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Gao H, Yu Y, Lv Y, Wang D, Li H, Li Z, Zhang Y, Chen L, Leng J. Metagenomic Sequencing Reveals the Taxonomic and Functional Characteristics of Rumen Micro-organisms in Gayals. Microorganisms 2023; 11:1098. [PMID: 37317072 DOI: 10.3390/microorganisms11051098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 04/06/2023] [Accepted: 04/19/2023] [Indexed: 06/16/2023] Open
Abstract
As a semi-wild breed, Gayals have a strong fiber degradation capacity, which is unique to the microbial structure and function of their rumen. In this study, the unique rumen microbial composition and function of Gayals were investigated by metagenomic sequencing, with the Yunnan yellow cattle as the control. We compared the differences in rumen micro-organisms between Gayals and the Yunnan Yellow cattle, and the results showed that there were differences in bacteria, archaea and fungi between Gayals and the Yunnan Yellow cattle, while no significant abundance changes were observed in the protozoa. In addition, the ratio of Firmicutes to Bacteroidetes (1.06) in Gayals was higher than that of the Yunnan Yellow cattle (0.66). Three enzymes (PTA, ACH and FTHFS) related to the acetate production pathway and five enzymes (BHBD, THL, PTB, BK and BCACT) involved in butyric acid production were annotated in this study. The CAZymes search results showed that the abundance of GH5, GH26, GH94, CBM11 and CBM63 in Gayals was higher than in the Yunnan Yellow cattle (p < 0.05). Furthermore, this research constructed a model of rumen micro-organisms degrading fibers according to the characteristics and differences in the rumen microbiota structures and functions of the two breeds. This study expands our knowledge of the rumen microbiota and the mechanisms of fiber degradation in Gayals.
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Affiliation(s)
- Huan Gao
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Ye Yu
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Yaqi Lv
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Deao Wang
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Haonan Li
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Zhe Li
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Yuchen Zhang
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Lan Chen
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Jing Leng
- Key Laboratory of Animal Nutrition and Feed Science of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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Wang H, Li P, Liu X, Zhang C, Lu Q, Xi D, Yang R, Wang S, Bai W, Yang Z, Zhou R, Cheng X, Leng J. The Composition of Fungal Communities in the Rumen of Gayals ( Bos frontalis), Yaks ( Bos grunniens), and Yunnan and Tibetan Yellow Cattle ( Bos taurs). Pol J Microbiol 2019; 68:505-514. [PMID: 31880894 PMCID: PMC7260705 DOI: 10.33073/pjm-2019-050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 11/14/2022] Open
Abstract
The rumen is a microbial-rich ecosystem in which rumen fungi play an important role in the feed digestion of ruminants. The composition of rumen fungi in free-range ruminants such as gayals, yaks, Tibetan yellow cattle, and the domesticated Yunnan yellow cattle was investigated by sequencing an internal transcribed spacer region 1 (ITS1) using Illumina MiSeq. A total of 285 092 optimized sequences and 904 operational taxonomic units (OTUs) were obtained from the four cattle breeds. The rumen fungi abundance and Chao and Simpson indexes were all higher in free-range ruminants than in domesticated ruminants. Three fungal phyla were identified by sequence comparison: Neocallimastigomycota, Basidiomycota, and Ascomycota. Basidiomycota and Ascomycota have very low abundance in the rumen of four breeds cattle but anaerobic fungi (AF) Neocallimastigomycota occurred in a high abundance. In Neocallimastigomycota, the dominant genera were Piromyces, Anaeromyces, Cyllamyces, Neocallimastix, and Orpionmyces in four cattle breeds. The composition of the major genera of Neocallimastigaceae varied greatly among the four cattle breeds. The unclassified genera were unequally distributed in gayals, yaks, Tibetan and Yunnan yellow cattle, accounting for 90.63%, 98.52%, 97.79%, and 27.01% respectively. It appears that free-range ruminants have more unknown rumen fungi than domesticated ruminants and the cattle breeds and animal diets had an impact on the diversity of rumen fungi.
