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References from Exploring the universal healthy human gut microbiota around the World. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1371/journal.pbio.1002533
10.1371/journal.pbio.1002533 · External reference
The road to metagenomics: from microbiology to DNA sequencing technologies and bioinformatics
10.3389/fgene.2015.00348 · 2015 · External reference
10.1264/jsme2.me16024
10.1264/jsme2.me16024 · External reference
A review of methods and databases for metagenomic classification and assembly
10.1093/bib/bbx120 · 2019 · External reference
10.1093/femsre/fuw046
10.1093/femsre/fuw046 · External reference
10.1111/1365-2656.13229
10.1111/1365-2656.13229 · External reference
10.1038/nature06244
10.1038/nature06244 · External reference
10.1038/nature07540
10.1038/nature07540 · External reference
10.1371/journal.pone.0034242
10.1371/journal.pone.0034242 · External reference
10.1126/science.aad3503
10.1126/science.aad3503 · External reference
10.1093/femsre/fuw045
10.1093/femsre/fuw045 · External reference
The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units
10.1038/s41598-018-32221-8 · 2018 · External reference
10.7717/peerj.4652
10.7717/peerj.4652 · External reference
Exclusivity offers a sound yet practical species criterion for bacteria despite abundant gene flow
10.1186/s12864-018-5099-6 · 2018 · External reference
10.1016/j.bbrc.2015.12.083
10.1016/j.bbrc.2015.12.083 · External reference
Quantitative assessment of shotgun metagenomics and 16S rDNA amplicon sequencing in the study of human gut microbiome
10.1089/omi.2018.0013 · 2018 · External reference
10.1371/journal.pone.0206484
10.1371/journal.pone.0206484 · External reference
Bacterial associations in the healthy human gut microbiome across populations
10.1038/s41598-021-82449-0 · 2021 · External reference
Benchmarking metagenomics tools for taxonomic classification
10.1016/j.cell.2019.07.010 · 2019 · External reference
10.1016/j.cub.2015.05.040
10.1016/j.cub.2015.05.040 · External reference
10.1038/s41586-019-1058-x
10.1038/s41586-019-1058-x · External reference
10.1016/j.cell.2019.01.001
10.1016/j.cell.2019.01.001 · External reference
10.1371/journal.pbio.1000546
10.1371/journal.pbio.1000546 · External reference
Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny
10.1186/s13059-019-1807-z · 2019 · External reference
Unresolved reference
External reference
10.1038/nature11209
10.1038/nature11209 · External reference
FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science
10.1038/s41467-019-11306-6 · 2019 · External reference
10.1038/s41591-019-0559-3
10.1038/s41591-019-0559-3 · External reference
10.1038/s41587-018-0008-8
10.1038/s41587-018-0008-8 · External reference
10.1038/s41587-018-0009-7
10.1038/s41587-018-0009-7 · External reference
10.1038/s41586-019-0965-1
10.1038/s41586-019-0965-1 · External reference
10.1038/nature17672
10.1038/nature17672 · External reference
10.1093/dnares/dsw002
10.1093/dnares/dsw002 · External reference
Subsistence strategies in traditional societies distinguish gut microbiomes
2015 · External reference
10.1038/nm.3914
10.1038/nm.3914 · External reference
Unresolved reference
External reference
Unresolved reference
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10.1093/bioinformatics/btw354
10.1093/bioinformatics/btw354 · External reference
10.1186/s13059-019-1891-0
10.1186/s13059-019-1891-0 · External reference
10.7717/peerj-cs.104
10.7717/peerj-cs.104 · External reference
Unresolved reference
External reference
10.1371/journal.pone.0061217
10.1371/journal.pone.0061217 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
10.1093/bioinformatics/btw313
10.1093/bioinformatics/btw313 · External reference
10.1371/journal.pcbi.1005404
10.1371/journal.pcbi.1005404 · External reference
10.1093/database/baaa062
10.1093/database/baaa062 · External reference
Kraken: ultrafast metagenomic sequence classification using exact alignments
