Phylogenetic diversity and dietary association of rumen Treponema revealed using group-specific 16S rRNA gene-based analysis

Bekele, Aschalew Z.; Koike, Satoshi; Kobayashi, Yasuo

doi:10.1111/j.1574-6968.2010.02191.x

Cited by 72 publications

(75 citation statements)

References 47 publications

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“…It appeared that versatile Butyrivibrio species that can degrade several types of polysaccharides (hemicellulose, starch, and pectin) are abundant in the liquid fraction irrespective of the diets. The two OTUs assigned to Treponema are thought to be associated with diets rich in concentrate as described previously (Bekele et al 2011). "Unclassified_Bacteroidetes" (seven OTUs) and "Unclassified_Clostridiales" (six OTUs) were the first and second most abundant unclassified groups in the Lq-H sample, while "Unclassified_Lachnospiraceae" (eight OTUs) was the most abundant unclassified group in the Lq-C sample.…”

Section: Resultsmentioning

confidence: 95%

Phylogenetic diversity of bacterial communities in bovine rumen as affected by diets and microenvironments

Kim

Morrison

2011

Folia Microbiol

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Phylogenetic analysis was conducted to examine ruminal bacteria in two ruminal fractions (adherent fraction vs. liquid fraction) collected from cattle fed with two different diets: forage alone vs. forage plus concentrate. One hundred forty-four 16S rRNA gene (rrs) sequences were obtained from clone libraries constructed from the four samples. These rrs sequences were assigned to 116 different operational taxonomic units (OTUs) defined at 0.03 phylogenetic distance. Most of these OTUs could not be assigned to any known genus. The phylum Firmicutes was represented by approximately 70% of all the sequences. By comparing to the OTUs already documented in the rumen, 52 new OTUs were identified. UniFrac, SONS, and denaturing gradient gel electrophoresis analyses revealed difference in diversity between the two fractions and between the two diets. This study showed that rrs sequences recovered from small clone libraries can still help identify novel species-level OTUs.

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Section: Resultsmentioning

confidence: 95%

Phylogenetic diversity of bacterial communities in bovine rumen as affected by diets and microenvironments

Kim

Morrison

2011

Folia Microbiol

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“…were among the gut-associated genera that were more prevalent in indoor samples. Treponema has previously been associated with digital dermatitis in cattle (31) and in the bovine rumen (32). Phocaeicola and Paludibacter have also been positively associated with valerate in the rumen (33) and were more prevalent in outdoor samples.…”

Section: Discussionmentioning

confidence: 98%

Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study

Doyle

Gleeson

O’Toole

et al. 2017

Appl Environ Microbiol

132

121

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In pasture-based systems, changes in dairy herd habitat due to seasonality results in the exposure of animals to different environmental niches. These niches contain distinct microbial communities that may be transferred to raw milk, with potentially important food quality and safety implications for milk producers. It is postulated that the extent to which these microorganisms are transferred could be limited by the inclusion of a teat preparation step prior to milking. High-throughput sequencing on a variety of microbial niches on farms was used to study the patterns of microbial movement through the dairy production chain and, in the process, to investigate the impact of seasonal housing and the inclusion/exclusion of a teat preparation regime on the raw milk microbiota from the same herd over two sampling periods, i.e., indoor and outdoor. Beta diversity and network analyses showed that environmental and milk microbiotas separated depending on whether they were sourced from an indoor or outdoor environment. Within these respective habitats, similarities between the milk microbiota and that of teat swab samples and, to a lesser extent, fecal samples were apparent. Indeed, SourceTracker identified the teat surface as the most significant source of contamination, with herd feces being the next most prevalent source of contamination. In milk from cows grazing outdoors, teat prep significantly increased the numbers of total bacteria present. In summary, sequence-based microbiota analysis identified possible sources of raw milk contamination and highlighted the influence of environment and farm management practices on the raw milk microbiota. IMPORTANCEThe composition of the raw milk microbiota is an important consideration from both a spoilage perspective and a food safety perspective and has implications for milk targeted for direct consumption and for downstream processing. Factors that influence contamination have been examined previously, primarily through the use of culture-based techniques. We describe here the extensive application of high-throughput DNA sequencing technologies to study the relationship between the milk production environment and the raw milk microbiota. The results show that the environment in which the herd was kept was the primary driver of the composition of the milk microbiota composition.KEYWORDS farm practices, food chain, food safety, metagenomics, microbial source tracking, raw milk microbiota T he impact of the dairy farm environment on the microbial composition of raw milk and raw milk products has been appreciated for some time (1). There are numerous niches that collectively constitute the dairy farm environment, and these harbor a vast array of microbes. The transfer of microbes from the farm environment to raw milk can be influenced be a number of factors, including farmer hygiene, husbandry practices,