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Affiliation(s)
- Houfu Wang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Pengfei Li
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Xuchuan Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Chunyong Zhang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Qiongfen Lu
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Renhui Yang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Shuling Wang
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China
| | - Wenshun Bai
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Zhen Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Rongkang Zhou
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Xiao Cheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
| | - Jing Leng
- Key Laboratory of Animal and Feed Science of Yunnan Provincial, Yunnan Agricultural University , Kunming , China ; Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming , China
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Sinnathamby G, Henderson G, Umair S, Janssen P, Bland R, Simpson H. The bacterial community associated with the sheep gastrointestinal nematode parasite Haemonchus contortus. PLoS One 2018; 13:e0192164. [PMID: 29420571 PMCID: PMC5805237 DOI: 10.1371/journal.pone.0192164] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/17/2018] [Indexed: 11/23/2022] Open
Abstract
Culture-independent methods were used to study the microbiota of adult worms, third-stage larvae and eggs, both in faeces and laid in vitro, of Haemonchus contortus, a nematode parasite of the abomasa of ruminants which is a major cause of production losses and ill-health. Bacteria were identified in eggs, the female reproductive tract and the gut of adult and third-stage larvae (L3). PCR amplification of 16S rRNA sequences, denaturing gradient gel electrophoresis (DGGE) and clone libraries were used to compare the composition of the microbial communities of the different life-cycle stages of the parasites, as well as parasites and their natural environments. The microbiomes of adult worms and L3 were different from those in the abomasum or faeces respectively. The H. contortus microbiota was mainly comprised of members of the phyla Proteobacteria, Firmicutes and Bacteroidetes. Bacteria were localised in the gut, inside eggs and within the uterus of adult female worms using the universal FISH Eub338 probe, which targets most bacteria, and were also seen in these tissues by light and transmission electron microscopy. Streptococcus/Lactococcus sp. were identified within the distal uterus with the probe Strc493. Sequences from the genera Weissella and Leuconostoc were found in all life-cycle stages, except eggs collected from faeces, in which most sequences belonged to Clostridium sp. Bacteria affiliated with Weissella/Leuconostoc were identified in both PCR-DGGE short sequences and clone libraries of nearly full length 16S rRNA bacterial sequences in all life-cycle stages and subsequently visualised in eggs by fluorescent in situ hybridisation (FISH) with group-specific probes. This strongly suggests they are vertically transmitted endosymbionts. As this study was carried out on a parasite strain which has been maintained in the laboratory, other field isolates will need to be examined to establish whether these bacteria are more widely dispersed and have potential as targets to control H. contortus infections.
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Affiliation(s)
- Gajenathirin Sinnathamby
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | | | - Saleh Umair
- AgResearch Ltd, Palmerston North, New Zealand
| | | | - Ross Bland
- AgResearch Ltd, Palmerston North, New Zealand
| | - Heather Simpson
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
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Boonsaen P, Kinjo M, Sawanon S, Suzuki Y, Koike S, Kobayashi Y. Partial characterization of phylogeny, ecology and function of the fibrolytic bacteriumRuminococcus flavefaciens OS14, newly isolated from the rumen of swamp buffalo. Anim Sci J 2017; 89:377-385. [DOI: 10.1111/asj.12927] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 08/17/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Phoompong Boonsaen
- Department of Animal Science; Faculty of Agriculture at Kamphaeng Saen; Kasetsart University; Nakhon Pathom Thailand
- Center for Advanced Studies for Agriculture and Food; Kasetsart University Institute for Advanced Studies; Kasetsart University; Bangkok Thailand
| | - Madoka Kinjo
- Laboratory of Animal Function and Nutrition; Research Faculty of Agriculture; Hokkaido University; Sapporo Japan
| | - Suriya Sawanon
- Department of Animal Science; Faculty of Agriculture at Kamphaeng Saen; Kasetsart University; Nakhon Pathom Thailand
- Center for Advanced Studies for Agriculture and Food; Kasetsart University Institute for Advanced Studies; Kasetsart University; Bangkok Thailand
| | - Yutaka Suzuki
- Laboratory of Animal Function and Nutrition; Research Faculty of Agriculture; Hokkaido University; Sapporo Japan
| | - Satoshi Koike
- Laboratory of Animal Function and Nutrition; Research Faculty of Agriculture; Hokkaido University; Sapporo Japan
| | - Yasuo Kobayashi
- Laboratory of Animal Function and Nutrition; Research Faculty of Agriculture; Hokkaido University; Sapporo Japan
