{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T20:10:20Z","timestamp":1791317420134,"version":"4.3.1"},"reference-count":70,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,3,24]],"date-time":"2025-03-24T00:00:00Z","timestamp":1742774400000},"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. Microbiol."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>The intestinal microbiota contributes to the colonization resistance of the gut towards bacterial pathogens. Antibiotic treatment often negatively affects the microbiome composition, rendering the host more susceptible for infections. However, a correct interpretation of such a perturbation requires quantitative microbiome profiling to reflect accurately the direction and magnitude of compositional changes within a microbiota. Standard 16S rRNA gene amplicon sequencing of microbiota samples offers compositional data in relative, but not absolute abundancies, and the presence of multiple copies of 16S rRNA genes in bacterial genomes introduces bias into compositional data. We explored whether improved sequencing data analysis influences the significance of the effect exerted by antibiotics on the faecal microbiota of young pigs using two veterinary antibiotics. Calculation of absolute abundances, either by flow cytometry-based bacterial cell counts or by spike-in of synthetic 16S rRNA genes, was employed and 16S rRNA gene copy numbers (GCN) were corrected.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Cell number determination exhibited large interindividual variability in two pig studies, using either tylosin or tulathromycin. Following tylosin application, flow cytometry-based cell counting revealed decreased absolute abundances of five families and ten genera. These results were not detectable by standard 16S analysis based on relative abundances. Here, GCN correction additionally uncovered significant decreases of <jats:italic>Lactobacillus<\/jats:italic> and <jats:italic>Faecalibacterium<\/jats:italic>. In another experimental setting with tulathromycin treatment, bacterial abundance quantification by flow cytometry and by a spike-in method yielded similar results only on the phylum level. Even though the spike-in method identified the decrease of four genera, analysis by fluorescence-activated cell sorting (FACS) uncovered eight significantly reduced genera, such as <jats:italic>Prevotella<\/jats:italic> and <jats:italic>Paraprevotella<\/jats:italic> upon antibiotic treatment. In contrast, analysis of relative abundances only showed a decrease of <jats:italic>Faecalibacterium<\/jats:italic> and <jats:italic>Rikenellaceae<\/jats:italic> RC9 gut group and, thus, a much less detailed antibiotic effect.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Flow cytometry is a laborious method, but identified a higher number of significant microbiome changes in comparison to common compositional data analysis and even revealed to be superior to a spike-in method. Calculation of absolute abundances and GCN correction are valuable methods that should be standards in microbiome analyses in veterinary as well as human medicine.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmicb.2025.1481197","type":"journal-article","created":{"date-parts":[[2025,3,24]],"date-time":"2025-03-24T10:55:11Z","timestamp":1742813711000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":19,"title":["Absolute abundance calculation enhances the significance of microbiome data in antibiotic treatment studies"],"prefix":"10.3389","volume":"16","author":[{"given":"Stefanie","family":"Wagner","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Weber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lena-Sophie","family":"Paul","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angelika","family":"Gr\u00fcmpel-Schl\u00fcter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeannette","family":"Kluess","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Klaus","family":"Neuhaus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thilo M.","family":"Fuchs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,3,24]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"e01202-20","DOI":"10.1128\/mSphere.01202-20","article-title":"Primer, pipelines, parameters: issues in 16S rRNA gene sequencing","volume":"6","author":"Abellan-Schneyder","year":"2021","journal-title":"mSphere"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"2629","DOI":"10.1128\/JB.186.9.2629-2635.2004","article-title":"Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons","volume":"186","author":"Acinas","year":"2004","journal-title":"J. Bacteriol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/2049-2618-2-11","article-title":"Copy righter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction","volume":"2","author":"Angly","year":"2014","journal-title":"Microbiome"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"804455","DOI":"10.3389\/fendo.2022.804455","article-title":"Taxonomic and functional fecal microbiota signatures associated with insulin resistance in non-diabetic subjects with overweight\/obesity within the frame of the PREDIMED-plus study","volume":"13","author":"Atzeni","year":"2022","journal-title":"Front. Endocrinol. (Lausanne)."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1093\/sysbio\/syy054","article-title":"EPA-ng: massively parallel evolutionary placement of genetic sequences","volume":"68","author":"Barbera","year":"2018","journal-title":"Syst. Biol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1186\/s12917-018-1704-9","article-title":"Intestinal microbiota mediates enterotoxigenic Escherichia coli-induced diarrhea in piglets","volume":"14","author":"Bin","year":"2018","journal-title":"BMC Vet. Res."