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Liu J, Han L, Hou S, Gui L, Yuan Z, Sun S, Wang Z, Yang B. Integrated metabolome and microbiome analysis reveals the effect of rumen-protected sulfur-containing amino acids on the meat quality of Tibetan sheep meat. Front Microbiol 2024; 15:1345388. [PMID: 38389537 PMCID: PMC10883651 DOI: 10.3389/fmicb.2024.1345388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/17/2024] [Indexed: 02/24/2024] Open
Abstract
Introduction This study investigated the effects of rumen-protected sulfur-containing amino acids (RPSAA) on the rumen and jejunal microbiota as well as on the metabolites and meat quality of the longissimus lumborum (LL) in Tibetan sheep. Methods By combining 16S rDNA sequencing with UHPLC-Q-TOF MS and Pearson correlation analysis, the relationship between gastrointestinal microbiota, muscle metabolites and meat quality was identified. Results The results showed that feeding RPSAA can increase the carcass weight, abdominal fat thickness (AP-2 group), and back fat thickness (AP-2 and AP-3 group) of Tibetan sheep. The water holding capacity (WHC), texture, and shear force (SF) of LL in the two groups also increased although the fatty acids content and brightness (L*) value significantly decreased in the AP-2 group. Metabolomics and correlation analysis further showed that RPSAA could significantly influence the metabolites in purine metabolism, thereby affecting L* and SF. In addition, RPSAA was beneficial for the fermentation of the rumen and jejunum. In both groups, the abundance of Prevotella 1, Lachnospiraceae NK3A20 group, Prevotella UCG-003, Lachnospiraceae ND3007 group in the rumen as well as the abundance of Eubacterium nodatum group and Mogibacterium group in the jejunum increased. In contrast, that of Turicibacter pathogens in the jejunum was reduced. The above microorganisms could regulate meat quality by regulating the metabolites (inosine, hypoxanthine, linoleic acid, palmitic acid, etc.) in purine and fatty acids metabolism. Discussion Overall, reducing the levels of crude proteins in the diet and feeding RPSAA is likely to improve the carcass quality of Tibetan sheep, with the addition of RPMET (AP-2) yielding the best edible quality, possibly due to its ability to influence the gastrointestinal microbiota to subsequently regulate muscle metabolites.
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Affiliation(s)
- JiQian Liu
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Lijuan Han
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Shengzhen Hou
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Linsheng Gui
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Zhenzhen Yuan
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Shengnan Sun
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Zhiyou Wang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Baochun Yang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
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Dixit S, Kumar S, Sharma R, Banakar PS, Singh M, Keshri A, Tyagi AK. Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review. Anim Biotechnol 2023; 34:3187-3205. [PMID: 35713100 DOI: 10.1080/10495398.2022.2078979] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.
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Affiliation(s)
- Sonam Dixit
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Sachin Kumar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Ritu Sharma
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - P S Banakar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Manvendra Singh
- Krishi Vigyan Kendra, Banda University of Agriculture and Technology, Banda, India
| | - Anchal Keshri
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - A K Tyagi
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
- Animal Nutrition and Physiology, Indian Council of Agricultural Research, New Delhi, India
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3
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Dixit S, Kumar S, Sharma R, Banakar PS, Deb R, Tyagi AK. Rumen microbial diversity, enteric methane emission and nutrient utilization of crossbred Karan-Fries cattle ( Bos taurus) and Murrah buffalo ( Bubalus bubalis) consuming varied roughage concentrate ratio. Anim Biotechnol 2023; 34:1857-1875. [PMID: 35352616 DOI: 10.1080/10495398.2022.2053696] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Dietary mix and host species have both been shown to have a significant impact on rumen microbial diversity, enteric methane emission and animal performance. The goal of this study was to see how the roughage concentrate ratio 70:30 (Low concentrate; LC) vs 40:60 (High concentrate; HC) and the host species crossbred cattle vs buffalo affected rumen microbial diversity, enteric methane emissions and nutrient utilization. Dry matter intake (kg/d) and dry matter percent digestibility were considerably (p < 0.05) higher in the HC ration and buffalo compared to LC ration and crossbred cattle, respectively. Both dietary mix and host species had a substantial (p < 0.05) impact on intake of various nutrients, including organic matter (OM), crude protein (CP), ether extract (EE), neutral detergent fiber (NDF), and acid detergent fiber (ADF). Increased concentrate proportion in the ration improved nitrogen balance, resulting in increased average daily gain and considerably reduced methane (g/d) output (p < 0.05). Furthermore, 16S rRNA genes were sequenced using Oxford Nanopore Technology (ONT) and subsequently annotated using the Centrifuge workflow to uncover ruminal bacterial diversity. Firmicutes was considerably (p < 0.01) greater in the LC diet, whereas, Bacteroidetes was higher in the HC ration. Genus Prevotella dominated all rumen samples, and buffalo fed LC ration had significantly (p < 0.01) higher Oscillospira abundance. At the species level, simple sugar-utilizing bacteria such as Prevotella spp. and Selenomonas ruminantium predominated in the crossbred cattle, but fibrolytic bacteria such as Oscillospira guilliermondii were statistically (p < 0.01) more abundant in the buffalo. Overall, dietary mix and host species have both been shown to have a significant impact on rumen microbial diversity, enteric methane emission and animal performance, however, host species remained a major driving force to change ruminal community composition as compared to roughage concentrate ratio under similar environmental conditions.