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Xue D, Chen H, Zhao X, Xu S, Hu L, Xu T, Jiang L, Zhan W. Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan Plateau. Syst Appl Microbiol 2017; 40:227-236. [PMID: 28495244 DOI: 10.1016/j.syapm.2017.03.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 12/16/2022]
Abstract
Yak and Tibetan sheep are the major indigenous ruminants on the Qinghai-Tibetan Plateau in China. The aim of this work was to study the differences in ruminal fermentation parameters and rumen prokaryotic community composition between hosts and feeding paradigms. The 16S rRNA genes targeting bacteria and archaea were sequenced using the MiSeq platform. The results showed that the prokaryotic community structure between yak and Tibetan sheep was significantly different (P<0.01). A significant difference in structure was also found between groups of yaks barn fed with a total mixed ration (TMR) and those naturally grazing (NG) (P=0.034), as well as for Tibetan sheep of the two groups (P=0.026). The core prokaryotic populations that existed in the rumen mostly dominated the structure. There was an obvious correlation of the prokaryotic community composition at the phylum and genus levels with the host or the feeding pattern. In addition, Tibetan sheep showed significantly higher yields of volatile fatty acids (VFAs) than yak, as did the NG group compared with the TMR group. In conclusion, both the host and feeding pattern may influence rumen microbial ecology system, with host effects being more important than those of the feeding pattern.
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Affiliation(s)
- Dan Xue
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, China; College of Life Sciences, Sichuan University, 610065 Chengdu, China; University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, China.
| | - Xinquan Zhao
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, China
| | - Shixiao Xu
- Northwest Plateau Institute of Biology, Chinese Academy of Sciences, 81001 Xining, China.
| | - Linyong Hu
- Northwest Plateau Institute of Biology, Chinese Academy of Sciences, 81001 Xining, China
| | - Tianwei Xu
- University of Chinese Academy of Sciences, 100049 Beijing, China; Northwest Plateau Institute of Biology, Chinese Academy of Sciences, 81001 Xining, China
| | - Lin Jiang
- State Key Laboratory of Soil Erosion and Dry Land Farming on the Loess Plateau, College of Forestry, Northwest A&F University, 712100 Yangling, China
| | - Wei Zhan
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, China; University of Chinese Academy of Sciences, 100049 Beijing, China
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Saltykova IV, Petrov VA, Logacheva MD, Ivanova PG, Merzlikin NV, Sazonov AE, Ogorodova LM, Brindley PJ. Biliary Microbiota, Gallstone Disease and Infection with Opisthorchis felineus. PLoS Negl Trop Dis 2016; 10:e0004809. [PMID: 27447938 PMCID: PMC4957795 DOI: 10.1371/journal.pntd.0004809] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/06/2016] [Indexed: 12/12/2022] Open
Abstract
Background There is increasing interest in the microbiome of the hepatobiliary system. This study investigated the influence of infection with the fish-borne liver fluke, Opisthorchis felineus on the biliary microbiome of residents of the Tomsk region of western Siberia. Methodology/Principal Findings Samples of bile were provided by 56 study participants, half of who were infected with O. felineus, and all of who were diagnosed with gallstone disease. The microbiota of the bile was investigated using high throughput, Illumina-based sequencing targeting the prokaryotic 16S rRNA gene. About 2,797, discrete phylotypes of prokaryotes were detected. At the level of phylum, bile from participants with opisthorchiasis showed greater numbers of Synergistetes, Spirochaetes, Planctomycetes, TM7 and Verrucomicrobia. Numbers of > 20 phylotypes differed in bile of the O. felineus-infected compared to non-infected participants, including presence of species of the genera Mycoplana, Cellulosimicrobium, Microlunatus and Phycicoccus, and the Archaeans genus, Halogeometricum, and increased numbers of Selenomonas, Bacteroides, Rothia, Leptotrichia, Lactobacillus, Treponema and Klebsiella. Conclusions/Significance Overall, infection with the liver fluke O. felineus modified the biliary microbiome, increasing abundance of bacterial and archaeal phylotypes. The microbiota of the alimentary tract and other sites of the body influences human health. Contrary to popular belief, the bile within the liver is not sterile, and may host a microbiome consisting of diverse species of microbes. The spectrum of microbial species and their numbers within the biliary system may be influenced by disease including infection with pathogens such as parasitic worms and with gallstone disease, liver cancer and other ailments. Here we examined the microbes in the bile of patients from western Siberia, Russia who were concurrently infected with a food-borne parasitic worm, the liver fluke Opisthorchis felineus. Infection with this liver fluke is common in western Siberia, as a consequence of dietary preference for undercooked or smoked fresh-water fishes that often carry the larva of the liver fluke. Using high throughput sequencing targeting a conserved bacterial gene and statistical analyses, numerous bacterial species were identified in the bile of the patients. Infection with the liver fluke modified the biliary microbiome, resulting in abundant and diverse species of bacteria and Archaea.
