works
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Parks, D. H., Chuvochina, M., Waite, D. W., Rinke, C., Skarshewski, A., Chaumeil, P.-A., & Hugenholtz, P. (2018) · Nature Biotechnology · doi:10.1038/nbt.4229 · Cited by 3,603 · see citing works
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.004 · Cited by 3,315 · see citing works
Reshaping Data with the reshape Package
Wickham, H. (2007) · Journal of Statistical Software · doi:10.18637/jss.v021.i12 · Cited by 3,167 · see citing works
Fast and accurate de novo genome assembly from long uncorrected readsPreprint
Vaser, R., Sović, I., Nagarajan, N., & Šikić, M. (2017) · Genome Research · doi:10.1101/gr.214270.116 · Cited by 3,059 · see citing works
Olm, M. R., Brown, C. T., Brooks, B., & Banfield, J. F. (2017) · The ISME Journal · doi:10.1038/ismej.2017.126 · Cited by 3,031 · see citing works
Environment dominates over host genetics in shaping human gut microbiota
Rothschild, D., Weissbrod, O., Barkan, E., Kurilshikov, A., Korem, T., Zeevi, D., Costea, P. I., Godneva, A., Kalka, I. N., Bar, N., et al. (2018) · Nature · doi:10.1038/nature25973 · Cited by 2,859 · see citing works
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
Wu, Y., Simmons, B. A., & Singer, S. W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv638 · Cited by 2,809 · see citing works
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
Laslett, D. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh152 · Cited by 2,714 · see citing works
Binning metagenomic contigs by coverage and composition
Alneberg, J., Bjarnason, B. S., de Bruijn, I., Schirmer, M., Quick, J., Ijaz, U. Z., Lahti, L., Loman, N. J., Andersson, A. F., & Quince, C. (2014) · Nature Methods · doi:10.1038/nmeth.3103 · Cited by 2,709 · see citing works
The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3893 · Cited by 2,624 · see citing works
Multivariable association discovery in population-scale meta-omics studies
Mallick, H., Rahnavard, A., McIver, L. J., Ma, S., Zhang, Y., Nguyen, L. H., Tickle, T. L., Weingart, G., Ren, B., Schwager, E. H., et al. (2021) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009442 · Cited by 2,596 · see citing works
Differential abundance analysis for microbial marker-gene surveys
Paulson, J. N., Stine, O. C., Bravo, H. C., & Pop, M. (2013) · Nature Methods · doi:10.1038/nmeth.2658 · Cited by 2,393 · see citing works
Bracken: estimating species abundance in metagenomics data
(2016) · doi:10.7717/peerj-cs.104 · Cited by 2,333 · see citing works
Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303 · see citing works
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
MetaHIT consortium, Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., et al. (2015) · Nature · doi:10.1038/nature15766 · Cited by 2,116 · see citing works
The Comprehensive Antibiotic Resistance Database
McArthur, A., Waglechner, N., Nizam, F., Yan, A., Azad, M. A., Baylay, A., Bhullar, K., Canova, M. J., de Pascale, G., Ejim, L., et al. (2013) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00419-13 · Cited by 2,053 · see citing works
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis
Scher, J. U., Sczesnak, A., Longman, R. S., Segata, N., Ubeda, C., Bielski, C., Rostron, T., Cerundolo, V., Pamer, E. G., Abramson, S. B., et al. (2013) · eLife · doi:10.7554/elife.01202 · Cited by 2,047 · see citing works
