{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T02:05:54Z","timestamp":1767837954175,"version":"3.49.0"},"reference-count":57,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2018,4,10]],"date-time":"2018-04-10T00:00:00Z","timestamp":1523318400000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010097","name":"China Association for Science and Technology","doi-asserted-by":"publisher","award":["CARS-44-A-4"],"award-info":[{"award-number":["CARS-44-A-4"]}],"id":[{"id":"10.13039\/100010097","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"DOI":"10.3389\/fmicb.2018.00733","type":"journal-article","created":{"date-parts":[[2018,4,10]],"date-time":"2018-04-10T04:22:17Z","timestamp":1523334137000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":31,"title":["Microbiome of Total Versus Live Bacteria in the Gut of Rex Rabbits"],"prefix":"10.3389","volume":"9","author":[{"given":"Xiangchao","family":"Fu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bo","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ping","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lihuan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bin","family":"Wen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hanzhong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shiqie","family":"Bai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gang","family":"Jia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2018,4,10]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1038\/nature09944","article-title":"Enterotypes of the human gut microbiome.","volume":"473","author":"Arumugam","year":"2011","journal-title":"Nature"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1038\/srep04202","article-title":"Stomach microbiota composition varies between patients with non-atrophic gastritis and patients with intestinal type of gastric cancer.","volume":"4","author":"Aviles-Jimenez","year":"2014","journal-title":"Sci. Rep."},{"key":"B3","doi-asserted-by":"publisher","first-page":"2940","DOI":"10.1128\/AEM.01333-08","article-title":"Discrimination of viable and dead fecal Bacteroidales bacteria by quantitative PCR with propidium monoazide.","volume":"75","author":"Bae","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"922","DOI":"10.1128\/AEM.05157-11","article-title":"Survival of host-associated bacteroidales cells and their relationship with Enterococcus spp., Campylobacter jejuni, Salmonella enterica serovar Typhimurium, and adenovirus in freshwater microcosms as measured by propidium monoazide-quantitative PCR.","volume":"78","author":"Bae","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"4679","DOI":"10.1128\/AEM.71.8.4679-4689.2005","article-title":"Genetic diversity of viable, injured, and dead fecal bacteria assessed by fluorescence-activated cell sorting and 16S rRNA gene analysis.","volume":"71","author":"Benamor","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"7438","DOI":"10.1128\/AEM.01071-12","article-title":"Selection for Cu-Tolerant bacterial communities with altered composition, but unaltered richness, via long-term Cu exposure.","volume":"78","author":"Berg","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1073\/pnas.0506655103","article-title":"Molecular analysis of the bacterial microbiota in the human stomach.","volume":"103","author":"Bik","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1038\/srep09342","article-title":"The bacterial communities associated with fecal types and body weight of rex rabbits.","volume":"5","author":"Bo","year":"2015","journal-title":"Sci. Rep."},{"key":"B9","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nmeth.2276","article-title":"Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.","volume":"10","author":"Bokulich","year":"2013","journal-title":"Nat. Methods"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0028742","article-title":"Complex carbohydrate utilization by the healthy human microbiome.","volume":"7","author":"Cantarel","year":"2011","journal-title":"PLoS One"},{"key":"B11","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data.","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. Methods"},{"key":"B12","doi-asserted-by":"publisher","first-page":"521.e248","DOI":"10.1111\/j.1365-2982.2012.01891.x","article-title":"Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome.","volume":"24","author":"Carroll","year":"2012","journal-title":"Neurogastroenterol. Motil."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1942","DOI":"10.3382\/ps.2014-03974","article-title":"Spatial heterogeneity and stability of bacterial community in the gastrointestinal tracts of broiler chickens.","volume":"93","author":"Choi","year":"2014","journal-title":"Poult. Sci."},{"key":"B14","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1126\/science.aad2602","article-title":"The ecology of the microbiome: networks, competition, and stability.","volume":"350","author":"Coyte","year":"2015","journal-title":"Science"},{"key":"B15","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1111\/j.1365-2672.1971.tb02307.x","article-title":"Transport and storage of faeces for bacteriological examination.","volume":"34","author":"Crowther","year":"1971","journal-title":"J. Appl. Bacteriol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1016\/j.cell.2014.09.043","article-title":"Alien invasions and Gut \u201cisland biogeography\u201d.","volume":"159","author":"Delong","year":"2014","journal-title":"Cell"},{"key":"B17","doi-asserted-by":"publisher","first-page":"3476","DOI":"10.1093\/bioinformatics\/btv401","article-title":"Error filtering, pair assembly and error correction for next-generation sequencing reads.","volume":"31","author":"Edgar","year":"2015","journal-title":"Bioinformatics"},{"key":"B18","first-page":"169","article-title":"A note on the total viable counts and selective enumeration of anaerobic bacteria in the caecal content, soft and hard faeces of rabbit.","volume":"46","author":"Emaldi","year":"2008","journal-title":"J. Appl. Microbiol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"813","DOI":"10.1007\/s00784-014-1297-z","article-title":"The effect of propidium monoazide treatment on the measured bacterial composition of clinical samples after the use of a mouthwash.","volume":"19","author":"Exterkate","year":"2015","journal-title":"Clin. Oral Investig."