Characterization of the rumen microbiome of Indian Kankrej cattle (Bos indicus) adapted to different forage diet

Abstract

Present study described rumen microbiome of Indian cattle (Kankrej breed) to better understand the microbial diversity and largely unknown functional capacity of the rumen microbiome under different dietary treatments. Kankrej cattle were gradually adapted to a high-forage diet (four animals with dry forage and four with green forage) containing 50 % (K1), 75 % (K2) to 100 % (K3) forage, and remaining concentrate diet, each for 6 weeks followed by analysis of rumen fiber adherent and fiber-free metagenomic community by shotgun sequencing using ion torrent PGM platform and EBI-metagenomics annotation pipeline. Taxonomic analysis indicated that rumen microbiome was dominated by Bacteroidetes followed by Firmicutes, Fibrobacter, Proteobacteria, and Tenericutes. Functional analysis based on gene ontology classified all reads in total 157 categories based on their functional role in biological, molecular, and cellular component with abundance of genes associated with hydrolase activity, membrane, transport, transferase, and different metabolism (such as carbohydrate and protein). Statistical analysis using STAMP revealed significant differences (P < 0.05) between solid and liquid fraction of rumen (in 65 categories), between all three treatments (in 56 categories), and between green and dry roughage (17 categories). Diet treatment also exerted significant difference in environmental gene tags (EGTs) involved in metabolic pathways for production of volatile fatty acids. EGTs for butyrate production were abundant in K2, whereas EGTs for propionate production was abundant during K1. Principal component analysis also demonstrated that diet proportion, fraction of rumen, and type of forage affected rumen microbiome at taxonomic as well as functional level.

Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies

“…Studies that decipher the community composition of anaerobic sludge has also been conducted by many research groups across the world (Guo et al, 2015; Sun et al, 2015; Ferrentino et al, 2016; Ju et al, 2016) but the studies conducting the detailed investigation of taxonomic as well as functional composition of pre- and post-treated anaerobic sludge are very few. Researchers have used different sequencing depths ranging from 0.1 GB to 3.3 GB to study functional composition using the Ion-torrent platform (Joshi et al, 2014; Patel et al, 2014; Rua et al, 2015; Hinsu et al, 2017; Motooka et al, 2017). Here, we employed ∼1 GB sequencing depth for shotgun metagenomic sequencing to inspect the microbial shifts in pre- and post-treated sludge along with their functional alterations.…”

Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches

“…We have previously characterized rumen microbiome of Kankrej cattle, Jaffrabadi and Mehsani buffalo fed with different roughage concentrations in the diet using amplicon and shotgun sequencing and demonstrated that bacterial community in the liquid and solid fractions of rumen are diverse and different proportions of roughage in the diet exerted significant impact on rumen bacterial population [42,45,48,53]. In the present study we further hypothesised that the importance of the role of bacterial species in the rumen is not only determine by their abundance but how functionally active they are.…”

Dynamic changes of yak (Bos grunniens) gut microbiota during growth revealed by polymerase chain reaction-denaturing gradient gel electrophoresis and metagenomics

“…Metagenomic sequencing represents a powerful alternative to ribosomal RNA (rRNA) sequencing for analyzing complex microbial communities [9], and this method avoids the need to culture individual microorganisms and eliminates cloning and polymerase chain reaction (PCR) biases [10]. Recently, Patel et al [11] found that diet proportion, fraction of rumen, and forage type affected rumen microbiome of Indian Kankrej cattle at taxonomic as well as functional levels by metagenomic sequencing. According to metagenomic analysis results, Zhu et al [6] found that ~37-Mbp contig sequences from gut microbes of the giant panda recovered putative genes coding cellulose-digesting related enzymes in Clostridium group I, showing that the giant pandas had evolved a number of traits to overcome the anatomical and physiological challenge of digesting a diet high in fibrous matter.…”