In depth analysis of rumen microbial and carbohydrate-active enzymes profile in Indian crossbred cattle

Jose, V. Lyju; More, Ravi Prabhakar; Thulasi, A.; Arumugaperumal, Arun

doi:10.1016/j.syapm.2017.02.003

Cited by 30 publications

(22 citation statements)

References 40 publications

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“…We detected up to 60 types of glycoside hydrolases in the flying squirrel's cecal metagenome (Supplementary Table 4 ). This high diversity of GH groups was comparable to the diversity detected in other mammalian herbivores (Brulc et al, 2009 ; Flint et al, 2012 ; Wang et al, 2013 ; Jose et al, 2017 ), whereas detailed combinations and relative abundances of GH groups seemed to differ among animals with distinct gut structures and dietary preferences (Supplementary Table 8 ). For example, there were relatively high abundances of GH3, GH43, and GH53 in the flying squirrel's cecal metagenome, with even enriched levels in the cecal metatranscriptome (Figure 8 ).…”

Section: Discussionsupporting

confidence: 80%

Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling

Liu

Wang

et al. 2018

Front. Microbiol.

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Mammalian herbivores rely on microbial activities in an expanded gut chamber to convert plant biomass into absorbable nutrients. Distinct from ruminants, small herbivores typically have a simple stomach but an enlarged cecum to harbor symbiotic microbes; however, knowledge of this specialized gut structure and characteristics of its microbial contents is limited. Here, we used leaf-eating flying squirrels as a model to explore functional characteristics of the cecal microbiota adapted to a high-fiber, toxin-rich diet. Specifically, environmental conditions across gut regions were evaluated by measuring mass, pH, feed particle size, and metabolomes. Then, parallel metagenomes and metatranscriptomes were used to detect microbial functions corresponding to the cecal environment. Based on metabolomic profiles, >600 phytochemical compounds were detected, although many were present only in the foregut and probably degraded or transformed by gut microbes in the hindgut. Based on metagenomic (DNA) and metatranscriptomic (RNA) profiles, taxonomic compositions of the cecal microbiota were dominated by bacteria of the Firmicutes taxa; they contained major gene functions related to degradation and fermentation of leaf-derived compounds. Based on functional compositions, genes related to multidrug exporters were rich in microbial genomes, whereas genes involved in nutrient importers were rich in microbial transcriptomes. In addition, genes encoding chemotaxis-associated components and glycoside hydrolases specific for plant beta-glycosidic linkages were abundant in both DNA and RNA. This exploratory study provides findings which may help to form molecular-based hypotheses regarding functional contributions of symbiotic gut microbiota in small herbivores with folivorous dietary habits.

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Section: Discussionsupporting

confidence: 80%

Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling

Liu

Wang

et al. 2018

Front. Microbiol.

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“…2 ) highlights their key involvement in lignocellulose degradation in the camel rumen. Compared to the bovine rumen’s microbiome [ 19 ], the contribution of Bacteroidetes species to the production of CAZymes in the camel rumen was relatively high (56% vs 40%) (Fig. 1 ), but in contrast, while in the bovine rumen, Proteobacteria accounted for > 10% of GH-encoding sequences, the equivalent frequency in the camel rumen was just 1.4%.…”

Section: Discussionmentioning

confidence: 99%

A metagenomic analysis of the camel rumen’s microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation

Gharechahi

Salekdeh

2018

Biotechnol Biofuels

104

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BackgroundThe diverse microbiome present in the rumen of ruminant animals facilitates the digestion of plant-based fiber. In this study, a shotgun metagenomic analysis of the microbes adhering to plant fiber in the camel rumen was undertaken to identify the key species contributing to lignocellulose degradation and short chain volatile fatty acids (VFA) fermentation.ResultsThe density of genes in the metagenome encoding glycoside hydrolases was estimated to be 25 per Mbp of assembled DNA, which is significantly greater than what has been reported in other sourced metagenomes, including cow rumen. There was also a substantial representation of sequences encoding scaffoldins, dockerins and cohesins, indicating the potential for cellulosome-mediated lignocellulose degradation. Binning of the assembled metagenome has enabled the definition of 65 high-quality genome bins which showed high diversity for lignocellulose degrading enzymes. Species associated to Bacteroidetes showed a high proportion of genes for debranching and oligosaccharide degrading enzymes, while those belonging to Firmicutes and Fibrobacteres were rich in cellulases and hemicellulases and thus these lineages were probably the key for ensuring the degradation of lignocellulose. The presence of many “polysaccharide utilization loci” (PULs) in Bacteroidetes genomes indicates their broad substrate specificity and high potential carbohydrate degradation ability. An analysis of VFA biosynthesis pathways showed that genes required for the synthesis of acetate were present in a range of species, except for Elusimicrobiota and Euryarchaeota. The production of propionate, exclusively via the succinate pathway, was carried out by species belonging to the phyla Bacteroidetes, Firmicutes, Spirochaetes and Fibrobacteres. Butyrate was generated via the butyrylCoA: acetate CoA-transferase pathway by Bacteroidetes and Lentisphaerae species, but generally via the butyrate kinase pathway by Firmicutes species.ConclusionThe analysis confirmed the camel rumen’s microbiome as a dense and yet largely untapped source of enzymes with the potential to be used in a range of biotechnological processes including biofuel, fine chemicals and food processing industries.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1214-9) contains supplementary material, which is available to authorized users.

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“…Novas β-galactosidases bem como tecnologias inovadoras ligadas à produção dessa enzima vêm sendo descobertas e estudadas pelos pesquisadores (DUAN et al, 2017;JOSE et al, 2017;LIU et al, 2017;YOU, Chang, et al, 2017;YOU, Zhang, et al, 2017). Erich et al (2015) realizaram uma triagem de 1,3 milhões de clones de metagenoma para descobrir novas β-galactosidases.…”

Section: Enzima β-Galactosidaseunclassified

Ciência e Tecnologia de Leite e Produtos Lácteos Sem Lactose

Dantas¹,

Verruck²,

Prudêncio³

2019

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In depth analysis of rumen microbial and carbohydrate-active enzymes profile in Indian crossbred cattle

Cited by 30 publications

References 40 publications

Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling

Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling

A metagenomic analysis of the camel rumen’s microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation

Ciência e Tecnologia de Leite e Produtos Lácteos Sem Lactose

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