{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T03:44:19Z","timestamp":1790653459731,"version":"4.1.0"},"reference-count":86,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,5,31]],"date-time":"2021-05-31T00:00:00Z","timestamp":1622419200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p>Research on the human microbiome has mainly been restricted to the identification of most abundant microbiota associated with health or disease. Their abundance may reflect their capacity to exploit their niche, however, metabolic functions exerted by low-abundant microrganisms can impact the dysbiotic signature of local microbial habitats. This scoping review aims to map the literature regarding the management of low-abundant microorganisms in studies investigating human microbiome samples. A systematic literature search was performed in 5 electronic databases, as well as grey literature. We selected clinical microbiome studies targeting human participants of any age, from any body site. We also included studies with secondary data which originated from human biofilm samples. All of the papers used next-generation sequencing (NGS) techniques in their methodology. A total of 826 manuscripts were retrieved, of which 42 were included in this review and 22 reported low-abundant bacteria (LB) in samples taken from 7 body sites (breast, gut, oral cavity, skin, stomach, upper respiratory tract (URT), and vagina). Four studies reported microbes at abundance levels between 5 and 20%, 8 studies reported between 1 and 5%, and 18 studies reported below 1%. Fifteen papers mentioned fungi and\/or archaea, and from those only 4 (fungi) and 2 (archaea) produced data regarding the abundance of these domains. While most studies were directed towards describing the taxonomy, diversity and abundance of the highly abundant species, low-abundant species have largely been overlooked. Indeed, most studies select a cut-off value at &amp;lt;1% for low-abundant organisms to be excluded in their analyses. This practice may compromise the true diversity and influence of all members of the human microbiota. Despite their low abundance and signature in biofilms, they may generate important markers contributing to dysbiosis, in a sort of \u2018butterfly effect\u2019. A detailed snapshot of the physiological, biological mechanisms at play, including virulence determinants in the context of a dysbiotic community, may help better understand the health-disease transition.<\/jats:p>","DOI":"10.3389\/fcimb.2021.689197","type":"journal-article","created":{"date-parts":[[2021,5,31]],"date-time":"2021-05-31T03:35:02Z","timestamp":1622432102000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":81,"title":["Low-Abundant Microorganisms: The Human Microbiome\u2019s Dark Matter, a Scoping Review"],"prefix":"10.3389","volume":"11","author":[{"given":"J\u00e9ssica Alves de","family":"Cena","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianying","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongmei","family":"Deng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nail\u00ea","family":"Dam\u00e9-Teixeira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thuy","family":"Do","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2021,5,31]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12864-016-3254-5","article-title":"Integrated Metagenomic Data Analysis Demonstrates That a Loss of Diversity in Oral Microbiota Is Associated With Periodontitis","volume":"18","author":"Ai","year":"2017","journal-title":"BMC Genomics"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0135620","article-title":"A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing Cpn60-Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types","volume":"10","author":"Albert","year":"2015","journal-title":"PloS One"},{"key":"B3","doi-asserted-by":"publisher","first-page":"31444","DOI":"10.3402\/jom.v8.31444","article-title":"Species-Level Core Oral Bacteriome Identified by 16S Rrna Pyrosequencing in a Healthy Young Arab Population","volume":"8","author":"Al-hebshi","year":"2016","journal-title":"J. Oral. Microbiol."