1
|
Ban C, Tian X, Lu Q, Lounglawan P, Wen G. Enhancing Rumen Fermentation and Bacteria Community in Sika Deer ( Cervus nippon) through Varying Levels of Dragon Fruit Peel Polyphenolic Extract: An In Vitro Study. Animals (Basel) 2024; 14:1139. [PMID: 38672287 PMCID: PMC11047680 DOI: 10.3390/ani14081139] [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: 03/05/2024] [Revised: 04/06/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
The aim of this study is to investigate the effect of dragon fruit peel polyphenolic extract (DFPE) on gas production, rumen fermentation, and bacterial communities in sika deer using an in vitro technique. Three treatments with different DFPE levels (DFPE0, base diet; DFPE5, base diet + 5 mg/g DFPE; DFPE10, base diet + 10 mg/g DFPE, respectively; n = 6) were implemented. The phenolic composition of DFPE, gas production (GP), ammonia nitrogen (NH3-N), volatile fatty acid (VFA), and bacteria communities was evaluated after 24 h of incubation. The results showed that GP and NH3-N were reduced by DFPE supplementation. Total VFA, isovaleric acid, and valeric acid were increased (p < 0.05) by the addition of DFPE. No changes (p > 0.05) were observed in pH, acetic acid, propionic acid, isobutyric acid, butyric acid, and the ratio of acetic acid to propionic acid. Additionally, the alpha indexes, including Sobs, Shannon, and Ace, were increased by DFPE supplementation. Moreover, at the phylum level, DFPE supplementation increased (p = 0.01) Bacteroidota but reduced (p < 0.01) Firmicutes. At the genus level, compared to DFPE0, the DFPE10 had increased relative abundances of Rikenellaceae_RC9_gut_group (p < 0.01), norank_f_Muribaculaceae (p = 0.01), Lachnospiraceae_NK3A20_group (p < 0.01), Christensenellaceae_R-7_group (p < 0.01), and NK4A214_group (p < 0.01), decreased relative abundances of Streptococcus (p < 0.01), Oribacterium (p = 0.01), and Enterococcus (p < 0.01). Compared to DFPE0, DFPE5 had no change (p > 0.05) in all bacteria at the genus level except for decreased relative abundance of Enterococcus (p < 0.01). These results indicated that DFPE may be able to be used as a feed additive to enhance fermentation parameters and improve ruminal bacteria communities in Sika deer.
Collapse
Affiliation(s)
- Chao Ban
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
| | - Xingzhou Tian
- College of Animal Science, Guizhou University, Guiyang 550025, China (Q.L.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Qi Lu
- College of Animal Science, Guizhou University, Guiyang 550025, China (Q.L.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Pipat Lounglawan
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
| | - Guilan Wen
- College of Animal Science, Guizhou University, Guiyang 550025, China (Q.L.)
| |
Collapse
|
2
|
Keum GB, Pandey S, Kim ES, Doo H, Kwak J, Ryu S, Choi Y, Kang J, Kim S, Kim HB. Understanding the Diversity and Roles of the Ruminal Microbiome. J Microbiol 2024; 62:217-230. [PMID: 38662310 DOI: 10.1007/s12275-024-00121-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 04/26/2024]
Abstract
The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.
Collapse
Affiliation(s)
- Gi Beom Keum
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sriniwas Pandey
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Eun Sol Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Hyunok Doo
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Jinok Kwak
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sumin Ryu
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Yejin Choi
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Juyoun Kang
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sheena Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Hyeun Bum Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea.
