Composition, spatial distribution, and diversity of the bacterial communities in the rumen of cows fed different forages.

Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
FEMS Microbiology Ecology (Impact Factor: 3.88). 09/2010; 74(3):612-22. DOI: 10.1111/j.1574-6941.2010.00977.x
Source: PubMed

ABSTRACT The species composition, distribution, and biodiversity of the bacterial communities in the rumen of cows fed alfalfa or triticale were investigated using 16S rRNA gene clone library analyses. The rumen bacterial community was fractionated and analyzed as three separate fractions: populations in the planktonic, loosely attached to rumen digesta particles, and tightly attached to rumen digesta particles. Six hundred and thirteen operational taxonomic units (OTUs) belonging to 32 genera, 19 families, and nine phyla of the domain Bacteria were identified from 1014 sequenced clones. Four hundred and fifty one of the 613 OTUs were identified as new species. These bacterial sequences were distributed differently among the three fractions in the rumen digesta of cows fed alfalfa or triticale. Chao 1 estimation revealed that, in both communities, the populations tightly attached to particulates were more diverse than the planktonic and those loosely attached to particulates. S-Libshuff detected significant differences in the composition between any two fractions in the rumen of cows with the same diet and between the communities fed alfalfa and triticale diets. The species richness estimated for the communities fed alfalfa and triticale is 1027 and 662, respectively. The diversity of the rumen bacterial community examined in this study is greater than previous studies have demonstrated and the differences in the community composition between two high-fiber diets have implications for sample selection for downstream metagenomics applications.