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Parks, D. H., Rinke, C., Chuvochina, M., Chaumeil, P.-A., Woodcroft, B. J., Evans, P. N., Hugenholtz, P., & Tyson, G. W. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0012-7 · Cited by 1,882 · see citing works
Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.001 · Cited by 1,591 · see citing works
A complete domain-to-species taxonomy for Bacteria and Archaea
Parks, D. H., Chuvochina, M. S., Chaumeil, P.-A., Rinke, C., Mussig, A. J., & Hugenholtz, P. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0501-8 · Cited by 1,542 · see citing works
A unified catalog of 204,938 reference genomes from the human gut microbiome
Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0603-3 · Cited by 1,367 · see citing works
Oliphant, K., & Allen-Vercoe, E. (2019) · Microbiome · doi:10.1186/s40168-019-0704-8 · Cited by 1,327 · see citing works
Gut microbiome of the Hadza hunter-gatherers
Schnorr, S. L., Candela, M., Rampelli, S., Centanni, M., Consolandi, C., Basaglia, G., Turroni, S., Biagi, E., Peano, C., Severgnini, M., et al. (2014) · Nature Communications · doi:10.1038/ncomms4654 · Cited by 1,317 · see citing works
A new genomic blueprint of the human gut microbiota
Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D. (2019) · Nature · doi:10.1038/s41586-019-0965-1 · Cited by 1,314 · see citing works
The microbiome, cancer, and cancer therapy
Helmink, B. A., Khan, M. A. W., Hermann, A., Gopalakrishnan, V., & Wargo, J. A. (2019) · Nature Medicine · doi:10.1038/s41591-019-0377-7 · Cited by 1,200 · see citing works
Kieft, K., Zhou, Z., & Anantharaman, K. (2020) · Microbiome · doi:10.1186/s40168-020-00867-0 · Cited by 1,108 · see citing works
Gupta, V. K., Paul, S., & Dutta, C. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01162 · Cited by 1,019 · see citing works
DNAPlotter: circular and linear interactive genome visualization
Carver, T. J., Thomson, N. R., Bleasby, A. J., Berriman, M., & Parkhill, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn578 · Cited by 888 · see citing works
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania
Smits, S. A., Leach, J., Sonnenburg, E. D., Gonzalez, C. G., Lichtman, J. S., Reid, G., Knight, R., Manjurano, A., Changalucha, J., Elias, J. E., et al. (2017) · Science · doi:10.1126/science.aan4834 · Cited by 886 · see citing works
Carbohydrate metabolism in Bifidobacteria
Pokusaeva, K., Fitzgerald, G. F., & van Sinderen, D. (2011) · Genes & Nutrition · doi:10.1007/s12263-010-0206-6 · Cited by 855 · see citing works
US immigration westernizes the human gut microbiome
Vangay, P., Johnson, A. J., Ward, T. L., Al-Ghalith, G. A., Shields-Cutler, R. R., Hillmann, B. M., Lucas, S. K., Beura, L. K., Thompson, E. A., Till, L. M., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.029 · Cited by 794 · see citing works
Impact of commonly used drugs on the composition and metabolic function of the gut microbiota
Vich Vila, A., Collij, V., Sanna, S., Sinha, T., Imhann, F., Bourgonje, A. R., Mujagic, Z., Jonkers, D. M. A. E., Masclee, A. A. M., Fu, J., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-14177-z · Cited by 791 · see citing works
New insights from uncultivated genomes of the global human gut microbiome
Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S., & Kyrpides, N. C. (2019) · Nature · doi:10.1038/s41586-019-1058-x · Cited by 737 · see citing works
Gibson, M. K., Forsberg, K. J., & Dantas, G. A. (2014) · The ISME Journal · doi:10.1038/ismej.2014.106 · Cited by 656 · see citing works