| |
Collapse
|
3
|
Dahl SA, Seifert J, Camarinha-Silva A, Cheng YC, Hernández-Arriaga A, Hudler M, Windisch W, König A. Microbiota and Nutrient Portraits of European Roe Deer (Capreolus capreolus) Rumen Contents in Characteristic Southern German Habitats. MICROBIAL ECOLOGY 2023; 86:3082-3096. [PMID: 37875737 PMCID: PMC10640537 DOI: 10.1007/s00248-023-02308-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023]
Abstract
Roe deer (Capreolus capreolus) are found in various habitats, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants still needs to be improved. There are only a few publications for individual species with a low number of samples. This study aims to identify a core microbiota for Bavarian roe deer and present nutrient and microbiota portraits of the individual habitat types. This study investigated the roe deer's rumen (reticulorumen) content from seven different characteristic Bavarian habitat types. The focus was on the composition of nutrients, fermentation products, and the rumen bacterial community. A total of 311 roe deer samples were analysed, with the most even possible distribution per habitat, season, age class, and gender. Significant differences in nutrient concentrations and microbial composition were identified for the factors habitat, season, and age class. The highest crude protein content (plant protein and microbial) in the rumen was determined in the purely agricultural habitat (AG), the highest value of non-fibre carbohydrates in the alpine mountain forest, and the highest fibre content (neutral detergent fibre, NDF) in the pine forest habitat. Maximum values for fibre content go up to 70% NDF. The proportion of metabolites (ammonia, lactate, total volatile fatty acids) was highest in the Agriculture-Beech-Forest habitat (ABF). Correlations can be identified between adaptations in the microbiota and specific nutrient concentrations, as well as in strong fluctuations in ingested forage. In addition, a core bacterial community comprising five genera could be identified across all habitats, up to 44% of total relative abundance. As with all wild ruminants, many microbial genera remain largely unclassified at various taxonomic levels. This study provides a more in-depth insight into the diversity and complexity of the roe deer rumen microbiota. It highlights the key microorganisms responsible for converting naturally available nutrients of different botanical origins.
Collapse
Affiliation(s)
- Sarah-Alica Dahl
- Wildlife Biology and Management Unit, Chair of Animal Nutrition and Metabolism, Technical University of Munich, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany.
| | - Jana Seifert
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 10, 70599, Stuttgart, Germany
| | - Amélia Camarinha-Silva
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 10, 70599, Stuttgart, Germany
| | - Yu-Chieh Cheng
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 10, 70599, Stuttgart, Germany
| | - Angélica Hernández-Arriaga
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 10, 70599, Stuttgart, Germany
| | - Martina Hudler
- Game Management and Wildlife Management, Weihenstephan-Triesdorf University of Applied Sciences, Hans-Carl-von-Carlowitz-Platz 3, 85354, Freising, Germany
| | - Wilhelm Windisch
- TUM School of Life Sciences, Technical University of Munich, Liesel-Beckmann-Straße 2, 85354, Freising, Germany
| | - Andreas König
- Wildlife Biology and Management Unit, Chair of Animal Nutrition and Metabolism, Technical University of Munich, Hans-Carl-von-Carlowitz-Platz 2, 85354, Freising, Germany
| |
Collapse
|
4
|
Wang D, Hu X, Li M, Liu J, Tang M, Liu W, Zhan J, Xu Y, Zhang W. Diet composition and interspecific niche of Taohongling Sika deer (Cervus nippon kopschi) and its sympatric Reeve’s muntjac (Muntiacus reevesi) and Chinese hare (Lepus sinensis) in winter (Animalia, Mammalia). Zookeys 2023; 1149:17-36. [DOI: 10.3897/zookeys.1149.96936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/30/2022] [Indexed: 02/24/2023] Open
Abstract
Species co-existence depends on how organisms utilize their environment and resources. Little is known about the winter diet composition and sympatric co-existence of South China sika deer and its companion species in Taohongling. In this study, high-throughput sequencing and metabarcoding trnL were used to study the diet composition and interspecific relationship including sika deer, Reeve’s muntjac, and Chinese hare. Our results show that 203 genera in 90 families are contained in the diet of sika deer, 203 genera in 95 families for Reeve’s muntjac, and 163 genera in 75 families for Chinese hare. Sika deer fed on Rubus chingii, Loropetalum chinense, and Eurya japonica in winter, accounting for 75.30%; Reeve’s muntjac consumed mainly R. chingii, E. japonica, and Euonymus grandiflorus, accounting for 68.80%, and Chinese hare mainly fed on R. chingii, Smilax china, and Rhus chinensis, accounting for 41.98%. The Shannon index showed no significant difference between groups (p > 0.05). The NMDS analysis found considerable overlap among three species. Sika deer and Reeve’s muntjac consumed similar forage plants but varied greatly in Chinese hare, which occupied the widest choice in winter, resulting in higher diet breadth and increased dietary divergence, thereby reducing competition and facilitating coexistence. The diet niche overlap index among them, as represented by Pianka’s index, ranging from 0.62 between sika deer and Chinese hare to 0.83 between sika deer and Reeve’s muntjac, which indicated a more similar niche and potential competition in closely related species. Our findings provide a new diet perspective of three herbivores, leading to a more comprehensive understanding of resource partitioning and species coexistence.