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.02360","article-title":"Keystone Species in Pregnancy Gingivitis: A Snapshot of Oral Microbiome During Pregnancy and Postpartum Period","volume":"9","author":"Balan","year":"2018","journal-title":"Front. Microbiol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/s41579-018-0024-1","article-title":"Keystone Taxa as Drivers of Microbiome Structure and Functioning","volume":"16","author":"Banerjee","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-020-00875-0","article-title":"Microbiome Definition Re-Visited: Old Concepts and New Challenges","volume":"8","author":"Berg","year":"2020","journal-title":"Microbiome"},{"key":"B7","doi-asserted-by":"publisher","first-page":"1169","DOI":"10.1038\/mi.2016.131","article-title":"Helicobacter Pylori Infection Is Associated With an Altered Gastric Microbiota in Children","volume":"10","author":"Brawner","year":"2017","journal-title":"Mucosal Immunol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1186\/s12866-015-0351-6","article-title":"The Truth About Metagenomics: Quantifying and Counteracting Bias in 16S rRNA Studies","volume":"15","author":"Brooks","year":"2015","journal-title":"BMC Microbiol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1128\/IAI.74.1.673-681.2006","article-title":"Cd4+-T-Cell Effector Functions and Costimulatory Requirements Essential for Surviving Mucosal Infection With Citrobacter Rodentium","volume":"74","author":"Bry","year":"2006","journal-title":"Infect. Immun."},{"key":"B10","doi-asserted-by":"publisher","first-page":"1932","DOI":"10.1016\/j.bbadis.2014.06.015","article-title":"Next Generation Sequencing Technology: Advances and Applications","volume":"1842","author":"Buermans","year":"2014","journal-title":"Biochim. Biophys. Acta (BBA)-Mol. Basis Dis."},{"key":"B11","doi-asserted-by":"publisher","first-page":"2631","DOI":"10.1128\/jb.00261-15","article-title":"Functional Analysis of Porphyromonas Gingivalis W83 Crispr-Cas Systems","volume":"197","author":"Burmistrz","year":"2015","journal-title":"J. Bacteriol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1177\/0022034512449462","article-title":"Progress Dissecting the Oral Microbiome in Caries and Health","volume":"24","author":"Burne","year":"2012","journal-title":"Adv. Dental Res."},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.00011","article-title":"Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects","volume":"10","author":"Camelo-Castillo","year":"2019","journal-title":"Front. Microbiol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"1074","DOI":"10.1111\/jcpe.12470","article-title":"Relationship Between Periodontitis-Associated Subgingival Microbiota and Clinical Inflammation by 16S Pyrosequencing","volume":"42","author":"Camelo-Castillo","year":"2015","journal-title":"J. Clin. Periodontol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2011-12-5-r50","article-title":"Moving Pictures of the Human Microbiome","volume":"12","author":"Caporaso","year":"2011","journal-title":"Genome Biol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1038\/nrmicro732","article-title":"The Damage-Response Framework of Microbial Pathogenesis","volume":"1","author":"Casadevall","year":"2003","journal-title":"Nat. Rev. Microbiol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1128\/AEM.01177-06","article-title":"Use of 16S rRNA and Rpob Genes as Molecular Markers for Microbial Ecology Studies","volume":"73","author":"Case","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1128\/aem.00547-18","article-title":"Bifidobacterium Pseudolongum in the Ceca of Rats Fed Hi-Maize Starch Has Characteristics of a Keystone Species in Bifidobacterial Blooms","volume":"84","author":"Centanni","year":"2018","journal-title":"Appl. Environ. Microbiol."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005361","article-title":"Boolean Analysis Reveals Systematic Interactions Among Low-Abundance Species in the Human Gut Microbiome","volume":"13","author":"Claussen","year":"2017","journal-title":"PloS Comput. Biol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"104606","DOI":"10.1016\/j.archoralbio.2019.104606","article-title":"Presence of Archaea in Dental Caries Biofilms","volume":"110","author":"Dame-Teixeira","year":"2020","journal-title":"Arch. Oral. Biol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-018-28550-3","article-title":"Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas","volume":"8","author":"Das","year":"2018","journal-title":"Sci. Rep."