Ou, J., Carbonero, F., Zoetendal, E. G., DeLany, J. P., Wang, M., Newton, K., Gaskins, H. R., & O’Keefe, S. J. (2013) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.112.056689 · Cited by 646 · see citing works
Stewart, R. D., Auffret, M. D., Warr, A., Walker, A. W., Roehe, R., & Watson, M. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0202-3 · Cited by 593 · see citing works
Subsistence strategies in traditional societies distinguish gut microbiomes
Obregon-Tito, A. J., Tito, R. Y., Metcalf, J., Sankaranarayanan, K., Clemente, J. C., Ursell, L. K., Zech Xu, Z., Van Treuren, W., Knight, R., Gaffney, P. M., et al. (2015) · Nature Communications · doi:10.1038/ncomms7505 · Cited by 587 · see citing works
Martínez, I., Stegen, J. C., Maldonado-Gómez, M. X., Eren, A. M., Siba, P. M., Greenhill, A. R., & Walter, J. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.03.049 · Cited by 576 · see citing works
Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans
Hagan, T., Cortese, M., Rouphael, N., Boudreau, C., Linde, C., Maddur, M. S., Das, J., Wang, H., Guthmiller, J., Zheng, N.-Y., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.010 · Cited by 572 · see citing works
The ancestral and industrialized gut microbiota and implications for human health
Sonnenburg, E. D., & Sonnenburg, J. L. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0191-8 · Cited by 489 · see citing works
Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.018 · Cited by 476 · see citing works
Interpreting prevotella and bacteroides as biomarkers of diet and lifestyle
Gorvitovskaia, A., Holmes, S. P., & Huse, S. M. (2016) · Microbiome · doi:10.1186/s40168-016-0160-7 · Cited by 461 · see citing works
Rienzi, S. C. D., Sharon, I., Wrighton, K. C., Koren, O., Hug, L. A., Thomas, B. C., Goodrich, J. K., Bell, J. T., Spector, T. D., Banfield, J. F., et al. (2013) · eLife · doi:10.7554/elife.01102 · Cited by 404 · see citing works
Accurate and complete genomes from metagenomes
Chen, L.-X., Anantharaman, K., Shaiber, A., Eren, A. M., & Banfield, J. F. (2020) · Genome Research · doi:10.1101/gr.258640.119 · Cited by 401 · see citing works
Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota
Rampelli, S., Schnorr, S. L., Consolandi, C., Turroni, S., Severgnini, M., Peano, C., Brigidi, P., Crittenden, A. N., Henry, A. G., & Candela, M. (2015) · Current Biology · doi:10.1016/j.cub.2015.04.055 · Cited by 399 · see citing works
Santoru, M. L., Piras, C., Murgia, A., Palmas, V., Camboni, T., Liggi, S., Ibba, I., Lai, M. A., Orrù, S., Blois, S., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-10034-5 · Cited by 387 · see citing works
sourmash: a library for MinHash sketching of DNA
Brown, C. T., & Irber, L. C. (2016) · The Journal of Open Source Software · doi:10.21105/joss.00027 · Cited by 385 · see citing works
Assembly of long error-prone reads using de Bruijn graphs
Lin, Y., Yuan, J., Kolmogorov, M., Shen, M. W., Chaisson, M., & Pevzner, P. A. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1604560113 · Cited by 384 · see citing works
The khmer software package: enabling efficient nucleotide sequence analysis
Crusoe, M., Alameldin, H. F., Awad, S., Boucher, E., Caldwell, A., Cartwright, R., Charbonneau, A. L., Constantinides, B., Edvenson, G., Fay, S. A., et al. (2015) · F1000Research · doi:10.12688/f1000research.6924.1 · Cited by 371 · see citing works
Complete, closed bacterial genomes from microbiomes using nanopore sequencing
Moss, E. L., Maghini, D. G., & Bhatt, A. S. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0422-6 · Cited by 371 · see citing works