1 Bookmark
  • [Show abstract] [Hide abstract]
    ABSTRACT: tRumen cannulation is the reference method for collection of representative samples ofrumen digesta. However, it is not always viable, which obliges to depend on less invasivetechniques, such as stomach tubing. The aim of this work was to study if the differencesin fermentation parameters and rumen microbial populations observed between species(sheep and goats), diets (forage and forage plus concentrate) and sampling times (pre-and post-feeding) are consistent when collecting the samples through stomach tube orrumen cannula, in an attempt to validate the use of the former as an alternative to the lat-ter. Four sheep and four goats, fitted with ruminal cannula, were fed either forage (F diet;alfalfa hay) or forage plus concentrate (1:1; FC diet), in two 15-day periods. At the end ofeach period (days 14 and 15), samples of rumen digesta were taken by stomach tube andrumen cannula, before and 4 h after morning feeding, for determination of ruminal fermen-tation parameters (pH, and lactate, ammonia and total VFA concentrations). The three mainrumen microbial groups (bacteria, protozoa and methanogenic archaea) and two fibrolyticbacteria (Ruminococcus flavefaciens and Fibrobacter succinogenes) were quantified by real-time PCR and, additionally, PCR-DGGE analysis of the bacterial community on the rumendigesta samples collected post-feeding was carried out. Overall, sampling through ruminalcannula and stomach tube gave similar results regarding fermentation parameters whencomparing species, diets and sampling times. Despite samples for microbiology assays con-tained liquid plus solid fractions when collected through rumen cannula and mostly liquidwhen collected through stomach tube, both techniques showed certain consistency in theeffects of treatments on the rumen microbiota (e.g., both revealed no differences between species in total bacteria, archaea and R. flavefaciens concentrations, and higher protozoanumbers in goats than in sheep). However, there was also some discrepancy regardingmicroorganism concentrations, particularly concerning sampling times (e.g., differencesbetween pre- and post-feeding samplings were only observed in rumen cannula samplesfor total bacteria and methanogenic archaea, and in stomach tube samples for R. flavefa-ciens concentrations). Therefore, this study supports that non-invasive stomach tubing is afeasible alternative to surgical rumen cannulation in sheep and goats to examine ruminalfermentation. Nonetheless, caution should be taken when using this technique to assessthe structure and composition of the rumen microbial community.
    Animal Feed Science and Technology 09/2014; 198:57-66. · 2.09 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The rumen compartment of the ruminant digestive tract is an enlarged fermentation chamber which houses a diverse collection of symbiotic microorganisms that provide the host animal with a remarkable ability to digest plant lignocellulosic materials. Characterization of the ruminal microbial community provides opportunities to improve animal food digestion efficiency, mitigate methane emission, and develop efficient fermentation systems to convert plant biomasses into biofuels. In this study, 16S rRNA gene amplicon pyrosequencing was applied in order to explore the structure of the bacterial community inhabiting the camel rumen. Using 76,333 quality-checked, chimera- and singleton-filtered reads, 4954 operational taxonomic units (OTUs) were identified at a 97% species level sequence identity. At the phylum level, more than 96% of the reads were affiliated to OTUs belonging to Bacteroidetes (51%), Firmicutes (31%), Proteobacteria (4.8%), Spirochaetes (3.5%), Fibrobacteres (3.1%), Verrucomicrobia (2.7%), and Tenericutes (0.95%). A total of 15% of the OTUs (746) that contained representative sequences from all major taxa were shared by all animals and they were considered as candidate members of the core camel rumen microbiome. Analysis of microbial composition through the solid and liquid fractions of rumen digesta revealed differential enrichment of members of Fibrobacter, Clostridium, Ruminococcus, and Treponema in the solid fraction, as well as members of Prevotella, Verrucomicrobia, Cyanobacteria, and Succinivibrio in the liquid fraction. The results clearly showed that the camel rumen microbiome was structurally similar but compositionally distinct from that of other ruminants, such as the cow. The unique characteristic of the camel rumen microbiome that differentiated it from those of other ruminants was the significant enrichment for cellulolytic bacteria.
    Systematic and Applied Microbiology 10/2014; · 3.31 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Background Infant microbiota is influenced by numerous factors, such as delivery mode, environment, prematurity and diet (breast milk or formula) and last but not least, the diet composition. In the diet composition, protein and carbohydrate are very important for the growth of microbiota, many infant fomulas (different ratio protein/carbohydrate) can regulate the development of gut microbiota by different metabolism. The effect of low-protein, high-carbohydrate infant formula on the establishment of microbiota remains unclear, and the effect of human breast milk on the gut microbiota of the rats has also not been reported.ResultsIn a 7 d intervention, a total of 36 neonatal SD rats (14 d old) were randomly assigned to the following groups: (1) breast-fed group (A group); (2) low-protein, high-carbohydrate infant formula-fed group (B group); (3) human breast milk-fed group (C group). After 7 days, we selected 6 rats at random from each group to study. Microbial composition in the contents of the large intestines was analysed by Miseq Sequencing. Significantly different (p<0.05) microbial colonisation patterns were observed in the large intestines of breast-fed group from low-protein, high-carbohydrate infant formula-fed and human breast milk-fed rats, but the microbiota of low-protein, high-carbohydrate infant formula-fed group and human breast milk-fed group have high similarity. At the phylum level, the absolute quantity of Bacteroidetes, Firmicutes and Proteobacteria (p<0.001) significantly differentiated in breast-fed group from low- protein, high- carbohydrate infant formula-fed and human breast milk-fed groups. Lachnospiraceae, Bacteroidaceae, Porphyromonadaceae and Prevotellaceae were the 4 top families in breast-fed group, but the top 4 families in low-protein, high- carbohydrate infant formula-fed and human breast milk-fed groups were the same, which were Bacteroidaceae, Enterobacteriaceae, Porphyromonadaceae and Lachnospiraceae. At the genus level, Bacteroides was the most abundant division, their OTUS abundance in three groups was 14.91%, 35.94%, 43.24% respectively.Conclusions This study showed that infant formula closer resembling human milk was more different than rats¿ breast milk and led to a microbiota profile similar to that for human breast milk-fed neonates. The finding could support a new thinking to develop infant formulas, and provide much more details than what is known previously.
    BMC Microbiology 11/2014; 14(1):279. · 2.98 Impact Factor


1 Download