},{"key":"B22","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1186\/s40168-018-0605-2","article-title":"Simple Statistical Identification and Removal of Contaminant Sequences in Marker-Gene and Metagenomics Data","volume":"6","author":"Davis","year":"2018","journal-title":"Microbiome"},{"key":"B23","doi-asserted-by":"publisher","first-page":"1238","DOI":"10.2337\/db12-0526","article-title":"Fecal Microbiota Composition Differs Between Children With \u03b2-Cell Autoimmunity and Those Without","volume":"62","author":"de Goffau","year":"2013","journal-title":"Diabetes"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.02243","article-title":"Low Microbial Diversity and Abnormal Microbial Succession Is Associated With Necrotizing Enterocolitis in Preterm Infants","volume":"8","author":"Dobbler","year":"2017","journal-title":"Front. Microbiol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/hdy.2010.152","article-title":"Applications of Next Generation Sequencing in Molecular Ecology of Non-Model Organisms","volume":"107","author":"Ekblom","year":"2011","journal-title":"Heredity"},{"key":"B26","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1016\/j.jmii.2014.07.005","article-title":"Application of Next-Generation Sequencing to Study Ascitic Microbiome in Cirrhotic Patients With or Without Spontaneous Bacterial Peritonitis","volume":"48","author":"Feng","year":"2015","journal-title":"J. Microbiol. Immunol. Infect."},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0102451","article-title":"Identifying Keystone Species in the Human Gut Microbiome From Metagenomic Timeseries Using Sparse Linear Regression","volume":"9","author":"Fisher","year":"2014","journal-title":"PloS One"},{"key":"B28","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1016\/j.chom.2010.08.004","article-title":"Enterobacteriaceae Act in Concert With the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis","volume":"8","author":"Garrett","year":"2010","journal-title":"Cell Host Microbe"},{"key":"B29","doi-asserted-by":"publisher","first-page":"e1000713","DOI":"10.1371\/journal.ppat.1000713","article-title":"Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals","volume":"6","author":"Ghannoum","year":"2010","journal-title":"PloS Pathog."},{"key":"B30","doi-asserted-by":"publisher","first-page":"717","DOI":"10.1038\/nrmicro2873","article-title":"The Keystone-Pathogen Hypothesis","volume":"10","author":"Hajishengallis","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1016\/j.tim.2016.02.010","article-title":"Dancing With the Stars: How Choreographed Bacterial Interactions Dictate Nososymbiocity and Give Rise to Keystone Pathogens, Accessory Pathogens, and Pathobionts","volume":"24","author":"Hajishengallis","year":"2016","journal-title":"Trends Microbiol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.1101\/gr.085464.108","article-title":"Microbial Community Profiling for Human Microbiome Projects: Tools, Techniques, and Challenges","volume":"19","author":"Hamady","year":"2009","journal-title":"Genome Res."},{"key":"B33","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1002\/alr.21428","article-title":"Sinus Culture Poorly Predicts Resident Microbiota","volume":"5","author":"Hauser","year":"2015","journal-title":"Int. Forum Allergy Rhinol"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0116705","article-title":"Complementary Amplicon-Based Genomic Approaches for the Study of Fungal Communities in Humans","volume":"10","author":"Heisel","year":"2015","journal-title":"PloS One"},{"key":"B35","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1111\/j.1600-0757.2005.00113.x","article-title":"Porphyromonas Gingivalis, Treponema Denticola, and Tannerella Forsythia: The \u2018Red Complex\u2019, a Prototype Polybacterial Pathogenic Consortium in Periodontitis","volume":"38","author":"Holt","year":"2005","journal-title":"Periodontol. 2000"},{"key":"B36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-018-26509-y","article-title":"Combining Amplicon Sequencing and Metabolomics in Cirrhotic Patients Highlights Distinctive Microbiota Features Involved in Bacterial Translocation, Systemic Inflammation and Hepatic Encephalopathy","volume":"8","author":"Iebba","year":"2018","journal-title":"Sci. Rep."},{"key":"B37","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1186\/s13550-017-0318-8","article-title":"Gut Microbiota and Physiologic Bowel 18 F-FDG Uptake","volume":"7","author":"Kang","year":"2017","journal-title":"EJNMMI Res."},{"key":"B38","doi-asserted-by":"publisher","first-page":"e1002541","DOI":"10.1371\/journal.pcbi.1002541","article-title":"A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: Drisee","volume":"8","author":"Keegan","year":"2012","journal-title":"PloS Comput. Biol."