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“…Some Treponema species have been shown to interact with cellulolytic bacteria and increase the degradation rate of cellulose (56), and Treponema spp. also are involved in degradation of soluble fibers (57). Recent studies also have identified abundant Treponema in a termite gut metagenome (58) and enriched in the gut microbiomes of humans with highly fibrous hunter-gatherer diets (59).…”

Section: Discussionmentioning

confidence: 99%

Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters

Jia

Wilkins

et al. 2016

Appl Environ Microbiol

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Cellulose and xylan are two major components of lignocellulosic biomass, which represents a potentially important energy source, as it is abundant and can be converted to methane by microbial action. However, it is recalcitrant to hydrolysis, and the establishment of a complete anaerobic digestion system requires a specific repertoire of microbial functions. In this study, we maintained 2-year enrichment cultures of anaerobic digestion sludge amended with cellulose or xylan to investigate whether a cellulose-or xylan-digesting microbial system could be assembled from sludge previously used to treat neither of them. While efficient methane-producing communities developed under mesophilic (35°C) incubation, they did not under thermophilic (55°C) conditions. Illumina amplicon sequencing results of the archaeal and bacterial 16S rRNA genes revealed that the mature cultures were much lower in richness than the inocula and were dominated by single archaeal (genus Methanobacterium) and bacterial (order Clostridiales) groups, although at finer taxonomic levels the bacteria were differentiated by substrates. Methanogenesis was primarily via the hydrogenotrophic pathway under all conditions, although the identity and growth requirements of syntrophic acetate-oxidizing bacteria were unclear. Incubation conditions (substrate and temperature) had a much greater effect than inoculum source in shaping the mature microbial community, although analysis based on unweighted UniFrac distance found that the inoculum still determined the pool from which microbes could be enriched. Overall, this study confirmed that anaerobic digestion sludge treating nonlignocellulosic material is a potential source of microbial cellulose-and xylan-digesting functions given appropriate enrichment conditions. C ellulose and xylan, two major structural components of plant cell walls, represent important resources for renewable energy (1-3). Cellulose, hemicellulose (the major component is xylan), and lignin make up 35 to 50%, 20 to 35%, and 10 to 25% of total lignocellulose by dry weight, respectively (4). Cellulose and xylan from lignocellulosic biomass not only represent new energy sources but also could reduce carbon dioxide emissions, as lignocellulosic biofuels are considered carbon neutral. However, digesting recalcitrant lignocellulosic components to fermentable sugars is a rate-limiting step (5), making lignocellulosic biofuels currently challenging to produce while being price competitive with fossil fuels (6, 7). Microbes have evolved strategies (8, 9) to digest lignocellulosic components concurrent with the evolution of plant cell walls, making the investigation of microbial cellulose and xylan digestion potentially important to this emerging energy source.Metagenomic and microbial diversity studies of ruminant animals (e.g., cow [10], sheep [11], and deer [12]) have revealed rich taxonomic and functional microbial diversity, including mechanisms for cellulose and xylan digestion. Microbial cellulose and xylan digestion systems have been ide...

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Phylogenetic diversity and dietary association of rumen Treponema revealed using group-specific 16S rRNA gene-based analysis

Cited by 72 publications

References 47 publications

Phylogenetic diversity of bacterial communities in bovine rumen as affected by diets and microenvironments

Phylogenetic diversity of bacterial communities in bovine rumen as affected by diets and microenvironments

Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study

Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters

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