2014 · External reference
10.1111/j.1574-6941.2006.00204.x
10.1111/j.1574-6941.2006.00204.x · External reference
10.4161/gmic.2.2.15416 · Admitted local publication
10.1128/aem.66.4.1654-1661.2000
10.1128/aem.66.4.1654-1661.2000 · External reference
Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov
10.1099/00207713-52-6-2141 · 2002 · External reference
10.1007/bf02100146
10.1007/bf02100146 · External reference
10.1016/s0039-6060(98)70127-8
10.1016/s0039-6060(98)70127-8 · External reference
The Sporobiota of the Human Gut
10.1080/19490976.2020.1863134 · 2021 · External reference
Clostridium species as probiotics: potentials and challenges
2020 · External reference
10.1099/ijs.0.64192-0
10.1099/ijs.0.64192-0 · External reference
10.1002/9781118960608
10.1002/9781118960608 · External reference
10.1099/ijsem.0.002226
10.1099/ijsem.0.002226 · External reference
10.1099/ijs.0.65208-0
10.1099/ijs.0.65208-0 · External reference
Butyricicoccus pullicaecorum gen. nov., sp. nov., an anaerobic, butyrate-producing bacterium isolated from the caecal content of a broiler chicken
10.1099/ijs.0.65730-0 · 2008 · External reference
Butyricicoccus porcorum sp. nov., a butyrate-producing bacterium from swine intestinal tract
10.1099/ijsem.0.002738 · 2018 · External reference
Phylogenetic evidence for the transfer of Eubacterium lentum to the genus Eggerthella as Eggerthella lenta gen. nov., comb. nov
10.1099/00207713-49-4-1725 · 1999 · External reference
Adlercreutzia equolifaciens gen. nov., sp. nov., an equol-producing bacterium isolated from human faeces, and emended description of the genus Eggerthella
10.1099/ijs.0.65404-0 · 2008 · External reference
Taxonomic Study of Bacteroides clostridiiformis subsp. clostridiiformis (Burri and Ankersmit) Holdeman and Moore and of Related Organisms: Proposal of Clostridium clostridiiformis (Burri and Ankersmit) comb. nov. and Clostridium symbiosum (Stevens) comb. nov
10.1099/00207713-26-2-195 · 1976 · External reference
Reclassification of the Clostridium clostridioforme and Clostridium sphenoides clades as Enterocloster gen. nov. and Lacrimispora gen. nov., including reclassification of 15 taxa
10.1099/ijsem.0.003698 · 2020 · External reference
10.1111/1462-2920.12173
10.1111/1462-2920.12173 · External reference
Oscillibacter valericigenes gen. nov., sp. nov., a valerate-producing anaerobic bacterium isolated from the alimentary canal of a Japanese corbicula clam
10.1099/ijs.0.64717-0 · 2007 · External reference
Dysosmobacter welbionis gen. nov., sp. nov., isolated from human faeces and emended description of the genus Oscillibacter
10.1099/ijsem.0.003547 · 2020 · External reference
10.1053/j.gastro.2014.07.020
10.1053/j.gastro.2014.07.020 · External reference
Physiologic hypoxia and oxygen homeostasis in the healthy intestine. A review in the theme: cellular responses to hypoxia. American Journal of Physiology-Cell
2015 · External reference
10.1073/pnas.1718635115
10.1073/pnas.1718635115 · External reference
10.1038/nature17645
10.1038/nature17645 · External reference
10.1093/gbe/evu050
10.1093/gbe/evu050 · External reference
10.1371/journal.pbio.3000661
10.1371/journal.pbio.3000661 · External reference
10.1126/science.aaf3951
10.1126/science.aaf3951 · External reference
10.1073/pnas.1419136111
10.1073/pnas.1419136111 · External reference
10.1073/pnas.1734063100
10.1073/pnas.1734063100 · External reference
10.1146/annurev.nutr.22.011602.092259
10.1146/annurev.nutr.22.011602.092259 · External reference
The microbiome of uncontacted Amerindians
10.1126/sciadv.1500183 · 2015 · External reference
10.1016/j.celrep.2015.03.049
10.1016/j.celrep.2015.03.049 · External reference
10.1038/nature18646
10.1038/nature18646 · External reference
Detection of increased plasma interleukin-6 levels and prevalence of Prevotella copri and Bacteroides vulgatus in the feces of type 2 diabetes patients
10.3389/fimmu.2017.01107 · 2017 · External reference
10.1136/gutjnl-2014-307649