Self-citationHigh-depth African genomes inform human migration and health
Choudhury, A., Aron, S., Botigué, L. R., Sengupta, D., Botha, G., Bensellak, T., Wells, G., Kumuthini, J., Shriner, D., Fakim, Y. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2859-7 · Cited by 355 · see citing works
Self-citationHigh-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED
Kaminski, J., Gibson, M. K., Franzosa, E. A., Segata, N., Dantas, G. A., & Huttenhower, C. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004557 · Cited by 325 · see citing works
Cohort Profile: Mandela's children: The 1990 birth to twenty study in South Africa
Richter, L., Norris, S. A., Pettifor, J. M., Yach, D., & Cameron, N. (2007) · International Journal of Epidemiology · doi:10.1093/ije/dym016 · Cited by 321 · see citing works
Self-citationBiology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut
Guerin, E., Shkoporov, A. N., Stockdale, S. R., Clooney, A. G., Ryan, F. J., Sutton, T., Draper, L. A., González-Tortuero, E., Ross, R. P., & Hill, C. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.10.002 · Cited by 297 · see citing works
Tyler, A. D., Mataseje, L., Urfano, C. J., Schmidt, L., Antonation, K. S., Mulvey, M. R., & Corbett, C. R. (2018) · Scientific Reports · doi:10.1038/s41598-018-29334-5 · Cited by 294 · see citing works
An Expanded Genomic Representation of the Phylum Cyanobacteria
Soo, R. M., Skennerton, C. T., Sekiguchi, Y., Imelfort, M., Paech, S. J., Dennis, P. G., Steen, J. A., Parks, D. H., Tyson, G. W., & Hugenholtz, P. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu073 · Cited by 290 · see citing works
Kengne, A. P., Bentham, J., Zhou, B., Peer, N., Matsha, T. E., Bixby, H., Cesare, M. D., Hajifathalian, K., Lu, Y., Taddei, C., et al. (2017) · International Journal of Epidemiology · doi:10.1093/ije/dyx078 · Cited by 267 · see citing works
Self-citationGlobal phylogeography and ancient evolution of the widespread human gut virus crAssphage
Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M. C., Levi, K., Dinsdale, E. A., Cinek, O., Aziz, R. K., McNair, K. A., Barr, J. J., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0494-6 · Cited by 247 · see citing works
Transmission of human-associated microbiota along family and social networks
Brito, I., Gurry, T., Zhao, S., Huang, K. H., Young, S., Shea, T. P., Naisilisili, W., Jenkins, A., Jupiter, S. D., Gevers, D., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0409-6 · Cited by 239 · see citing works
Parasite-Microbiota Interactions With the Vertebrate Gut: Synthesis Through an Ecological Lens
Leung, J. M., Graham, A. L., & Knowles, S. C. L. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00843 · Cited by 214 · see citing works
Gut microbiome transition across a lifestyle gradient in Himalaya
Jha, A. R., Davenport, E., Gautam, Y., Bhandari, D., Tandukar, S., Ng, K. M., Fragiadakis, G. K., Holmes, S., Gautam, G. P., Leach, J. D., et al. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2005396 · Cited by 184 · see citing works
Ramsay, M., Crowther, N. J., Tambo, E., Agongo, G., Baloyi, V., Dikotope, S. A., Gómez-Olivé, F. X., Jaff, N. G., Sorgho, H., Wagner, R. G., et al. (2016) · Global Health · doi:10.1017/gheg.2016.17 · Cited by 183 · see citing works
Self-citationRecovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategyPreprint
Sieber, C. M. K., Probst, A. J., Sharrar, A. M., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/107789 · Cited by 173 · see citing works