},{"key":"B39","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1016\/j.chom.2013.07.007","article-title":"Fusobacterium Nucleatum Potentiates Intestinal Tumorigenesis and Modulates the Tumor-Immune Microenvironment","volume":"14","author":"Kostic","year":"2013","journal-title":"Cell Host Microbe"},{"key":"B40","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-019-55290-9","article-title":"Differences in the Intestinal Microbiome of Healthy Children and Patients With Newly Diagnosed Crohn\u2019s Disease","volume":"9","author":"Kowalska-Duplaga","year":"2019","journal-title":"Sci. Rep."},{"key":"B41","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1186\/s13073-016-0327-7","article-title":"Capturing the Diversity of the Human Gut Microbiota Through Culture-Enriched Molecular Profiling","volume":"8","author":"Lau","year":"2016","journal-title":"Genome Med."},{"key":"B42","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1186\/s12866-016-0689-4","article-title":"Decontamination of 16S Rrna Gene Amplicon Sequence Datasets Based on Bacterial Load Assessment by Qpcr","volume":"16","author":"Lazarevic","year":"2016","journal-title":"BMC Microbiol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"6176","DOI":"10.1073\/pnas.0308766101","article-title":"Methanogenic Archaea and Human Periodontal Disease","volume":"101","author":"Lepp","year":"2004","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0063139","article-title":"Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome","volume":"8","author":"Li","year":"2013","journal-title":"PloS One"},{"key":"B45","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1186\/1471-2164-11-488","article-title":"Molecular Analysis of the Diversity of Vaginal Microbiota Associated With Bacterial Vaginosis","volume":"11","author":"Ling","year":"2010","journal-title":"BMC Genomics"},{"key":"B46","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1016\/j.atherosclerosis.2018.11.038","article-title":"The Intestinal Microbiota Associated With Cardiac Valve Calcification Differs From That of Coronary Artery Disease","volume":"284","author":"Liu","year":"2019","journal-title":"Atherosclerosis"},{"key":"B47","doi-asserted-by":"publisher","first-page":"e3","DOI":"10.1093\/nar\/gks828","article-title":"Composition-Based Classification of Short Metagenomic Sequences Elucidates the Landscapes of Taxonomic and Functional Enrichment of Microorganisms","volume":"41","author":"Liu","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"B48","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41368-019-0045-2","article-title":"Salivary Mycobiome Dysbiosis and its Potential Impact on Bacteriome Shifts and Host Immunity in Oral Lichen Planus","volume":"11","author":"Li","year":"2019","journal-title":"Int. J. Oral. Sci."},{"key":"B49","doi-asserted-by":"publisher","first-page":"434","DOI":"10.1038\/nbt.2198","article-title":"Performance Comparison of Benchtop High-Throughput Sequencing Platforms","volume":"30","author":"Loman","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"e30087","DOI":"10.1371\/journal.pone.0030087","article-title":"Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community Dna Sample","volume":"7","author":"Luo","year":"2012","journal-title":"PloS One"},{"key":"B51","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1146\/annurev-anchem-062012-092628","article-title":"Next-Generation Sequencing Platforms","volume":"6","author":"Mardis","year":"2013","journal-title":"Annu. Rev. Anal. Chem."},{"key":"B52","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1007\/s40142-015-0076-8","article-title":"Understanding the Basics of NGS: From Mechanism to Variant Calling","volume":"3","author":"Muzzey","year":"2015","journal-title":"Curr. Genet. Med. Rep."},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.00197","article-title":"Impact of Westernized Diet on Gut Microbiota in Children on Leyte Island","volume":"8","author":"Nakayama","year":"2017","journal-title":"Front. Microbiol."},{"key":"B54","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s40168-017-0373-4","article-title":"The Gut Mycobiome of the Human Microbiome Project Healthy Cohort","volume":"5","author":"Nash","year":"2017","journal-title":"Microbiome"},{"key":"B55","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.jtos.2018.11.005","article-title":"Biogeography of the Human Ocular Microbiota","volume":"17","author":"Ozkan","year":"2019","journal-title":"Ocul. Surf."