Collapse
|
5
|
Battelli M, Colombini S, Parma P, Galassi G, Crovetto GM, Spanghero M, Pravettoni D, Zanzani SA, Manfredi MT, Rapetti L. In vitro effects of different levels of quebracho and chestnut tannins on rumen methane production, fermentation parameters, and microbiota. Front Vet Sci 2023; 10:1178288. [PMID: 37152691 PMCID: PMC10154982 DOI: 10.3389/fvets.2023.1178288] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/29/2023] [Indexed: 05/09/2023] Open
Abstract
Both condensed and hydrolysable tannins (CTs and HTs, respectively) have the ability to reduce enteric CH4 production in ruminants. However, the precise mechanism of action is not fully understood. Among the proposed hypotheses are the reduction of ruminal digestibility, direct control action on protozoa, reduction of archaea, and a hydrogen sink mechanism. In this in vitro study, which simulated rumen fermentation, two additives, one containing CTs (70% based on DM) from quebracho and one with HTs (75% based on DM) from chestnut, at four levels of inclusion (2, 4, 6, 8% on an as-fed basis) were added to the fermentation substrate and tested against a negative control. Both types of tannins significantly reduced total gas (GP) and CH4 (ml/g DM) production during the 48 h of incubation. The lower GP and CH4 production levels were linked to the reduction in dry matter digestibility caused by CTs and HTs. Conversely, no significant differences were observed for the protozoan and archaeal populations, suggesting a low direct effect of tannins on these rumen microorganisms in vitro. However, both types of tannins had negative correlations for the families Bacteroidales_BS11 and F082 and positive correlations for the genera Prevotella and Succinivibrio. Regarding the fermentation parameters, no differences were observed for pH and total volatile fatty acid production, while both CTs and HTs linearly reduced the NH3 content. CTs from quebracho were more effective in reducing CH4 production than HTs from chestnut. However, for both types of tannins, the reduction in CH4 production was always associated with a lower digestibility without any changes in archaea or protozoa. Due to the high variability of tannins, further studies investigating the chemical structure of the compounds and their mechanisms of action are needed to understand the different results reported in the literature.
Collapse
Affiliation(s)
- Marco Battelli
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Stefania Colombini
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Pietro Parma
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Gianluca Galassi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Gianni Matteo Crovetto
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Milan, Italy
| | - Mauro Spanghero
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Davide Pravettoni
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Lodi, Italy
| | | | - Maria Teresa Manfredi
- Department of Veterinary Medicine and Animal Sciences, University of Milan, Lodi, Italy
| | - Luca Rapetti
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Milan, Italy
- *Correspondence: Luca Rapetti,
| |
Collapse
|
6
|
Betancur-Murillo CL, Aguilar-Marín SB, Jovel J. Prevotella: A Key Player in Ruminal Metabolism. Microorganisms 2022; 11:microorganisms11010001. [PMID: 36677293 PMCID: PMC9866204 DOI: 10.3390/microorganisms11010001] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Ruminants are foregut fermenters that have the remarkable ability of converting plant polymers that are indigestible to humans into assimilable comestibles like meat and milk, which are cornerstones of human nutrition. Ruminants establish a symbiotic relationship with their microbiome, and the latter is the workhorse of carbohydrate fermentation. On the other hand, during carbohydrate fermentation, synthesis of propionate sequesters H, thus reducing its availability for the ultimate production of methane (CH4) by methanogenic archaea. Biochemically, methane is the simplest alkane and represents a downturn in energetic efficiency in ruminants; environmentally, it constitutes a potent greenhouse gas that negatively affects climate change. Prevotella is a very versatile microbe capable of processing a wide range of proteins and polysaccharides, and one of its fermentation products is propionate, a trait that appears conspicuous in P. ruminicola strain 23. Since propionate, but not acetate or butyrate, constitutes an H sink, propionate-producing microbes have the potential to reduce methane production. Accordingly, numerous studies suggest that members of the genus Prevotella have the ability to divert the hydrogen flow in glycolysis away from methanogenesis and in favor of propionic acid production. Intended for a broad audience in microbiology, our review summarizes the biochemistry of carbohydrate fermentation and subsequently discusses the evidence supporting the essential role of Prevotella in lignocellulose processing and its association with reduced methane emissions. We hope this article will serve as an introduction to novice Prevotella researchers and as an update to others more conversant with the topic.