Links between environment, diet, and the hunter-gatherer microbiome
Fragiadakis, G. K., Smits, S. A., Sonnenburg, E. D., Treuren, W. V., Reid, G., Knight, R. D., Manjurano, A. M., Changalucha, J. M., Domínguez-Bello, M. G., Leach, J. D., et al. (2018) · Gut Microbes · doi:10.1080/19490976.2018.1494103 · Cited by 164 · see citing works
Ajayi, I. O., Adebamowo, C., Adami, H., Dalal, S., Diamond, M. B., Bajunirwe, F., Guwatudde, D., Njelekela, M. A., Nankya-Mutyoba, J., Chiwanga, F. S., et al. (2016) · BMC Public Health · doi:10.1186/s12889-016-3789-z · Cited by 155 · see citing works
Role of the Microbiota in the Modulation of Vaccine Immune Responses
Ciabattini, A., Olivieri, R., Lazzeri, E., & Medaglini, D. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01305 · Cited by 151 · see citing works
Sato, M. P., Ogura, Y., Nakamura, K., Nishida, R., Gotoh, Y., Hayashi, M., Hisatsune, J., Sugai, M., Itoh, T., & Hayashi, T. (2019) · DNA Research · doi:10.1093/dnares/dsz017 · Cited by 143 · see citing works
Evolution of the gut microbiome following acute HIV-1 infection
Rocafort, M., Noguera-Julián, M., Rivera, J., Pastor, L., Guillén, Y., Langhorst, J., Parera, M., Mandomando, I., Carrillo, J., Urrea, V., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0687-5 · Cited by 137 · see citing works
Campbell, T., Sun, X., Patel, V. H., Sanz, C., Morgan, D., & Dantas, G. A. (2020) · The ISME Journal · doi:10.1038/s41396-020-0634-2 · Cited by 131 · see citing works
Angelakis, E., Bachar, D., Yasir, M., Musso, D., Djossou, F., Gaborit, B., Brah, S., Diallo, A., Ndombe, G. M., Mediannikov, O., et al. (2018) · New Microbes and New Infections · doi:10.1016/j.nmni.2018.10.009 · Cited by 111 · see citing works
de la Cuesta‐Zuluaga, J., Corrales-Agudelo, V., Velásquez-Mejía, E. P., Carmona, J. A., Abad, J. M., & Escobar, J. S. (2018) · Scientific Reports · doi:10.1038/s41598-018-29687-x · Cited by 110 · see citing works
Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana
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., et al. (2019) · Genome Biology · doi:10.1186/s13059-018-1616-9 · Cited by 110 · see citing works
Kabudula, C. W., Houle, B. C., Collinson, M., Kahn, K., Gómez-Olivé, F. X., Clark, S. J., & Tollman, S. M. (2017) · BMC Public Health · doi:10.1186/s12889-017-4312-x · Cited by 108 · see citing works
Self-citationSystematically investigating the impact of medication on the gut microbiome
Maier, L., & Typas, A. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.11.001 · Cited by 90 · see citing works
Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation
Brewster, R., Tamburini, F. B., Asiimwe, E., Oduaran, O. H., Hazelhurst, S., & Bhatt, A. S. (2019) · Trends in Microbiology · doi:10.1016/j.tim.2019.05.006 · Cited by 79 · see citing works
Self-citationYinda, C. K., Vanhulle, E., Conceição-Neto, N., Beller, L., Deboutte, W., Shi, C., Ghogomu, S. M., Maes, P., Van Ranst, M., & Matthijnssens, J. (2019) · mSphere · doi:10.1128/msphere.00585-18 · Cited by 75 · see citing works
SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes
Lu, J., & Salzberg, S. L. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008439 · Cited by 75 · see citing works
Lokmer, A., Cian, A., Froment, A., Gantois, N., Viscogliosi, É., Chabé, M., & Ségurel, L. (2019) · PLoS ONE · doi:10.1371/journal.pone.0211139 · Cited by 71 · see citing works
Koslicki, D., & Falush, D. (2016) · mSystems · doi:10.1128/msystems.00020-16 · Cited by 68 · see citing works