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Affiliation(s)
- Sonam Dixit
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Sachin Kumar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Ritu Sharma
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - P S Banakar
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
| | - Rajib Deb
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Amrish Kumar Tyagi
- Rumen Biotechnology Laboratory, Department of Animal Nutrition, National Dairy Research Institute, Karnal, India
- Animal Nutrition and Physiology, Indian Council of Agricultural Research, New Delhi, India
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4
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Hinsu AT, Tulsani NJ, Panchal KJ, Pandit RJ, Jyotsana B, Dafale NA, Patil NV, Purohit HJ, Joshi CG, Jakhesara SJ. Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages. Sci Rep 2021; 11:9400. [PMID: 33931716 PMCID: PMC8087840 DOI: 10.1038/s41598-021-88943-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/12/2021] [Indexed: 02/07/2023] Open
Abstract
In dromedary camels, which are pseudo-ruminants, rumen or C1 section of stomach is the main compartment involved in fiber degradation, as in true ruminants. However, as camels are adapted to the harsh and scarce grazing conditions of desert, their ruminal microbiota makes an interesting target of study. The present study was undertaken to generate the rumen microbial profile of Indian camel using 16S rRNA amplicon and shotgun metagenomics. The camels were fed three diets differing in the source of roughage. The comparative metagenomic analysis revealed greater proportions of significant differences between two fractions of rumen content followed by diet associated differences. Significant differences were also observed in the rumen microbiota collected at different time-points of the feeding trial. However, fraction related differences were more highlighted as compared to diet dependent changes in microbial profile from shotgun metagenomics data. Further, 16 genera were identified as part of the core rumen microbiome of Indian camels. Moreover, glycoside hydrolases were observed to be the most abundant among all Carbohydrate-Active enzymes and were dominated by GH2, GH3, GH13 and GH43. In all, this study describes the camel rumen microbiota under different dietary conditions with focus on taxonomic, functional, and Carbohydrate-Active enzymes profiles.
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Affiliation(s)
- Ankit T Hinsu
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India
| | - Nilam J Tulsani
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India
| | - Ketankumar J Panchal
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India
| | - Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India
| | | | - Nishant A Dafale
- ICAR-Central Arid Zone Research Institute, Jodhpur, 342003, India
| | - Niteen V Patil
- ICAR-National Research Centre On Camel, Bikaner, 334001, India.,ICAR-Central Arid Zone Research Institute, Jodhpur, 342003, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India.,Gujarat Biotechnology Research Centre, Gandhinagar, 382010, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science & A.H., Anand Agricultural University, Anand, 388001, India.
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5
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Hinsu AT, Patel AB, Pandit RJ, Thakkar JR, Shah RK, Jakhesara SJ, Koringa PG, Joshi CG. MetaRNAseq analysis of surti buffalo rumen content reveals that transcriptionally active microorganisms need not be abundant. Mol Biol Rep 2020; 47:5101-5114. [PMID: 32557173 DOI: 10.1007/s11033-020-05581-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/10/2020] [Indexed: 11/26/2022]
Abstract
The present study describes rumen microbiota composition and their functional profiles in Indian Surti buffaloes by metagenomic (MG) and metatranscriptomic (MT) approaches. The study compares samples from buffaloes fed three different proportion of roughages; green and dry type of roughage; and different rumen liquor fractions. Irrespective of sample, Bacteroidetes and Firmicutes were the most predominant bacterial phyla, followed by Proteobacteria, Fibrobacteres and Actinobacteria while, Prevotella, Bacteroides, Ruminococcus and Clostridium were the most abundant genera. Different proportions of taxa were observed in both MG and MT approaches indicating the differences in organisms present and organisms active in the rumen. Higher proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data. Functionally, higher proportions of genes involved in Carbohydrate metabolism, Amino acid metabolism and Translation were observed in both data. Genes involved in Metabolism were observed to be underrepresented in MT data while, those involved in Genetic information processing were overrepresented in MT data. Further, genes involved in Carbohydrate metabolism were overexpressed compared to genes involved in Amino acid metabolism in MT data compared to MG data which had higher proportion of genes involved in Amino acid metabolism than Carbohydrate metabolism. In all significant differences were observed between both approaches, different fractions of rumen liquor (liquid and solid) and different proportions of roughage in diet.
