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

Gharechahi, Javad; Salekdeh, Ghasem Hosseini

doi:10.1186/s13068-018-1214-9

Cited by 104 publications

(98 citation statements)

References 70 publications

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“…Recent studies on the camel gastrointestinal tract metagenome detected at least 27 bacterial phyla. Whereas in the forestomach a higher number of bacteria were associated with amino acid metabolism, replication and repair, carbohydrate metabolism was enriched in the large intestine and faeces (Gharechahi & Salekdeh 2018;He et al 2018). A novel thermo-stable xylanase showing a high activity in a broad pH and temperature range was discovered in the dromedary rumen metagenome, suggesting a potential application in some industrial sectors (e.g.…”

Section: Gut Bacterial Communitiesmentioning

confidence: 99%

Old World camels in a modern world – a balancing act between conservation and genetic improvement

Burger¹,

Ciani

Faye

2019

Animal Genetics

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Old World camels have served humans in cross-continental caravans, transporting people and goods, connecting different cultures and providing milk, meat, wool and draught since their domestication around 3000-6000 years ago. In a world of modern transport and fast connectivity, these beasts of burden seem to be out-dated. However, a growing demand for sustainable milk and meat production, especially in countries affected by climate change and increasing desertification, brings dromedaries (Camelus dromedarius) and Bactrian camels (Camelus bactrianus) back onstage and into the focus of animal breeders and scientists. In this review on the molecular genetics of these economically important species we give an overview about the evolutionary history, domestication and dispersal of Old World camels, whereas highlighting the need for conservation of wild two-humped camels (Camelus ferus) as an evolutionarily unique and highly endangered species. We provide cutting-edge information on the current molecular resources and on-going sequencing projects. We cannot emphasise enough the importance of balancing the need for improving camel production traits with maintaining the genetic diversity in two domestic species with specific physiological adaptation to a desert environment.

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Section: Gut Bacterial Communitiesmentioning

confidence: 99%

Old World camels in a modern world – a balancing act between conservation and genetic improvement

Burger¹,

Ciani

Faye

2019

Animal Genetics

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“…As is well known, the ruminant gastrointestinal microbiota can produce a wide array of CAZymes involved in the utilization of lignocellulosic biomass, which is the most abundant and bio-renewable resource on earth [14,24,25]. In our study, a large repertoire of genes coding for carbohydrate-degrading enzymes were identi ed in the yak fecal microbiome.…”

Section: Diversity Of Carbohydrate-degrading Enzymes and Microbial Comentioning

confidence: 84%

Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community

Gong

Zhou

Luo

et al. 2020

Preprint

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Background: Yaks are able to utilize the gastrointestinal microbiota to digest plant materials. Although the cellulolytic bacteria in the yak rumen have been reported, there is still limited information on the diversity of the major microorganisms and putative carbohydrate-metabolizing enzymes for the degradation of complex lignocellulosic biomass in its gut ecosystem. Results: Here, this study aimed to decode biomass-degrading genes and genomes in the yak fecal microbiota using deep metagenome sequencing. A comprehensive catalog comprising 4.5 million microbial genes from the yak feces were established based on metagenomic assemblies from 92 Gb sequencing data. We identified a full spectrum of genes encoding carbohydrate-active enzymes, three-quarters of which were assigned to highly diversified enzyme families involved in the breakdown of complex dietary carbohydrates, including 120 families of glycoside hydrolases, 25 families of polysaccharide lyases, and 15 families of carbohydrate esterases. Inference of taxonomic assignments to the carbohydrate-degrading genes revealed the major microbial contributors were Bacteroidaceae, Ruminococcaceae, Rikenellaceae, Clostridiaceae, and Prevotellaceae. Furthermore, 68 prokaryotic genomes were reconstructed and the genes encoding glycoside hydrolases involved in plant-derived polysaccharide degradation were identified in these uncultured genomes, many of which were novel species with lignocellulolytic capability. Conclusions: Our findings shed light on a great diversity of carbohydrate-degrading enzymes in the yak gut microbial community and uncultured species, which provides a useful genetic resource for future studies on the discovery of novel enzymes for industrial applications.

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“…Studies demonstrated that members of the Bacteroidetes phylum that contain a varied combination of CAZymes (Carbohydrate-Active Enzymes) in the form of PULs (polysaccharide utilization loci), which encode multiple proteins include the detection, sequestration, hydrolysis and transport of complex carbohydrates (Gharechahi & Salekdeh 2018). It is reported that particular PUL can be used to predict the substrate specificity of microbial strains and the presence of many PULs in Bacteroidetes genomes indicates their broad substrate specifcity and high potential carbohydrate degradation ability (Stewart et PeerJ reviewing PDF | (2018:11:32825:3:0:ACCEPTED 5 Aug 2019)…”

Section: Discussionmentioning

confidence: 99%

Peer Review #2 of "Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau (v0.1)"

2019

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The rumen microbiota of ruminants plays a vital role in fiber digestion, and environmental factors affect its community structure. The yak (Bos grunniens) is the main livestock species that inhabits the Qinghai-Tibet Plateau (QTP) at regions located at high-altitude of 3000-5000 m. This work investigated the rumen bacterial community of yak that grazed on the QTP during the whole year to evaluate the relationship between the rumen bacterial community and the nutrient composition of forage plant at three stages. In this study, the diversity of the rumen prokaryotic community composition was monitored in 10 fullgrazing yak in an alpine meadow of the QTP. The nutrient composition of three forage growth stages was determined: re-green stage (REGY), grassy stage (GY), and withered stage (WGY). High-throughput sequencing of bacterial 16S rRNA gene was used. The results showed that the nutritive composition of the alpine meadow changed with the seasons: crude protein (CP) (13.22%) was high in forage during REGY (spring), while neutral detergent fiber (NDF) (59.00%) was high during WGY (winter). Microbial diversity and richness were highest during REGY and the average number of operational taxonomic units from 30 samples was 4470. The microbial composition was dominated by members of Bacteroidetes (51.82%), followed by Firmicutes (34.08%), and the relative microbial abundance changed in the three forage growth stages. Unweighted UniFrac distance PcoA showed that the bacterial community structure differed between REGY, GY, and WGY. Furthermore, taxonomic groups did not present differences regarding gender in these three stages. The rumen microbiota was enriched with functional potentials that were related to ABC transporters, the Two component system, Aminoacyl-tRNA biosynthesis, and metabolism of Purine, Pyrimidine, Starch and sucrose metabolism. Significant differences were found in the composition, diversity, and function of yak ruminal microorganisms during different forage growth stages. This indicates that microbial changes in the rumen depend on changes in the forage nutritional composition. These

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

Cited by 104 publications

References 70 publications

Old World camels in a modern world – a balancing act between conservation and genetic improvement

Old World camels in a modern world – a balancing act between conservation and genetic improvement

Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community

Peer Review #2 of "Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau (v0.1)"

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