Collapse
Affiliation(s)
- Claudia Lorena Betancur-Murillo
- Escuela de Ciencias Básicas, Tecnología e Ingeniería, Universidad Nacional Abierta y a Distancia, UNAD, Bogotá 111511, Colombia
| | | | - Juan Jovel
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
- Correspondence:
| |
Collapse
|
7
|
Si H, Li S, Nan W, Sang J, Xu C, Li Z. Integrated Transcriptome and Microbiota Reveal the Regulatory Effect of 25-Hydroxyvitamin D Supplementation in Antler Growth of Sika Deer. Animals (Basel) 2022; 12:ani12243497. [PMID: 36552417 PMCID: PMC9774409 DOI: 10.3390/ani12243497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/21/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
The level of plasma 25-hydroxyvitamin D (25(OH)D) is associated with the growth of the antler, a fast-growing bone organ of Cervidae. However, the benefits of 25(OH)D supplementation on antler growth and the underlying mechanisms remain unclear. Here, the antler growth profile and transcriptome, plasma parameters, rumen bacteria, and metabolites (volatile fatty acids and amino acids) were determined in sika deer in a 25(OH)D supplementation group (25(OH)D, n = 8) and a control group (Ctrl, n = 8). 25(OH)D supplementation significantly increased the antler weight and growth rate. The levels of IGF-1,25(OH)D and 1,25-dihydroxyvitamin D were significantly higher in the 25(OH)D group than in the Ctrl group, while the levels of LDL-C were lower. The levels of valerate and branched-chain amino acids in the rumen fluid were significantly different between the 25(OH)D and Ctrl groups. The bacterial diversity indices were not significantly different between the two groups. However, the relative abundances of the butyrate-producing bacteria (families Lachnospiraceae and Succinivibrionaceae) and the pyruvate metabolism pathway were higher in the 25(OH)D group. The transcriptomic profile of the antler was significantly different between the 25(OH)D and Ctrl groups, with 356 up- and 668 down-regulated differentially expressed genes (DEGs) in the 25(OH)D group. The up-regulated DEGs were enriched in the proteinaceous extracellular matrix and collagen, while the down-regulated DEGs were enriched in the immune system and lipid metabolism pathways. Overall, these results provide novel insights into the effects of 25(OH)D supplementation on the host metabolism, rumen microbiota, and antler transcriptome of sika deer.
Collapse
Affiliation(s)
- Huazhe Si
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Songze Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Weixiao Nan
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Jianan Sang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Chao Xu
- Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
- Correspondence: (C.X.); (Z.L.)
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Jilin Agricultural University, Changchun 130118, China
- Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (C.X.); (Z.L.)