10.1136/gutjnl-2014-307649 · External reference
Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients
10.1073/pnas.0804812105 · 2008 · External reference
Unresolved reference
2022 · External reference
Dysbiosis in the gut bacterial microbiome of patients with uveitis, an inflammatory disease of the eye
10.1007/s12088-018-0746-9 · 2018 · External reference
Isolation and characterization of anaerobic bacteria from frozen rumen liquid and its potential Characterizations
10.3923/ijds.2017.47.51 · 2017 · External reference
Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study
10.1186/s12866-016-0708-5 · 2016 · External reference
Diversity in gut bacterial community of school-age children in Asia
10.1038/srep08397 · 2015 · External reference
10.3390/nu10081105
10.3390/nu10081105 · External reference
10.2217/fmb-2016-0130
10.2217/fmb-2016-0130 · External reference
10.1038/nature09944
10.1038/nature09944 · External reference
10.1038/nature11550
10.1038/nature11550 · External reference
10.3390/microorganisms7010014
10.3390/microorganisms7010014 · External reference
10.1128/mmbr.00051-12
10.1128/mmbr.00051-12 · External reference
10.1016/j.cell.2021.02.052
10.1016/j.cell.2021.02.052 · External reference
10.1038/nature10571
10.1038/nature10571 · External reference
10.1038/nature18927
10.1038/nature18927 · External reference
10.1038/nature08937
10.1038/nature08937 · External reference
Unresolved reference
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10.1038/nature12820
10.1038/nature12820 · External reference
The effects of vegetarian and vegan diets on gut microbiota
10.3389/fnut.2019.00047 · 2019 · External reference
Japanese traditional dietary fungus koji Aspergillus oryzae functions as a prebiotic for Blautia coccoides through glycosylceramide: Japanese dietary fungus koji is a new prebiotic
2016 · External reference
10.1016/j.cell.2014.09.053
10.1016/j.cell.2014.09.053 · External reference
Unresolved reference
2019 · External reference
Host-associated microbiomes are predicted by immune system complexity and climate
2020 · External reference
10.1017/s0007114514004127
10.1017/s0007114514004127 · External reference
10.3389/fmicb.2017.01162
10.3389/fmicb.2017.01162 · External reference
10.1038/nature25973
10.1038/nature25973 · External reference
Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador
10.4269/ajtmh.20-0831 · 2021 · External reference
10.1038/s41396-020-0634-2
10.1038/s41396-020-0634-2 · External reference
10.1038/s41564-017-0072-8
10.1038/s41564-017-0072-8 · External reference
10.1016/j.chom.2014.09.013
10.1016/j.chom.2014.09.013 · External reference
Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle
10.1186/s40168-016-0160-7 · 2016 · External reference
bifidobacteria as probiotic agents–physiological effects and clinical benefits
10.1111/j.1365-2036.2005.02615.x · 2005 · External reference
Review on Bifidobacterium bifidum BGN4: functionality and nutraceutical applications as a probiotic microorganism
10.3390/ijms17091544 · 2016 · External reference
Searching for the bacterial effector: The example of the multi-skilled commensal bacterium Faecalibacterium prausnitzii
10.3389/fmicb.2018.00346 · 2018 · External reference
Faecalibacterium prausnitzii: A Next-Generation Probiotic in Gut Disease Improvement
10.1155/2021/6666114 · 2021 · External reference
Gut microbiota and diarrhea: an updated review
10.3389/fcimb.2021.625210 · 2021 · External reference
High iron-sequestrating bifidobacteria inhibit enteropathogen growth and adhesion to intestinal epithelial cells in vitro
10.3389/fmicb.2016.01480 · 2016 · External reference
Low dietary fiber intake increases Collinsella abundance in the gut microbiota of overweight and obese pregnant women
10.1080/19490976.2017.1406584 · 2018 · External reference
Traditional human populations and nonhuman primates show parallel gut microbiome adaptations to analogous ecological conditions
10.1128/msystems.00815-20 · 2020 · External reference