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Affiliation(s)
- Ankit T Hinsu
- Department of Animal Genetics & Breeding, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Avani B Patel
- Department of Animal Genetics & Breeding, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Jalpa R Thakkar
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Ravi K Shah
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India.
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6
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He B, Jin S, Cao J, Mi L, Wang J. Metatranscriptomics of the Hu sheep rumen microbiome reveals novel cellulases. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:153. [PMID: 31249617 PMCID: PMC6587244 DOI: 10.1186/s13068-019-1498-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/14/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Cellulosic biomass has great potential as a renewable biofuel resource. Robust, high-performance enzymes are needed to effectively utilize this valuable resource. In this study, metatranscriptomics was used to explore the carbohydrate-active enzymes (CAZymes), especially glycoside hydrolases (GHs), present in the rumen microbiome of Hu sheep. Select CAZymes were experimentally verified and characterized after cloning and expression in E. coli. RESULTS The metatranscriptomes of six Hu sheep rumen microbiomes yielded 42.3 Gbp of quality-checked sequence data that represented in total 2,380,783 unigenes after de novo assembling using Trinity and clustered with CD-HIT-EST. Annotation using the CAZy database revealed that 2.65% of the unigenes encoded GHs, which were assigned to 111 different CAZymes families. Firmicutes (18.7%) and Bacteroidetes (13.8%) were the major phyla to which the unigenes were taxonomically assigned. In total, 14,489 unigenes were annotated to 15 cellulase-containing GH families, with GH3, GH5 and GH9 being the predominant. From these putative cellulase-encoding unigenes, 4225 open reading frames (ORFs) were predicted to contain 2151 potential cellulase catalytic modules. Additionally, 147 ORFs were found to encode proteins that contain carbohydrate-binding modules (CBMs). Heterogeneous expression of 30 candidate cDNAs from the GH5 family in E. coli BL21 showed that 17 of the tested proteins had endoglucanase activity, while 7 exhibited exoglucanase activity. Interestingly, two of the GH5 proteins (Cel5A-h28 and Cel5A-h11) showed high specific activity against carboxymethylcellulose (CMC) and p-nitrophenyl-β-d-cellobioside (pNPC) (222.2 and 142.8 U/mg), respectively. The optimal pH value for activity of Cel5A-h11 and Cel5A-h28 was 6.0 for both enzymes, and optimal temperatures were 40 and 50 °C, respectively. Both enzymes retained over 70 and 60%, respectively, of their original activities after incubation at 40 °C for 60 min. However, their activities were rapidly diminished upon exposure to higher temperatures. Cel5A-h11 and Cel5A-h28 retained more than 80 and 60% of their maximal enzymatic activities after incubation for 16 h in buffered solutions in the pH range from 4.0 to 9.0. CONCLUSION The metatranscriptomic results revealed that the rumen microbiome of Hu sheep encoded a repertoire of new enzymes capable of cellulose degradation and metatranscriptomics was an effective method to discover novel cellulases for biotechnological applications.