| |
Collapse
|
8
|
Comparative study of the function and structure of the gut microbiota in Siberian musk deer and Forest musk deer. Appl Microbiol Biotechnol 2022; 106:6799-6817. [DOI: 10.1007/s00253-022-12158-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 11/02/2022]
|
9
|
Gastrointestinal Biogeography of Luminal Microbiota and Short-Chain Fatty Acids in Sika Deer (Cervus nippon). Appl Environ Microbiol 2022; 88:e0049922. [PMID: 35950850 PMCID: PMC9469704 DOI: 10.1128/aem.00499-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gut microbiota of sika deer has been widely investigated, but the spatial distribution of symbiotic microbes among physical niches in the gastrointestinal tract remains to be established. While feces are the most commonly used biological samples in these studies, the accuracy of fecal matter as a proxy of the microbiome at other gastrointestinal sites is as yet unknown. In the present study, luminal contents obtained along the longitudinal axis of deer gastrointestinal tract (rumen, reticulum, omasum, abomasum, small intestine, cecum, colon, and rectum) were subjected to 16S rRNA gene sequencing for profiling of the microbial composition, and samples from the rumen, small intestine, and cecum were subjected to metabolomic analysis to evaluate short-chain fatty acid (SCFA) profiles. Prevotella bacteria were the dominant gastric core microbes, while Christensenellaceae_R-7_group was predominantly observed in the intestine. While the eight gastrointestinal sites displayed variations in microbial diversity, abundance, and function, they could be clustered into stomach, small intestine, and large intestine segments, and the results further highlighted a specific microbial niche of the small intestine. SCFA levels in the rumen, small intestine, and cecum were significantly different, with Bacteroidetes and Spirochaetes were shown to play a critical role in SCFA production. Finally, the rectal microbial composition was significantly correlated with colonic and cecum communities but not those of the small intestine and four gastric sites. Quantification of the compositions and biogeographic relationships between gut microbes and SCFAs in sika deer should provide valuable insights into the interactions contributing to microbial functions and metabolites. IMPORTANCE Feces or specific segments of the gastrointestinal tract (in particular, the rumen) were sampled to explore the gut microbiome. The gastrointestinal biogeography of the luminal microbiota in ruminants, which is critical to guide accurate sampling for different purposes, is poorly understood at present. The microbial community of the rectal sample (as a proxy of fecal sample) showed higher correlation with those of other large intestinal sites relative to the small intestine or stomach, suggesting that the microbial composition is specifically shaped by the unique physiological characteristics of different gastrointestinal niches. In addition, significant differences in microbiomes and SCFAs were observed among the different gastrointestinal sites.
Collapse
|
10
|
Effect of Methionine Supplementation on Serum Metabolism and the Rumen Bacterial Community of Sika Deer ( Cervus nippon). Animals (Basel) 2022; 12:ani12151950. [PMID: 35953939 PMCID: PMC9367550 DOI: 10.3390/ani12151950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Methionine is the first or second limiting amino acid for ruminants, such as sika deer, and has a variety of biological functions such as antioxidant activity, immune response, and protein synthesis. This study aimed to investigate the effects of methionine supplementation on antler growth, serum biochemistry, rumen fermentation, and the bacterial community of sika deer during the antler-growing period. Twelve 4-year-old male sika deer were randomly assigned to three dietary groups supplemented with 0 g/day (n = 4, CON), 4.0 g/day (n = 4, LMet), and 6.0 g/day (n = 4, HMet) methionine. No significant difference (p > 0.05) was found in the production performance between the three groups, but antler weight was higher in both the LMet and HMet groups than in the CON group. Methionine supplementation significantly increased the serum glutathione peroxidase activity (p < 0.05). The serum immunoglobulin G level was significantly higher in the HMet group than in the other two groups (p < 0.05). No significant effect was found on the apparent amino acid digestibility of the three groups, but cysteine and methionine digestibility were higher in the LMet group. The serum hydroxylysine level was significantly lower in the LMet and HMet groups, whereas the serum lysine level was significantly lower in the HMet group compared with the CON group (p < 0.05). The LMet group had the highest but a nonsignificant total volatile fatty acid content and significantly higher microbial protein content in the rumen than the CON group (p < 0.05). The phyla Bacteroidetes, Firmicutes, and Proteobacteria were dominant in the rumen of the sika deer. The principal coordinate analysis (PCoA) and analysis of similarities (ANOSIM) results showed a significant change in the bacterial composition of the three groups (p < 0.05). The relative abundance of Prevotella and Rikenellaceae-RC9 was significantly higher in the LMet group compared with the CON group and CON and HMet groups, respectively. These results revealed that methionine supplementation improved the antioxidant activity and immune status, affecting amino acid metabolism and rumen microbial composition of the sika deer.