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Affiliation(s)
- Irina V. Saltykova
- Central Research Laboratory, Siberian State Medical University, Tomsk, Russian Federation
- Laboratory of Catalytic Research, Tomsk State University, Tomsk, Russian Federation
- Research Center for Neglected Diseases of Poverty, Department of Microbiology, Immunology and Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, D.C., United States of America
- * E-mail:
| | - Vjacheslav A. Petrov
- Central Research Laboratory, Siberian State Medical University, Tomsk, Russian Federation
| | - Maria D. Logacheva
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russian Federation
| | - Polina G. Ivanova
- Central Research Laboratory, Siberian State Medical University, Tomsk, Russian Federation
| | - Nikolay V. Merzlikin
- Surgical diseases department of Pediatric faculty, Siberian State Medical University, Tomsk, Russian Federation
| | - Alexey E. Sazonov
- Central Research Laboratory, Siberian State Medical University, Tomsk, Russian Federation
| | - Ludmila M. Ogorodova
- Department of Faculty Pediatrics, Siberian State Medical University, Tomsk, Russian Federation
| | - Paul J. Brindley
- Research Center for Neglected Diseases of Poverty, Department of Microbiology, Immunology and Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, D.C., United States of America
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Glendinning L, Wright S, Pollock J, Tennant P, Collie D, McLachlan G. Variability of the Sheep Lung Microbiota. Appl Environ Microbiol 2016; 82:3225-3238. [PMID: 26994083 PMCID: PMC4959240 DOI: 10.1128/aem.00540-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/15/2016] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED Sequencing technologies have recently facilitated the characterization of bacterial communities present in lungs during health and disease. However, there is currently a dearth of information concerning the variability of such data in health both between and within subjects. This study seeks to examine such variability using healthy adult sheep as our model system. Protected specimen brush samples were collected from three spatially disparate segmental bronchi of six adult sheep (age, 20 months) on three occasions (day 0, 1 month, and 3 months). To further explore the spatial variability of the microbiotas, more-extensive brushing samples (n = 16) and a throat swab were taken from a separate sheep. The V2 and V3 hypervariable regions of the bacterial 16S rRNA genes were amplified and sequenced via Illumina MiSeq. DNA sequences were analyzed using the mothur software package. Quantitative PCR was performed to quantify total bacterial DNA. Some sheep lungs contained dramatically different bacterial communities at different sampling sites, whereas in others, airway microbiotas appeared similar across the lung. In our spatial variability study, we observed clustering related to the depth within the lung from which samples were taken. Lung depth refers to increasing distance from the glottis, progressing in a caudal direction. We conclude that both host influence and local factors have impacts on the composition of the sheep lung microbiota. IMPORTANCE Until recently, it was assumed that the lungs were a sterile environment which was colonized by microbes only during disease. However, recent studies using sequencing technologies have found that there is a small population of bacteria which exists in the lung during health, referred to as the "lung microbiota." In this study, we characterize the variability of the lung microbiotas of healthy sheep. Sheep not only are economically important animals but also are often used as large animal models of human respiratory disease. We conclude that, while host influence does play a role in dictating the types of microbes which colonize the airways, it is clear that local factors also play an important role in this regard. Understanding the nature and influence of these factors will be key to understanding the variability in, and functional relevance of, the lung microbiota.