Collinson, M., White, M. J., Bocquier, P., McGarvey, S. T., Afolabi, S. A., Clark, S. J., Kahn, K., & Tollman, S. M. (2014) · Global Health Action · doi:10.3402/gha.v7.23514 · Cited by 67 · see citing works
Self-citationOduaran, O. H., Tamburini, F. B., Sahibdeen, V., Brewster, R., Gómez-Olivé, F. X., Kahn, K., Norris, S. A., Tollman, S. M., Twine, R., Wade, A. N., et al. (2020) · BMC Microbiology · doi:10.1186/s12866-020-02017-w · Cited by 64 · see citing works
Self-citationKabudula, C. W., Houle, B. C., Collinson, M., Kahn, K., Gómez-Olivé, F. X., Tollman, S. M., & Clark, S. J. (2017) · The Lancet Global Health · doi:10.1016/s2214-109x(17)30297-8 · Cited by 56 · see citing works
Self-citationStreptomyces, shared microbiome member of soil and gut, as ‘old friends’ against colon cancer
Bolourian, A., & Mojtahedi, Z. (2018) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiy120 · Cited by 49 · see citing works
The Unfolding Counter-Transition in Rural South Africa: Mortality and Cause of Death, 1994–2009
Houle, B. C., Clark, S. J., Gómez-Olivé, F. X., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0100420 · Cited by 46 · see citing works
Self-citationEmerging evidence linking the gut microbiome to neurologic disorders
Griffiths, J. A., & Mazmanian, S. K. (2018) · Genome Medicine · doi:10.1186/s13073-018-0609-3 · Cited by 44 · see citing works
Bawah, A. A., Houle, B. C., Alam, N., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0157281 · Cited by 43 · see citing works
Global phylogeography and ancient evolution of the widespread human gut virus crAssphagePreprint
Edwards, R. A., Vega, A. A., Norman, H., Ohaeri, M. C., Levi, K., Dinsdale, E. A., Cinek, O., Aziz, R. K., McNair, K. A., Barr, J. J., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/527796 · Cited by 43 · see citing works
Santosa, A., & Byass, P. (2016) · PLoS ONE · doi:10.1371/journal.pone.0155753 · Cited by 42 · see citing works
Struo: a pipeline for building custom databases for common metagenome profilers
de la Cuesta‐Zuluaga, J., Ley, R. E., & Youngblut, N. D. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz899 · Cited by 37 · see citing works
Complete genome sequence of Treponema succinifaciens type strain (6091T)
Han, C. S., Gronow, S., Teshima, H., Lapidus, A. L., Nolan, M., Lucas, S. M., Hammon, N. M., Deshpande, S., Cheng, J., Zeytun, A., et al. (2011) · Standards in Genomic Sciences · doi:10.4056/sigs.1984594 · Cited by 33 · see citing works
Trönnberg, L., Hawksworth, D., Hansen, A., et al. (2010) · Transactions of the Royal Society of Tropical Medicine and Hygiene · doi:10.1016/j.trstmh.2010.06.009 · Cited by 32 · see citing works
Gut microbiome transition across a lifestyle gradient in HimalayaPreprint
Jha, A. R., Davenport, E., Gautam, Y., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/253450 · Cited by 32 · see citing works
Jacobson, D. K., Honap, T. P., Ozga, A. T., Méda, N., Kagone, T., Carabin, H., Spicer, P., Tito, R. Y., Obregón-Tito, A. J., Marin-Reyes, L., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-81257-w · Cited by 22 · see citing works
Links between environment, diet, and the hunter-gatherer microbiomePreprint
Fragiadakis, G. K., Smits, S. A., Sonnenburg, E. D., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/319673 · Cited by 20 · see citing works
Sonnenburg, J. L., & Sonnenburg, E. D. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.10.010 · Cited by 7 · see citing works
harrietr: Wrangle Phylogenetic Distance Matrices and Other Utilities