Collapse
|
11
|
Xing X, Ai C, Wang T, Li Y, Liu H, Hu P, Wang G, Liu H, Wang H, Zhang R, Zheng J, Wang X, Wang L, Chang Y, Qian Q, Yu J, Tang L, Wu S, Shao X, Li A, Cui P, Zhan W, Zhao S, Wu Z, Shao X, Dong Y, Rong M, Tan Y, Cui X, Chang S, Song X, Yang T, Sun L, Ju Y, Zhao P, Fan H, Liu Y, Wang X, Yang W, Yang M, Wei T, Song S, Xu J, Yue Z, Liang Q, Li C, Ruan J, Yang F. The first high-quality reference genome of sika deer provides insights for high-tannin adaptation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022:S1672-0229(22)00075-4. [PMID: 35718271 PMCID: PMC10372904 DOI: 10.1016/j.gpb.2022.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/07/2022] [Accepted: 05/08/2022] [Indexed: 10/18/2022]
Abstract
Sika deer are known to prefer oak leaves, which are rich in tannins and toxic to most mammals; however, the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear. In identifying the mechanism responsible for the tolerance of a highly toxic diet, we have made a major advancement by explaining the genomics of sika deer. We generated the first high-quality, chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments. Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food, especially the expansion of the UGT family 2 subfamily B of UGT genes. The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation. Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.
Collapse
Affiliation(s)
- Xiumei Xing
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| | - Cheng Ai
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Tianjiao Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yang Li
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Huitao Liu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Pengfei Hu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Guiwu Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Huamiao Liu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Hongliang Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Ranran Zhang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Junjun Zheng
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Xiaobo Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lei Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yuxiao Chang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jinghua Yu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Lixin Tang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Shigang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiujuan Shao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Alun Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Peng Cui
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wei Zhan
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, China
| | - Sheng Zhao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhichao Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiqun Shao
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yimeng Dong
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Min Rong
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yihong Tan
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xuezhe Cui
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Shuzhuo Chang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Xingchao Song
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Tongao Yang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Limin Sun
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Yan Ju
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Pei Zhao
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Huanhuan Fan
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Ying Liu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Xinhui Wang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Wanyun Yang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Min Yang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Tao Wei
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Shanshan Song
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Jiaping Xu
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Zhigang Yue
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing 100083, China.
| | - Chunyi Li
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Fuhe Yang
- Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| |
Collapse
|
12
|
Yildirim E, Ilina L, Laptev G, Filippova V, Brazhnik E, Dunyashev T, Dubrovin A, Novikova N, Tiurina D, Tarlavin N, Laishev K. The structure and functional profile of ruminal microbiota in young and adult reindeers ( Rangifer tarandus) consuming natural winter-spring and summer-autumn seasonal diets. PeerJ 2021; 9:e12389. [PMID: 34900412 PMCID: PMC8627130 DOI: 10.7717/peerj.12389] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/04/2021] [Indexed: 01/04/2023] Open
Abstract
Background The key natural area of Russian reindeer (Rangifer tarandus, Nenets breed) is arctic zones, with severe climatic conditions and scarce feed resources, especially in the cold winter season. The adaptation of reindeer to these conditions is associated not only with the genetic potential of the animal itself. The rumen microbiome provides significant assistance in adapting animals to difficult conditions by participating in the fiber digestion. The aim of our study is to investigate the taxonomy and predicted metabolic pathways of the ruminal microbiota (RM) during the winter–spring (WS) and summer–autumn (SA) seasons, in calves and adult reindeer inhabiting the natural pastures of the Yamalo-Nenetsky Autonomous District of the Russian Federation. Methods The RM in reindeer was studied using the Next Generation Sequencing method with the MiSeq (Illumina, San Diego, CA, USA) platform. Reconstruction and prediction of functional profiles of the metagenome, gene families, and enzymes were performed using the software package PICRUSt2 (v.2.3.0). Results The nutritional value of WS and SA diets significantly differed. Crude fiber content in the WS diet was higher by 22.4% (p < 0.05), compared to SA, indicating possibly poorer digestibility and necessity of the adaptation of the RM to this seasonal change. A total of 22 bacterial superphyla and phyla were found in the rumen, superphylum Bacteroidota and phylum Firmicutes being the dominating taxa (up to 48.1% ± 4.30% and 46.1% ± 4.80%, respectively); while only two archaeal phyla presented as minor communities (no more then 0.54% ± 0.14% totally). The percentages of the dominating taxa were not affected by age or season. However, significant changes in certain minor communities were found, with seasonal changes being more significant than age-related ones. The percentage of phylum Actinobacteriota significantly increased (19.3-fold) in SA, compared to WS (p = 0.02) in adults, and the percentage of phylum Cyanobacteria increased up to seven-fold (p = 0.002) in adults and calves. Seasonal changes in RM can improve the ability of reindeer to withstand the seasons characterized by a low availability of nutrients. The PICRUSt2 results revealed 257 predicted metabolic pathways in RM: 41 pathways were significantly (p < 0.05) influenced by season and/or age, including the processes of synthesis of vitamins, volatile fatty acids, and pigments; metabolism of protein, lipids, and energy; pathogenesis, methanogenesis, butanediol to pyruvate biosynthesis, cell wall biosynthesis, degradation of neurotransmitters, lactic acid fermentation, and biosynthesis of nucleic acids. A large part of these changeable pathways (13 of 41) was related to the synthesis of vitamin K homologues. Conclusion The results obtained improve our knowledge on the structure and possible metabolic pathways of the RM in reindeer, in relation to seasonal changes.