},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1002606","article-title":"Microbial Co-occurrence relationships in the human microbiome.","volume":"8","author":"Faust","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1016\/j.mimet.2011.09.007","article-title":"Molecular pathogen detection in biosolids with a focus on quantitative PCR using propidium monoazide for viable cell enumeration.","volume":"87","author":"Frankenhuyzen","year":"2011","journal-title":"J. Microbiol. Methods"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1038\/srep18761","article-title":"Microbial community profiling shows dysbiosis in the lesional skin of Vitiligo subjects.","volume":"6","author":"Ganju","year":"2016","journal-title":"Sci. Rep."},{"key":"B23","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/S0301-6226(97)00111-5","article-title":"Caeco-colic digestion in the growing rabbit: impact of nutritional factors and related disturbances.","volume":"51","author":"Gidenne","year":"1997","journal-title":"Livest. Prod. Sci."},{"key":"B24","doi-asserted-by":"publisher","first-page":"81","DOI":"10.4995\/wrs.2004.579","article-title":"Impact of caecotrophy on rate of passage, intake and faecal excretion pattern in the growing rabbit.","volume":"12","author":"Gidenne","year":"2010","journal-title":"World Rabbit Sci."},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0074957","article-title":"Bacterial community mapping of the mouse gastrointestinal tract.","volume":"8","author":"Gu","year":"2013","journal-title":"PLoS One"},{"key":"B26","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1007\/s00248-014-0389-2","article-title":"Detecting the nonviable and heat-tolerant bacteria in activated sludge by minimizing DNA from dead cells.","volume":"67","author":"Guo","year":"2014","journal-title":"Microb. Ecol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.mimet.2015.12.002","article-title":"Propidium monoazide treatment to distinguish between live and dead methanogens in pure cultures and environmental samples.","volume":"121","author":"Heise","year":"2015","journal-title":"J. Microbiol. Methods"},{"key":"B28","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.mimet.2015.12.002","article-title":"Propidium monoazide treatment to distinguish between live and dead methanogens in pure cultures and environmental samples.","volume":"121","author":"Heise","year":"2016","journal-title":"J. Microbiol. Methods"},{"key":"B29","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1128\/AEM.2.3.164-170.1954","article-title":"Improved preservation of Treponema pallidum and other bacteria by freezing with glycerol.","volume":"2","author":"Hollander","year":"1954","journal-title":"Appl. Microbiol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1258\/002367784780891307","article-title":"Phase relationship of the circadian rhythms of feed intake, caecal motility and production of soft and hard faeces in domestic rabbits.","volume":"18","author":"H\u00f6rnicke","year":"1984","journal-title":"Lab. Anim."},{"key":"B31","doi-asserted-by":"publisher","first-page":"M276","DOI":"10.1111\/j.1750-3841.2011.02191.x","article-title":"Determination of lactic microflora of kefir grains and kefir beverage by using culture-dependent and culture-independent methods.","volume":"76","author":"Kesmen","year":"2011","journal-title":"J. Food Sci."},{"key":"B32","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1007\/978-1-60761-175-2_12","article-title":"Cytoscape: a community-based framework for network modeling.","volume":"563","author":"Killcoyne","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"1081","DOI":"10.1038\/ismej.2015.198","article-title":"Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention.","volume":"10","author":"Leah","year":"2015","journal-title":"ISME J."},{"key":"B34","doi-asserted-by":"publisher","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","article-title":"UniFrac: a new phylogenetic method for comparing microbial communities.","volume":"71","author":"Lozupone","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"B35","doi-asserted-by":"publisher","first-page":"5936","DOI":"10.3748\/wjg.15.5936","article-title":"Diarrhoea-predominant irritable bowel syndrome distinguishable by 16S rRNA gene phylotype quantification.","volume":"15","author":"Lyra","year":"2009","journal-title":"World J. Gastroenterol."},{"key":"B36","doi-asserted-by":"publisher","first-page":"1891","DOI":"10.1038\/ismej.2015.261","article-title":"Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China.","volume":"10","author":"Ma","year":"2016","journal-title":"ISME J."},{"key":"B37","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: fast length adjustment of short reads to improve genome assemblies.","volume":"27","author":"Mago","year":"2011","journal-title":"Bioinformatics"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1038\/srep16116","article-title":"Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function.","volume":"5","author":"Mao","year":"2015","journal-title":"Sci. Rep."