},{"key":"B56","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1111\/j.1600-0757.2012.00453.x","article-title":"Composition and Development of Oral Bacterial Communities","volume":"64","author":"Palmer","year":"2014","journal-title":"Periodontol. 2000"},{"key":"B57","doi-asserted-by":"publisher","first-page":"846","DOI":"10.1177\/0022034514542468","article-title":"Newly Identified Pathogens Associated With Periodontitis: A Systematic Review","volume":"93","author":"Perez-Chaparro","year":"2014","journal-title":"J. Dent. Res."},{"key":"B58","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0058487","article-title":"The Dental Plaque Microbiome in Health and Disease","volume":"8","author":"Peterson","year":"2013","journal-title":"PloS One"},{"key":"B59","doi-asserted-by":"publisher","first-page":"609","DOI":"10.2307\/1312990","article-title":"Challenges in the Quest for Keystones: Identifying Keystone Species is Difficult\u2014But Essential to Understanding How Loss of Species Will Affect Ecosystems","volume":"46","author":"Power","year":"1996","journal-title":"BioScience"},{"key":"B60","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0154653","article-title":"Microbiome of Deep Dentinal Caries Lesions in Teeth With Symptomatic Irreversible Pulpitis","volume":"11","author":"Rocas","year":"2016","journal-title":"PloS One"},{"key":"B61","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/j.chom.2013.07.012","article-title":"Fusobacterium Nucleatum Promotes Colorectal Carcinogenesis by Modulating E-Cadherin\/\u03b2-Catenin Signaling Via Its FadA Adhesin","volume":"14","author":"Rubinstein","year":"2013","journal-title":"Cell Host Microbe"},{"key":"B62","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0160856","article-title":"Microbiota in Breast Milk of Chinese Lactating Mothers","volume":"11","author":"Sakwinska","year":"2016","journal-title":"PloS One"},{"key":"B63","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1093\/jinfdis\/jiq061","article-title":"Perspective: Alpha-Bugs, Their Microbial Partners, and the Link to Colon Cancer","volume":"203","author":"Sears","year":"2011","journal-title":"J. Infect. Dis."},{"key":"B64","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.1038\/nbt1486","article-title":"Next-Generation DNA Sequencing","volume":"26","author":"Shendure","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"B65","doi-asserted-by":"publisher","first-page":"25443","DOI":"10.3402\/jom.v6.25443","article-title":"Metatranscriptomics Reveals Overall Active Bacterial Composition in Caries Lesions","volume":"6","author":"Sim\u00f3n-Soro","year":"2014","journal-title":"J. Oral. Microbiol."},{"key":"B66","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1016\/j.annepidem.2016.03.007","article-title":"Impact of Age and Sex on the Composition and Abundance of the Intestinal Microbiota in Individuals With and Without Enteric Infections","volume":"26","author":"Singh","year":"2016","journal-title":"Ann. Epidemiol."},{"key":"B67","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0137725","article-title":"Comparison of Fecal Microbiota in Children With Autism Spectrum Disorders and Neurotypical Siblings in the Simons Simplex Collection","volume":"10","author":"Son","year":"2015","journal-title":"PloS One"},{"key":"B68","volume-title":"Evolution & Detection of non-Coding RNA, and Transcriptome Analyses of Two non-Model Systems","author":"Srivastava","year":"2011"},{"key":"B69","volume-title":"Porphyromonas Gingivalis\u2013an Oral Keystone Pathogen Challenging the Human Immune System","author":"Stobernack","year":"2019"},{"key":"B70","doi-asserted-by":"publisher","first-page":"467","DOI":"10.7326\/M18-0850","article-title":"Prisma Extension for Scoping Reviews (Prisma-Scr): Checklist and Explanation","volume":"169","author":"Tricco","year":"2018","journal-title":"Ann. Intern. Med."