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Affiliation(s)
- Laura Glendinning
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Steven Wright
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Jolinda Pollock
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, United Kingdom
- Monogastric Science Research Centre, Scotland's Rural College (SRUC), Edinburgh, Midlothian, United Kingdom
| | - Peter Tennant
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - David Collie
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Gerry McLachlan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Midlothian, United Kingdom
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De Barbieri I, Gulino L, Hegarty R, Oddy V, Maguire A, Li L, Klieve A, Ouwerkerk D. Production attributes of Merino sheep genetically divergent for wool growth are reflected in differing rumen microbiotas. Livest Sci 2015. [DOI: 10.1016/j.livsci.2015.05.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Evaluation of bacterial and archaeal diversity in the rumen of Xiangxi yellow cattle (Bos taurus) fed Miscanthus sinensis or common mixed feedstuff. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0783-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Osés SM, Diez AM, Melero B, Luning PA, Jaime I, Rovira J. Characterization by culture-dependent and culture-independent methods of the bacterial population of suckling-lamb packaged in different atmospheres. Food Microbiol 2013; 36:216-22. [PMID: 24010600 DOI: 10.1016/j.fm.2013.05.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/24/2013] [Accepted: 05/20/2013] [Indexed: 02/04/2023]
Abstract
This study offers insight into the dynamics of bacterial populations in fresh cuts of suckling lamb under four different atmospheric conditions: air (A), and three Modified Atmosphere Packaging (MAP) environments, 15%O2/30%CO2/55%N2 (C, commercial), 70%O2/30%CO2 (O), and 15%O2/85%CO2 (H) for 18 days. Microbial analyses by both conventional methods and PCR-DGGE were performed. Controversial and surprising results emerged from comparing both methods in relation to the genus Pseudomonas. Thus, conventional methods detected the presence of high numbers of Pseudomonas colonies, although PCR-DGGE only detected this genus in air-packaged samples. PCR-DGGE detected higher microbial diversity in the control samples (A) than in the modified atmospheres (C, O, H), having atmosphere H the fewest number of species. Brochothrix thermosphacta, LAB (Carnobacterium divergens and Lactobacillus sakei), and Escherichia spp. were detected in all the atmospheres throughout storage. Moreover, previously undescribed bacteria from lamb meat such as Enterobacter hormaechei, Staphylococcus equorum and Jeotgalicoccus spp. were also isolated in this study by DGGE. Additionally, qPCR analysis was used to detect and characterize strains of Escherichia coli. Virulence genes (stx1, stx2 and eae) were detected throughout storage in 97% of the samples. A high CO2 atmosphere was the most effective packaging combination doubling storage time in comparison with commercial atmosphere.
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Affiliation(s)
- Sandra M Osés
- Department of Biotechnology and Food Science, University of Burgos, Burgos, Spain
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Sirohi SK, Singh N, Dagar SS, Puniya AK. Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem. Appl Microbiol Biotechnol 2012; 95:1135-54. [PMID: 22782251 DOI: 10.1007/s00253-012-4262-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/20/2012] [Accepted: 06/22/2012] [Indexed: 12/30/2022]
Abstract
Rumen microbial community comprising of bacteria, archaea, fungi, and protozoa is characterized not only by the high population density but also by the remarkable diversity and the most complex microecological interactions existing in the biological world. This unprecedented biodiversity is quite far from full elucidation as only about 15-20 % of the rumen microbes are identified and characterized till date using conventional culturing and microscopy. However, the last two decades have witnessed a paradigm shift from cumbersome and time-consuming classical methods to nucleic acid-based molecular approaches for deciphering the rumen microbial community. These techniques are rapid, reproducible and allow both the qualitative and quantitative assessment of microbial diversity. This review describes the different molecular methods and their applications in elucidating the rumen microbial community.
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Affiliation(s)
- Sunil Kumar Sirohi
- Nutrition Biotechnology Laboratory, Dairy Cattle Nutrition Division, National Dairy Research Institute, Karnal, 132001, Haryana, India.
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