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1513","DOI":"10.1017\/S095026881700036X","article-title":"Salmonella in the pork production chain and its impact on human health in the European Union","volume":"145","author":"Bonardi","year":"2017","journal-title":"Epidemiol. Infect."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.mimet.2018.09.015","article-title":"PCR-based quantification of taxa-specific abundances in microbial communities: quantifying and avoiding common pitfalls","volume":"153","author":"Bonk","year":"2018","journal-title":"J. Microbiol. Methods"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1111\/1755-0998.13730","article-title":"Pitfalls in the statistical analysis of microbiome amplicon sequencing data","volume":"23","author":"Boshuizen","year":"2023","journal-title":"Mol. Ecol. Resour."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1016\/j.chom.2023.04.003","article-title":"The natural product chlorotonil a preserves colonization resistance and prevents relapsing Clostridioides difficile infection","volume":"31","author":"Bublitz","year":"2023","journal-title":"Cell Host Microbe"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"e0125448","DOI":"10.1371\/journal.pone.0125448","article-title":"Antibiotics in early life alter the gut microbiome and increase disease incidence in a spontaneous mouse model of autoimmune insulin-dependent diabetes","volume":"10","author":"Candon","year":"2015","journal-title":"PLoS One"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"2106","DOI":"10.1093\/bioinformatics\/bts342","article-title":"Associating microbiome composition with environmental covariates using generalized Uni Frac distances","volume":"28","author":"Chen","year":"2012","journal-title":"Bioinformatics"},{"key":"ref14","first-page":"128","article-title":"The influence of probios or tylosin on growth of pigs and development of the gastrointestinal tract","author":"Collington","year":"1972"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"e40553","DOI":"10.7554\/eLife.40553","article-title":"Gut microbiota density influences host physiology and is shaped by host and microbial factors","volume":"8","author":"Contijoch","year":"2019","journal-title":"eLife"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"e0217050","DOI":"10.1371\/journal.pone.0217050","article-title":"Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples","volume":"14","author":"Czech","year":"2019","journal-title":"PLoS One"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"5588","DOI":"10.1128\/JCM.43.11.5588-5592.2005","article-title":"Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge","volume":"43","author":"De La Cochetiere","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"4554","DOI":"10.1073\/pnas.1000087107","article-title":"Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation","volume":"108","author":"Dethlefsen","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1038\/s41587-020-0548-6","article-title":"PICRUSt2 for prediction of metagenome functions","volume":"38","author":"Douglas","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1093\/jn\/nxz293","article-title":"A health-conscious food pattern is associated with prediabetes and gut microbiota in the Malm\u00f6 offspring study","volume":"150","author":"Ericson","year":"2020","journal-title":"J. Nutr."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1099\/00207713-47-2-590","article-title":"List of bacterial names with standing in nomenclature: a folder available on the internet","volume":"47","author":"Euz\u00e9by","year":"1997","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"10","DOI":"10.3389\/fcimb.2020.00403","article-title":"How to count our microbes? The effect of different quantitative microbiome profiling approaches","volume":"10","author":"Galazzo","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"006242","DOI":"10.1099\/ijsem.0.006242","article-title":"Valid publication of names of two domains and seven kingdoms of prokaryotes","volume":"74","author":"G\u00f6ker","year":"2024","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1007\/BF00416597","article-title":"Enrichment and isolation of Acetitomaculum ruminis, gen. Nov., sp. nov.: acetogenic bacteria from the bovine rumen","volume":"151","author":"Greening","year":"1989","journal-title":"Arch. Microbiol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"e16566","DOI":"10.1111\/1462-2920.16566","article-title":"Mock microbial community meta-analysis using different trimming of amplicon read lengths","volume":"26","author":"Haider","year":"2024","journal-title":"Environ. Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"717723","DOI":"10.3389\/fimmu.2021.717723","article-title":"A comprehensive analysis of the colonic flora diversity, short chain fatty acid metabolism, transcripts, and biochemical indexes in heat-stressed pigs","volume":"12","author":"Hu","year":"2021","journal-title":"Front. Immunol."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"e0227285","DOI":"10.1371\/journal.pone.0227285","article-title":"Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling","volume":"15","author":"Jian","year":"2020","journal-title":"PLoS One"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"2427","DOI":"10.1890\/06-1736.1","article-title":"Partitioning diversity into independent alpha and beta components","volume":"88","author":"Jost","year":"2007","journal-title":"Ecology"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1007\/s10872-007-0008-7","article-title":"Effects of fixation and storage on flow cytometric analysis of marine bacteria","volume":"63","author":"Kamiya","year":"2007","journal-title":"J. Oceanogr."