},{"key":"B39","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.cell.2012.10.052","article-title":"Xenobiotics shape the physiology and gene expression of the active human gut microbiome.","volume":"152","author":"Maurice","year":"2013","journal-title":"Cell"},{"key":"B40","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1038\/nrmicro1901","article-title":"Microbiology in the post-genomic era.","volume":"6","author":"Medini","year":"2008","journal-title":"Nat. Rev. Microbiol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"1082","DOI":"10.1038\/oby.2012.8","article-title":"Women with and without metabolic disorder differ in their gut microbiota composition.","volume":"20","author":"Munukka","year":"2012","journal-title":"Obesity"},{"key":"B42","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1099\/00221287-148-1-257","article-title":"Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set.","volume":"148","author":"Nadkarni","year":"2002","journal-title":"Microbiology"},{"key":"B43","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1111\/j.1574-6968.2008.01429.x","article-title":"Novel approaches toward preferential detection of viable cells using nucleic acid amplification techniques.","volume":"291","author":"Nocker","year":"2009","journal-title":"FEMS Microbiol. Lett."},{"key":"B44","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1016\/j.mimet.2006.04.015","article-title":"Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells.","volume":"67","author":"Nocker","year":"2006","journal-title":"J. Microbiol. Methods"},{"key":"B45","doi-asserted-by":"publisher","first-page":"5111","DOI":"10.1128\/AEM.02987-06","article-title":"Use of propidium monoazide for live\/dead distinction in microbial ecology.","volume":"73","author":"Nocker","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"B46","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1016\/j.tibtech.2012.05.007","article-title":"Cultivation of unculturable soil bacteria.","volume":"30","author":"Pham","year":"2012","journal-title":"Trends Biotechnol."},{"key":"B47","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1177\/2050640614520867","article-title":"Gelatin tannate ameliorates acute colitis in mice by reinforcing mucus layer and modulating gut microbiota composition: emerging role for \u2018gut barrier protectors\u2019 in IBD?","volume":"2","author":"Scaldaferri","year":"2014","journal-title":"United European Gastroenterol. J."},{"key":"B48","first-page":"357","article-title":"Coprophagy in animals: a review.","volume":"81","author":"Soave","year":"1991","journal-title":"Cornell Vet."},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.1038\/srep00170","article-title":"Bacterial biogeography of the human digestive tract.","volume":"1","author":"Stearns","year":"2011","journal-title":"Sci. Rep."},{"key":"B50","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v022.i05","article-title":"Interactive multivariate data analysis in R with the ade4 and ade4TkGUI Packages.","volume":"22","author":"Thioulouse","year":"2007","journal-title":"J. Stat. Softw."},{"key":"B51","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1038\/nature07540","article-title":"A core gut microbiome in obese and lean twins.","volume":"457","author":"Turnbaugh","year":"2009","journal-title":"Nature"},{"key":"B52","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1038\/ismej.2012.114","article-title":"New perspectives on viable microbial communities in low-biomass cleanroom environments.","volume":"7","author":"Vaishampayan","year":"2013","journal-title":"ISME J."},{"key":"B53","doi-asserted-by":"publisher","first-page":"2537","DOI":"10.1128\/AEM.02288-07","article-title":"Removal of free extracellular DNA from environmental samples by ethidium monoazide and propidium monoazide.","volume":"74","author":"Wagner","year":"2008","journal-title":"Appl. Environ. Microbiol."},{"key":"B54","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1038\/ismej.2011.109","article-title":"Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers.","volume":"6","author":"Wang","year":"2012","journal-title":"ISME J."},{"key":"B55","doi-asserted-by":"publisher","first-page":"1669","DOI":"10.1038\/ismej.2015.235","article-title":"Correlation detection strategies in microbial data sets vary widely in sensitivity and precision.","volume":"10","author":"Weiss","year":"2016","journal-title":"ISME J."},{"key":"B56","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.mimet.2011.02.004","article-title":"Quantification of viable Legionella pneumophila cells using propidium monoazide combined with quantitative PCR.","volume":"85","author":"Y\u00e1\u00f1ez","year":"2011","journal-title":"J. Microbiol. Methods"},{"key":"B57","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0117441","article-title":"The dynamic distribution of porcine microbiota across different ages and gastrointestinal tract segments.","volume":"10","author":"Zhao","year":"2015","journal-title":"PLoS One"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fmicb.2018.00733\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,31]],"date-time":"2020-10-31T11:45:52Z","timestamp":1604144752000},"score":1,"resource":{"primary":{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fmicb.2018.00733\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,4,10]]},"references-count":57,"alternative-id":["10.3389\/fmicb.2018.00733"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2018.00733","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,4,10]]},"article-number":"733"}}