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Affiliation(s)
- Bo He
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Shuwen Jin
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jiawen Cao
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Lan Mi
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jiakun Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
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Saggese I, Bona E, Conway M, Favero F, Ladetto M, Liò P, Manzini G, Mignone F. STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow. BMC Bioinformatics 2018; 19:184. [PMID: 30066630 PMCID: PMC6069750 DOI: 10.1186/s12859-018-2174-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
Background De novo assembly of RNA-seq data allows the study of transcriptome in absence of a reference genome either if data is obtained from a single organism or from a mixed sample as in metatranscriptomics studies. Given the high number of sequences obtained from NGS approaches, a critical step in any analysis workflow is the assembly of reads to reconstruct transcripts thus reducing the complexity of the analysis. Despite many available tools show a good sensitivity, there is a high percentage of false positives due to the high number of assemblies considered and it is likely that the high frequency of false positive is underestimated by currently used benchmarks. The reconstruction of not existing transcripts may false the biological interpretation of results as – for example – may overestimate the identification of “novel” transcripts. Moreover, benchmarks performed are usually based on RNA-seq data from annotated genomes and assembled transcripts are compared to annotations and genomes to identify putative good and wrong reconstructions, but these tests alone may lead to accept a particular type of false positive as true, as better described below. Results Here we present a novel methodology of de novo assembly, implemented in a software named STAble (Short-reads Transcriptome Assembler). The novel concept of this assembler is that the whole reads are used to determine possible alignments instead of using smaller k-mers, with the aim of reducing the number of chimeras produced. Furthermore, we applied a new set of benchmarks based on simulated data to better define the performance of assembly method and carefully identifying true reconstructions. STAble was also used to build a prototype workflow to analyse metatranscriptomics data in connection to a steady state metabolic modelling algorithm. This algorithm was used to produce high quality metabolic interpretations of small gene expression sets obtained from already published RNA-seq data that we assembled with STAble. Conclusions The presented results, albeit preliminary, clearly suggest that with this approach is possible to identify informative reactions not directly revealed by raw transcriptomic data.
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Affiliation(s)
- Igor Saggese
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte Orientale, 15121, Alessandria, Italy
| | - Elisa Bona
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte Orientale, 15121, Alessandria, Italy
| | - Max Conway
- Computer Laboratory, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Francesco Favero
- Dipartimento di Scienze della Salute, Università degli Studi del Piemonte Orientale, 28100, Novara, Italy
| | - Marco Ladetto
- AO SS Antonio e Biagio e Cesare Arrigo, 15121, Alessandria, Italy.,Dipartimento di Biotecnologie e Scienze per la Salute, Università di Torino, 10124, Torino, Italy
| | - Pietro Liò
- Computer Laboratory, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Giovanni Manzini
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte Orientale, 15121, Alessandria, Italy.,Istituto di Informatica e Telematica, CNR, 56124, Pisa, Italy
| | - Flavio Mignone
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte Orientale, 15121, Alessandria, Italy.
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Pandit RJ, Hinsu AT, Patel SH, Jakhesara SJ, Koringa PG, Bruno F, Psifidi A, Shah SV, Joshi CG. Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches. Syst Appl Microbiol 2018; 41:374-385. [PMID: 29555111 DOI: 10.1016/j.syapm.2018.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 01/17/2023]
Abstract
Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.
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Affiliation(s)
- Ramesh J Pandit
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Ankit T Hinsu
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Shriram H Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Fosso Bruno
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Amendola 165/A, 70126 Bari, Italy
| | - Androniki Psifidi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK; Department of Clinical Science and Services, Royal Veterinary College, North Mymms, Hertfordshire, UK
| | - S V Shah
- Livestock Research Station, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand 388 001, Gujarat, India.
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9
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Edwards JE, Forster RJ, Callaghan TM, Dollhofer V, Dagar SS, Cheng Y, Chang J, Kittelmann S, Fliegerova K, Puniya AK, Henske JK, Gilmore SP, O'Malley MA, Griffith GW, Smidt H. PCR and Omics Based Techniques to Study the Diversity, Ecology and Biology of Anaerobic Fungi: Insights, Challenges and Opportunities. Front Microbiol 2017; 8:1657. [PMID: 28993761 PMCID: PMC5622200 DOI: 10.3389/fmicb.2017.01657] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/15/2017] [Indexed: 11/25/2022] Open
Abstract
Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys. However, the true extent of their diversity may be even more extensively underestimated as anaerobic fungi continue being discovered in yet unexplored gut and non-gut environments. Additionally many studies are now known to have used primers that provide incomplete coverage of the Neocallimastigomycota. For ecological studies the internal transcribed spacer 1 region (ITS1) has been the taxonomic marker of choice, but due to various limitations the large subunit rRNA (LSU) is now being increasingly used. How the continued expansion of our knowledge regarding anaerobic fungal diversity will impact on our understanding of their biology and ecological role remains unclear; particularly as it is becoming apparent that anaerobic fungi display niche differentiation. As a consequence, there is a need to move beyond the broad generalization of anaerobic fungi as fiber-degraders, and explore the fundamental differences that underpin their ability to exist in distinct ecological niches. Application of genomics, transcriptomics, proteomics and metabolomics to their study in pure/mixed cultures and environmental samples will be invaluable in this process. To date the genomes and transcriptomes of several characterized anaerobic fungal isolates have been successfully generated. In contrast, the application of proteomics and metabolomics to anaerobic fungal analysis is still in its infancy. A central problem for all analyses, however, is the limited functional annotation of anaerobic fungal sequence data. There is therefore an urgent need to expand information held within publicly available reference databases. Once this challenge is overcome, along with improved sample collection and extraction, the application of these techniques will be key in furthering our understanding of the ecological role and impact of anaerobic fungi in the wide range of environments they inhabit.