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1017\/S175173111000193X","article-title":"Probiotics \u2013 do they have a role in the pig industry?","volume":"5","author":"Kenny","year":"2011","journal-title":"Animal"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"15485","DOI":"10.1073\/pnas.1205147109","article-title":"Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin","volume":"109","author":"Kim","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"876","DOI":"10.4014\/jmb.1512.12004","article-title":"Effects of the antibiotics growth promoter tylosin on swine gut microbiota","volume":"26","author":"Kim","year":"2016","journal-title":"J. Microbiol. Biotechnol."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"e2836","DOI":"10.7717\/peerj.2836","article-title":"Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons","volume":"5","author":"Lagkouvardos","year":"2017","journal-title":"PeerJ"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1186\/s12934-017-0793-7","article-title":"Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F420 autofluorescence","volume":"16","author":"Lambrecht","year":"2017","journal-title":"Microb. Cell Factories"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"e02634-18","DOI":"10.1128\/AEM.02634-18","article-title":"Towards quantitative microbiome community profiling using internal standards","volume":"85","author":"Lin","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1038\/s41522-020-00160-w","article-title":"Analysis of microbial compositions: a review of normalization and differential abundance analysis","volume":"6","author":"Lin","year":"2020","journal-title":"NPJ Biofilms Microbiomes"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1017\/S0007114521002968","article-title":"Long-term association between diet quality and characteristics of the gut microbiome in the multiethnic cohort study","volume":"128","author":"Ma","year":"2021","journal-title":"Br. J. Nutr."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"fuad039","DOI":"10.1093\/femsre\/fuad039","article-title":"Faecalibacterium: a bacterial genus with promising human health applications","volume":"47","author":"Martin","year":"2023","journal-title":"FEMS Microbiol. Rev."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/19490976.2020.1870402","article-title":"Association between antibiotics and gut microbiome dysbiosis in children: systematic review and meta-analysis","volume":"13","author":"McDonnell","year":"2021","journal-title":"Gut Microbes"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"e00206-19","DOI":"10.1128\/IAI.00206-19","article-title":"Antibiotic-induced shifts in fecal microbiota density and composition during hematopoietic stem cell transplantation","volume":"87","author":"Morjaria","year":"2019","journal-title":"Infect. Immun."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"2719","DOI":"10.1038\/s41467-019-10656-5","article-title":"Establishing microbial composition measurement standards with reference frames","volume":"10","author":"Morton","year":"2019","journal-title":"Nat. Commun."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"D613","DOI":"10.1093\/nar\/gkt1111","article-title":"LPSN\u2014list of prokaryotic names with standing in nomenclature","volume":"42","author":"Parte","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"1825","DOI":"10.1099\/ijsem.0.002786","article-title":"LPSN\u2013List of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on","volume":"68","author":"Parte","year":"2018","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"5607","DOI":"10.1099\/ijsem.0.004332","article-title":"List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ","volume":"70","author":"Parte","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1186\/s42523-021-00082-8","article-title":"A diet-specific microbiota drives Salmonella Typhimurium to adapt its in vivo response to plant-derived substrates","volume":"3","author":"Prax","year":"2021","journal-title":"Anim. Microbiome"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"7131","DOI":"10.1016\/j.watres.2013.07.051","article-title":"Monitoring microbiological changes in drinking water systems using a fast and reproducible flow cytometric method","volume":"47","author":"Prest","year":"2013","journal-title":"Water Res."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"1823","DOI":"10.1093\/bioinformatics\/bts252","article-title":"SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes","volume":"28","author":"Pruesse","year":"2012","journal-title":"Bioinformatics"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"633","DOI":"10.1038\/s41586-021-03241-8","article-title":"Multi-kingdom ecological drivers of microbiota assembly in preterm infants","volume":"591","author":"Rao","year":"2021","journal-title":"Nature"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1038\/s43705-021-00033-z","article-title":"Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling","volume":"1","author":"Reitmeier","year":"2021","journal-title":"ISME Commun."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"100148","DOI":"10.1016\/j.xpro.2020.100148","article-title":"Comparing circadian rhythmicity in the human gut microbiome","volume":"1","author":"Reitmeier","year":"2020","journal-title":"STAR Protoc."