Collapse
Affiliation(s)
- Elena Yildirim
- Molecular Genetic laboratory, BIOTROF+ LTD, Saint-Petersburg, Russia
| | - Larisa Ilina
- Molecular Genetic laboratory, BIOTROF+ LTD, Saint-Petersburg, Russia
| | - Georgy Laptev
- Molecular Genetic laboratory, BIOTROF+ LTD, Saint-Petersburg, Russia
| | | | - Evgeni Brazhnik
- Molecular Genetic laboratory, BIOTROF+ LTD, Saint-Petersburg, Russia
| | - Timur Dunyashev
- Molecular Genetic laboratory, BIOTROF+ LTD, Saint-Petersburg, Russia
| | - Andrey Dubrovin
- Molecular Genetic laboratory, BIOTROF+ LTD, Saint-Petersburg, Russia
| | - Natalia Novikova
- Molecular Genetic laboratory, BIOTROF+ LTD, Saint-Petersburg, Russia
| | - Daria Tiurina
- Molecular Genetic laboratory, BIOTROF+ LTD, Saint-Petersburg, Russia
| | - Nikolay Tarlavin
- Molecular Genetic laboratory, BIOTROF+ LTD, Saint-Petersburg, Russia
| | - Kasim Laishev
- Department of Animal Husbandry and Environmental Management of the Arctic, Federal Research Center of Russian Academy Sciences, Pushkin, Saint-Petersurg, Russia
| |
Collapse
|
13
|
Barraza A, Montes-Sánchez JJ, Caamal-Chan MG, Loera-Muro A. Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities. MICROBIOLOGY-SGM 2021; 167. [PMID: 34661515 DOI: 10.1099/mic.0.001092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.
Collapse
Affiliation(s)
- Aarón Barraza
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC. La Paz, BCS, 23096, Mexico
| | - Juan J Montes-Sánchez
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC. Guerrero Negro, BCS, 23940, Mexico
| | - M Goretty Caamal-Chan
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC. La Paz, BCS, 23096, Mexico
| | - Abraham Loera-Muro
- CONACYT-Centro de Investigaciones Biológicas del Noroeste, SC. La Paz, BCS, 23096, Mexico
| |
Collapse
|
14
|
Zhang Y, Choi SH, Nogoy KM, Liang S. Review: The development of the gastrointestinal tract microbiota and intervention in neonatal ruminants. Animal 2021; 15:100316. [PMID: 34293582 DOI: 10.1016/j.animal.2021.100316] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/23/2022] Open
Abstract
The complex microbiome colonizing the gastrointestinal tract (GIT) of ruminants plays an important role in the development of the immune system, nutrient absorption and metabolism. Hence, understanding GIT microbiota colonization in neonatal ruminants has positive impacts on host health and productivity. Microbes rapidly colonize the GIT after birth and gradually develop into a complex microbial community, which allows the possibility of GIT microbiome manipulation to enhance newborn health and growth and perhaps induce lasting effects in adult ruminants. This paper reviews recent advances in understanding how host-microbiome interactions affect the GIT development and health of neonatal ruminants. Following initial GIT microbiome colonization, continuous exposure to host-specific microorganisms is necessary for GIT development and immune system maturation. Furthermore, the early GIT microbial community structure is significantly affected by early life events, such as maternal microbiota exposure, dietary changes, age and the addition of prebiotics, probiotics and synbiotics, supporting the idea of microbial programming in early life. However, the time window in which interventions can optimally improve production and reduce gastrointestinal disease as well as the role of key host-specific microbiota constituents and host immune regulation requires further study.
