Culture-Independent Analysis of Fecal Microbiota in Cattle

Ozutsumi, Yuhei; Hayashi, Hidenori; Sakamoto, Mitsuo; Itabashi, Hideyuki; Benno, Yoshimi

doi:10.1271/bbb.69.1793

Cited by 58 publications

(42 citation statements)

References 10 publications

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“…The microarray approach revealed an unprecedented diversity with B1400 OTUs grouped in 40 phyla (7 of which were also detected by cloning) in comparison, with previous studies on the human gut (14 phyla (Andersson et al, 2008)), cow rumen (12 phyla (Tajima et al, 2001;Ozutsumi et al, 2005;Karnati et al, 2007)) chicken ceca (5 phyla (Lan et al, 2002;Zhu et al, 2002)) and other gastrointestinal tracts of several mammalian (overall 22 phyla ). The high number of phyla was partially confirmed by the rarefaction's curves at 80% sequence homology and the high OTU-level richness was also confirmed by the estimated values previously published (GodoyVitorino et al, 2008).…”

Section: Discussionsupporting

confidence: 70%

Developmental microbial ecology of the crop of the folivorous hoatzin

et al. 2010

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The hoatzin (Opisthocomus hoazin) is a South American strict folivorous bird, with a crop microbial ecosystem that ferments dietary plants. Chicks progressively become independent from the adultfed regurgitated crop liquids, and we hypothesized that the crop bacterial ecosystem develops through ecological succession mechanisms, as they grow into adults. The aim of this work was to compare the crop bacterial community in hoatzins from three age groups: newly hatched chicks, juveniles and adults by sequencing 16S rRNA genes and using the G2 PhyloChip. Cloning yielded a total of 2123 nearly full-length sequences binned into 294 operational taxonomic units (OTUs) (with o97% homology) belonging to 7 phyla, with 91% of novel OTUs. The microarray identified a diverse bacterial community dominated by Firmicutes and Bacteroidetes, with B1400 taxa grouped in 40 phyla that included those detected by cloning. In comparison with the adult, the hoatzin chick crop had a greater abundance of Flavobacteriaceae, Clostridiaceae and Lachnospiraceae but lacked phyla DSS1, Deferribacteres and Termite group 1, which were mostly present in adults. The overall community structure of the crop of the hoatzin changes with age in a complex manner, probably responding to new niches made available through dietary changes related to the transition from dependent to independent feeding.

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Section: Discussionsupporting

confidence: 70%

Developmental microbial ecology of the crop of the folivorous hoatzin

et al. 2010

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“…Members of the phylum Actinobacteria were not found in the colon contents of seals [25], but have been found and are part of the fecal bacterial community of Holstein cattle and humans [41,42]. One member of this phylum, Mycobacterium terrae which represented 13 clones, each clone showing 96% sequence similar to M. terrae (HM770865), is found ubiquitously in the environment.…”

Section: Discussionmentioning

confidence: 99%

Analysis of the bacterial diversity in the fecal material of the endangered Yangtze finless porpoise, Neophocaena phocaenoides asiaeorientalis

et al. 2011

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The aim of this study was to determine the bacteria present in the fecal material of the endangered Yangtze finless porpoise, Neophocaena phocaenoides asiaeorientalis. Fecal samples were collected from 12 Yangtze finless porpoises living in the wild at Poyang Lake, located in Jiangxi Province, China. To determine the bacterial diversity, a 16S rRNA gene clone library using the bacterial PCR primers fD1 and rP2, was prepared. A total of 138 near-full-length sequences were analyzed and 39 operational taxonomic units (OTUs) were identified. Sequences showing C97% similarity were grouped together as an OTU. Six different phyla were identified in which 38 OTUs were classified. Most of the OTUs contained sequences belonged to the phylum Firmicutes (51.3%), followed by Tenericutes (17.9%), Proteobacteria (15.4%), Actinobacteria (7.7%), Deinococcus-Thermus (2.6%) and Cyanobacteria (2.6%). A phylum could not be assigned for one clone within one OTU (2.6%). It appears that the Yangtze finless porpoise has a more diverse range of bacteria compared to other aquatic mammals, such as seals.

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“…While the rumen microbiota are also dominated by the Firmicutes and Bacteroidetes (7,22,23), the majority of organisms present in the rumen differ from those present in the feces (12,13,24).…”

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confidence: 99%

Newly Cultured Bacteria with Broad Diversity Isolated from Eight-Week Continuous Culture Enrichments of Cow Feces on Complex Polysaccharides

Ziemer

2014

Appl Environ Microbiol

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One of the functions of the mammalian large intestinal microbiota is the fermentation of plant cell wall components. In ruminant animals, the majority of their nutrients are obtained via pregastric fermentation; however, up to 20% can be recovered from microbial fermentation in the large intestine. Eight-week continuous culture enrichments of cattle feces with cellulose and xylan-pectin were used to isolate bacteria from this community. A total of 459 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented: Firmicutes (51.9%), Bacteroidetes (30.9%), Proteobacteria (11.1%), Actinobacteria (3.5%), Synergistetes (1.5%), and Fusobacteria (1.1%). The majority of bacterial isolates had <98.5% identity to cultured bacteria with sequences in the Ribosomal Database Project and thus represent new species and/or genera. Within the Firmicutes isolates, most were classified in the families Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, and Clostridiaceae I. The majority of the Bacteroidetes were most closely related to Bacteroides thetaiotaomicron, B. ovatus, and B. xylanisolvens and members of the Porphyromonadaceae family. Many of the Firmicutes and Bacteroidetes isolates were related to species demonstrated to possess enzymes which ferment plant cell wall components; the others were hypothesized to cross-feed these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 98% of the isolates not represented as previously cultured, there are new opportunities to study the genomic and metabolic capacities of these members of the complex intestinal microbiota.A function of the gut microbiota in mammalian herbivores and omnivores is the fermentation of plant cell wall components; mammals lack the enzymes required to breakdown ␤-(1,4) bonds and other linkages between the monosaccharides that make up plant cell walls (1, 2). The plant cell wall is made up of cellulose and hemicelluloses, the primary structural components of plants, and contain smaller and variable amounts of pectins, ␤-glucans, oligosaccharides, lignins, and glycoproteins (3).The physiology of ruminant animals, such as cattle, goats, and sheep, includes a foregut, where fermentation occurs and which allows the animal to directly utilize the short-chain fatty acids (SCFAs) produced by the anaerobic microbial fermentation of plant cell walls for energy (2). Thus, ruminal fermentation provides between 60% and 80% of the animal's energy requirements (4, 5). Ruminants obtain energy from the SCFAs produced in the large intestine, which provides from 0 to 20% of their dietary requirements, similar to the levels reported for other mammals (4, 5).A number of intestinal microbial metagenomes, including those of cattle (6, 7), human (8, 9), pig (10), and chicken (11), have been demonstrated to be enriched in carbohydrate transport and metabolism genes. Ley et al. (1) found that the type of diet (herbivorous, omnivorous, or carnivorous) strongly predic...

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Culture-Independent Analysis of Fecal Microbiota in Cattle

Cited by 58 publications

References 10 publications

Developmental microbial ecology of the crop of the folivorous hoatzin

Developmental microbial ecology of the crop of the folivorous hoatzin

Analysis of the bacterial diversity in the fecal material of the endangered Yangtze finless porpoise, Neophocaena phocaenoides asiaeorientalis

Newly Cultured Bacteria with Broad Diversity Isolated from Eight-Week Continuous Culture Enrichments of Cow Feces on Complex Polysaccharides

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