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Affiliation(s)
- Joan E. Edwards
- Laboratory of Microbiology, Wageningen University & ResearchWageningen, Netherlands
| | - Robert J. Forster
- Lethbridge Research and Development Centre, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - Tony M. Callaghan
- Department for Quality Assurance and Analytics, Bavarian State Research Center for AgricultureFreising, Germany
| | - Veronika Dollhofer
- Department for Quality Assurance and Analytics, Bavarian State Research Center for AgricultureFreising, Germany
| | | | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, Nanjing Agricultural UniversityNanjing, China
| | - Jongsoo Chang
- Department of Agricultural Science, Korea National Open UniversitySeoul, South Korea
| | - Sandra Kittelmann
- Grasslands Research Centre, AgResearch Ltd.Palmerston North, New Zealand
| | - Katerina Fliegerova
- Institute of Animal Physiology and Genetics, Czech Academy of SciencesPrague, Czechia
| | - Anil K. Puniya
- College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences UniversityLudhiana, India
- Dairy Microbiology Division, ICAR-National Dairy Research InstituteKarnal, India
| | - John K. Henske
- Department of Chemical Engineering, University of California, Santa BarbaraSanta Barbara, CA, United States
| | - Sean P. Gilmore
- Department of Chemical Engineering, University of California, Santa BarbaraSanta Barbara, CA, United States
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa BarbaraSanta Barbara, CA, United States
| | - Gareth W. Griffith
- Institute of Biological Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & ResearchWageningen, Netherlands
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Sidhu C, Vikram S, Pinnaka AK. Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies. Front Microbiol 2017; 8:1382. [PMID: 28769920 PMCID: PMC5515832 DOI: 10.3389/fmicb.2017.01382] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/07/2017] [Indexed: 01/06/2023] Open
Abstract
Sewage waste represents an ecosystem of complex and interactive microbial consortia which proliferate with different kinetics according to their individual genetic as well as metabolic potential. We performed metagenomic shotgun sequencing on Ion-Torrent platform, to explore the microbial community structure, their biological interactions and associated functional capacity of pre-treated/raw sludge (RS) and post-treated/dried sludge (DS) of wastewater treatment plant. Bacterial phylotypes belonging to Epsilonproteobacteria (∼45.80%) dominated the RS with relatively few Archaea (∼1.94%) whereas DS has the dominance of beta- (30.23%) and delta- (13.38%) classes of Proteobacteria with relatively greater abundance of Archaea (∼7.18%). In particular, Epsilonproteobacteria appears as a primary energy source in RS and sulfur-reducing bacteria with methanogens seems to be in the potential syntrophic association in DS. These interactions could be ultimately responsible for carrying out amino-acid degradation, aromatic compound degradation and degradation of propionate and butyrate in DS. Our data also reveal the presence of key genes in the sludge microbial community responsible for degradation of polycyclic aromatic hydrocarbons. Potential pathogenic microbes and genes for the virulence factors were found to be relatively abundant in RS which clearly reflect the necessity of treatment of RS. After treatment, potential pathogens load was reduced, indicating the sludge hygienisation in DS. Additionally, the interactions found in this study would reveal the biological and environmental cooperation among microbial communities for domestic wastewater treatment.
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Affiliation(s)
- Chandni Sidhu
- Microbial Type Culture Collection and Gene Bank, Council of Scientific and Industrial Research-Institute of Microbial TechnologyChandigarh, India
| | - Surendra Vikram
- Microbial Type Culture Collection and Gene Bank, Council of Scientific and Industrial Research-Institute of Microbial TechnologyChandigarh, India.,Centre for Microbial Ecology and Genomics, Department of Genetics, University of PretoriaPretoria, South Africa
| | - Anil Kumar Pinnaka
- Microbial Type Culture Collection and Gene Bank, Council of Scientific and Industrial Research-Institute of Microbial TechnologyChandigarh, India
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