da Silva, A. G. (2017) · doi:10.32614/cran.package.harrietr · Cited by 2 · see citing works
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Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population
Manara, S., Selma-Royo, M., Huang, K. D., Asnicar, F., Armanini, F., Blanco-Miguez, A., Cumbo, F., Golzato, D., Manghi, P., Pinto, F., et al. (2023) · Current Biology · doi:10.1016/j.cub.2023.04.011 · Cited by 30 · see citing works
- Authors
- Tamburini, F. B., Maghini, D., Oduaran, O. H., Brewster, R., Hulley, M. R., Sahibdeen, V., Norris, S. A., Tollman, S., Kahn, K., Wagner, R. G., Wade, A. N., Wafawanaka, F., Gómez-Olivé, F. X., Twine, R., Lombard, Z., H3Africa AWI-Gen Collaborative Centre, Agongo, G., Alberts, M., Ali, S., Asiki, G., Baloyi, V., Boua, P. R., Brandenburg, J.-T., Ceballos, F. C., Chikowore, T., Choma, S., Choudhury, A., Crowther, N., Debpuur, C., Gondwe, M., Hazelhurst, S., Kahn, K., Khayeka-Wandabwa, C., Kisiangani, I., Kyobutungi, C., Lombard, Z., Mashaba, G., Mashinya, F., Mathema, T., Micklesfield, L., Mohamed, S., Mthembu, B., Mukomana, F., Nonterah, E., Norris, S. A., Oduaran, O., Oduro, A. R., Gómez-Olivé, F. X., Ramsay, M., Sankoh, O., Sengupta, D., Smyth, N., Soo, C., Soodyall, H., Sorgho, H., Swiel, Y., Tambo, E., Tindana, P., Tinto, H., Tluway, F., Tollman, S., Twine, R., Wade, A., Wagner, R., Wandera, H., Kabudula, C., Ohene-Kwofie, D., Wafawanaka, F., Hazelhurst, S., & Bhatt, A. S.
- Affiliations
- Stanford University (US)
- Stanford Medicine (US)
- National Health Laboratory Service (ZA)
- University of the Witwatersrand (ZA)
- Corresponding author
- Bhatt, Ami S.
- ORCID
- Tamburini, Fiona B.
- Maghini, Dylan
- Oduaran, Ovokeraye H.
- Brewster, Ryan
- Hulley, Michaella R.
- Sahibdeen, Venesa
- Agongo, Godfred
- Alberts, Marianne
- Ali, Stuart
- Asiki, Gershim
- Baloyi, Vukosi
- Boua, Palwendé Romuald
- Brandenburg, Jean-Tristan
- Ceballos, Francisco Camiña
- Chikowore, Tinashe
- Choma, Solomon
- Choudhury, Ananyo
- Crowther, Nigel
- Debpuur, Cornelius
- Kisiangani, Isaac
- Kyobutungi, Catherine
- Mashinya, Felistas
- Micklesfield, Lisa
- Mohamed, Shukri
- Mukomana, Freedom
- Nonterah, Engelbert
- Oduro, Abraham R.
- Ramsay, Michèle
- Sankoh, Osman
- Sengupta, Dhriti
- Soo, Cassandra
- Soodyall, Himla
- Swiel, Yaniv
- Tambo, Ernest
- Tinto, Halidou
- Tluway, Furahini
- Wandera, Henry
- Kabudula, Chodziwadziwa
- Bhatt, Ami S.
- Venue
- Nature Communications
- Published
- 2022-02-22
- Volume
- 13
- Issue
- 1
- Pages
- 926-926
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC8863827
- OpenAlex
- W4212782842
- Cited by
- 88
- References
- 123
- Citations by year
- 2026: 17 · 2025: 30 · 2024: 19 · 2023: 14 · 2022: 7 · 2020: 1
- FWCI
- 5.71
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Science Foundation (GRFP)
- Stanford CEHG
- Stanford Graduate Fellowship
- U.S. Department of Health & Human Services | NIH | Fogarty International Center
- U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (R01 AI148623)
- U.S. Department of Health & Human Services | National Institutes of Health (P30 CA124435)
- Stanford Center for Innovation in Global Health; Rosenkranz Prize
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- human gut microbiome, rural-urban transition, South Africa, microbial diversity, beta diversity, undescribed taxa, Treponema, Lentisphaerae
- MeSH terms
- Gastrointestinal Microbiome, Adult, Female, Humans, Rural Population, South Africa, Metagenomics, Microbiota
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