},{"key":"B71","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-015-0107-4","article-title":"Ecology of Bacteria in the Human Gastrointestinal Tract-Identification of Keystone and Foundation Taxa","volume":"3","author":"Trosvik","year":"2015","journal-title":"Microbiome"},{"key":"B72","doi-asserted-by":"publisher","first-page":"804","DOI":"10.1038\/nature06244","article-title":"The Human Microbiome Project","volume":"449","author":"Turnbaugh","year":"2007","journal-title":"Nature"},{"key":"B73","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1016\/J.ENG.2017.01.008","article-title":"The Human Microbiota in Health and Disease","volume":"3","author":"Wang","year":"2017","journal-title":"Engineering"},{"key":"B74","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.02244","article-title":"Profiling of Oral Microbiota in Early Childhood Caries Using Single-Molecule Real-Time Sequencing","volume":"8","author":"Wang","year":"2017","journal-title":"Front. Microbiol."},{"key":"B75","doi-asserted-by":"publisher","first-page":"8639","DOI":"10.12659\/MSM.911768","article-title":"Gut Microbiota Disruption in Septic Shock Patients: A Pilot Study","volume":"24","author":"Wan","year":"2018","journal-title":"Med. Sci. Monit.: Int. Med. J. Exp. Clin. Res."},{"key":"B76","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000352","article-title":"Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples","volume":"5","author":"White","year":"2009","journal-title":"PloS Comput. Biol."},{"key":"B77","doi-asserted-by":"publisher","first-page":"298","DOI":"10.3390\/ijms21010298","article-title":"Targeting the 16s Rrna Gene for Bacterial Identification in Complex Mixed Samples: Comparative Evaluation of Second (Illumina) and Third (Oxford Nanopore Technologies) Generation Sequencing Technologies","volume":"21","author":"Winand","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"B78","doi-asserted-by":"publisher","first-page":"e00325","DOI":"10.1128\/mSystems.00325-19","article-title":"A Cross-Sectional Study of Compositional and Functional Profiles of Gut Microbiota in Sardinian Centenarians","volume":"4","author":"Wu","year":"2019","journal-title":"MSystems"},{"key":"B79","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41368-020-0082-x","article-title":"Oral Microbiome: Possible Harbinger for Children\u2019s Health","volume":"12","author":"Xiao","year":"2020","journal-title":"Int. J. Oral. Sci."},{"key":"B80","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1093\/ecco-jcc\/jjy188","article-title":"Il23r-Protective Coding Variant Promotes Beneficial Bacteria and Diversity in the Ileal Microbiome in Healthy Individuals Without Inflammatory Bowel Disease","volume":"13","author":"Zakrzewski","year":"2019","journal-title":"J. Crohn\u2019s Colitis"},{"key":"B81","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2019.00004","article-title":"Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut","volume":"9","author":"Zeng","year":"2019","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B82","first-page":"161","article-title":"Genoma, Microbioma Y Epigenoma Humano. Una Visi\u00f3n Contempor\u00e1nea De La Tr\u00edada Ecol\u00f3gica","volume":"71","author":"Zer\u00f3n","year":"2014","journal-title":"Rev. ADM"},{"key":"B83","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1186\/s13059-015-0821-z","article-title":"Identification of Low Abundance Microbiome in Clinical Samples Using Whole Genome Sequencing","volume":"16","author":"Zhang","year":"2015","journal-title":"Genome Biol."},{"key":"B84","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.03246","article-title":"A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples","volume":"9","author":"Zhang","year":"2019","journal-title":"Front. Microbiol."},{"key":"B85","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1016\/j.biopha.2018.01.146","article-title":"Human Oral Microbiota and its Modulation for Oral Health","volume":"99","author":"Zhang","year":"2018","journal-title":"BioMed. Pharmacother."},{"key":"B86","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41426-018-0202-2","article-title":"Altered Gut Microbiota After Traumatic Splenectomy Is Associated With Endotoxemia","volume":"7","author":"Zhu","year":"2018","journal-title":"Emerg. Microbes Infect."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2021.689197\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,5,31]],"date-time":"2021-05-31T03:35:09Z","timestamp":1622432109000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2021.689197\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,31]]},"references-count":86,"alternative-id":["10.3389\/fcimb.2021.689197"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2021.689197","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,5,31]]},"article-number":"689197"}}