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1186\/s42523-022-00221-9","article-title":"An insight into the commercial piglet's microbial gut colonization: from birth towards weaning","volume":"4","author":"Saladrigas-Garc\u00eda","year":"2022","journal-title":"Anim. Microbiome"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1016\/B978-0-12-407863-5.00012-5","article-title":"Use of internal standards for quantitative metatranscriptome and metagenome analysis","volume":"531","author":"Satinsky","year":"2013","journal-title":"Methods Enzymol."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"5074","DOI":"10.3390\/jcm10215074","article-title":"Gut microbiome in chronic coronary syndrome patients","volume":"10","author":"Sawicka-Smiarowska","year":"2021","journal-title":"J. Clin. Med."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"e01049","DOI":"10.1128\/msystems.01049-23","article-title":"Interrelation between gut microbiota, SCFA, and fatty acid composition in pigs","volume":"9","author":"Sebasti\u00e0","year":"2024","journal-title":"mSystems"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1016\/j.tibtech.2015.06.011","article-title":"Proteobacteria: microbial signature of dysbiosis in gut microbiota","volume":"33","author":"Shin","year":"2015","journal-title":"Trends Biotechnol."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1186\/s40168-016-0175-0","article-title":"Adjusting microbiome profiles for differences in microbial load by spike-in bacteria","volume":"4","author":"St\u00e4mmler","year":"2016","journal-title":"Microbiome"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1038\/nrmicro2989","article-title":"\u201cBlooming\u201d in the gut: how dysbiosis might contribute to pathogen evolution","volume":"11","author":"Stecher","year":"2013","journal-title":"Nat. Rev. Microbiol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"18675","DOI":"10.1038\/s41598-019-55328-y","article-title":"Identification of the core bacteria in rectums of diarrheic and non-diarrheic piglets","volume":"9","author":"Sun","year":"2019","journal-title":"Sci. Rep."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1186\/s40168-018-0491-7","article-title":"Absolute quantitation of microbiota abundance in environmental samples","volume":"6","author":"Tkacz","year":"2018","journal-title":"Microbiome"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"9095","DOI":"10.1038\/s41598-018-27314-3","article-title":"Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls","volume":"8","author":"Tourlousse","year":"2018","journal-title":"Sci. Rep."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"e23","DOI":"10.1093\/nar\/gkw984","article-title":"Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing","volume":"45","author":"Tourlousse","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1111\/jam.13364","article-title":"Probiotic roles of Lactobacillus sp. in swine: insights from gut microbiota","volume":"122","author":"Valeriano","year":"2017","journal-title":"J. Appl. Microbiol."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"6740","DOI":"10.1038\/s41467-021-27098-7","article-title":"Temporal variability in quantitative human gut microbiome profiles and implications for clinical research","volume":"12","author":"Vandeputte","year":"2021","journal-title":"Nat. Commun."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1038\/nature24460","article-title":"Quantitative microbiome profiling links gut community variation to microbial load","volume":"551","author":"Vandeputte","year":"2017","journal-title":"Nature"},{"key":"ref65","doi-asserted-by":"publisher","first-page":"e57923","DOI":"10.1371\/journal.pone.0057923","article-title":"The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses","volume":"8","author":"Vetrovsky","year":"2013","journal-title":"PLoS One"},{"key":"ref66","doi-asserted-by":"publisher","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Wang","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"2901","DOI":"10.1099\/ijs.0.049270-0","article-title":"Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria","volume":"63","author":"Williams","year":"2013","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"9793","DOI":"10.1039\/D1FO01468D","article-title":"Gut microbiota-dependent catabolites of tryptophan play a predominant role in the protective effects of turmeric polysaccharides against DSS-induced ulcerative colitis","volume":"12","author":"Yang","year":"2021","journal-title":"Food Funct."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"e0205784","DOI":"10.1371\/journal.pone.0205784","article-title":"Analysis of gut microbiota and the effect of lauric acid against necrotic enteritis in Clostridium perfringens and Eimeria side-by-side challenge model","volume":"14","author":"Yang","year":"2019","journal-title":"PLoS One"},{"key":"ref70","doi-asserted-by":"publisher","first-page":"762","DOI":"10.3389\/fmicb.2015.00762","article-title":"Reutericyclin producing Lactobacillus reuteri modulates development of fecal microbiota in weanling pigs","volume":"6","author":"Yang","year":"2015","journal-title":"Front. Microbiol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1481197\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,24]],"date-time":"2025-03-24T10:55:20Z","timestamp":1742813720000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1481197\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,24]]},"references-count":70,"alternative-id":["10.3389\/fmicb.2025.1481197"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1481197","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,24]]},"article-number":"1481197"}}