Collapse
Affiliation(s)
- Y Zhang
- Department of Animal Science, College of Animal Sciences, Jilin University, Changchun 130062, China; Department of Animal Science, Chungbuk National University, Cheongju 28644, South Korea
| | - S H Choi
- Department of Animal Science, Chungbuk National University, Cheongju 28644, South Korea
| | - K M Nogoy
- Department of Animal Science, Chungbuk National University, Cheongju 28644, South Korea
| | - S Liang
- Department of Animal Science, College of Animal Sciences, Jilin University, Changchun 130062, China.
| |
Collapse
|
15
|
Cairo PLG, Nogueira SSC, Altino VS, Vandenheede M, Schroyen M, Taminiau B, Daube G, Gross E, Bindelle J, Nogueira-Filho SLG. Individual differences in behaviour and gut bacteria are associated in collared peccary (Mammalia, Tayassuidae). J Appl Microbiol 2021; 131:2748-2762. [PMID: 33971065 DOI: 10.1111/jam.15133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 11/28/2022]
Abstract
AIMS We tested the hypothesis that the behaviour of an individual is associated with the diversity of its gut bacteria, using the collared peccary (Pecari tajacu) as a model. METHODS AND RESULTS In all, 24 adult male collared peccaries received either low- (n = 12) or high-fibre diet (n = 12) to induce contrasting gut fermentation profiles. They were submitted to three short-term challenges, allowing us to rate the animals in a coping-style dimension named 'calmness'. At the end of the experimental period, we collected samples of peccaries' forestomach contents to characterize bacterial diversity. We found a significant positive association between individual 'calmness' z-scores and the bacterial evenness index in gut bacteria (and a similar trend with the Simpson's diversity index), suggesting a more homogeneous bacterial community of calmer individuals. We also found a positive association between fibres digestibility and gut bacterial diversity in the peccaries' forestomach, but no effect of the dietary fibre level. CONCLUSIONS Gut bacteria evenness increases with 'calmness' z-scores, suggesting a more homogeneous bacterial community of calmer individuals, compared with the more heterogeneous of the most distressed ones. Our results also suggest associations between the digestibility of ADF with the gut bacterial diversity indices and with the relative abundance of the Actinobacteria phylum. SIGNIFICANCE AND IMPACT OF THE STUDY Our data showed that the hosts' individual behavioural differences are potentially aligned with gut bacterial diversity. The behaviour-microbiota link is correlated with host feed efficiency and, ultimately, may have implications for animal health and welfare of farm animals.
Collapse
Affiliation(s)
- P L G Cairo
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - S S C Nogueira
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil.,Instituto Nacional de Ciência e Tecnologia em Estudos Interdisciplinares e Transdiciplinares em Ecologia e Evolução (INCT IN-TREE), Salvador, Bahia, Brazil
| | - V S Altino
- Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - M Vandenheede
- Department of Veterinary Management of Animal Resources, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - M Schroyen
- Department of AgroBioChem, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium
| | - B Taminiau
- Department of Food Sciences, Fundamental and Applied Research of Animals & Health (FARAH), University of Liège, Liège, Belgium
| | - G Daube
- Department of Food Sciences, Fundamental and Applied Research of Animals & Health (FARAH), University of Liège, Liège, Belgium
| | - E Gross
- Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - J Bindelle
- Department of AgroBioChem/TERRA, Gembloux Agro-Bio Tech, Precision Livestock and Nutrition Unit/AgricultureIsLife, University of Liège, Gembloux, Belgium
| | - S L G Nogueira-Filho
- Instituto Nacional de Ciência e Tecnologia em Estudos Interdisciplinares e Transdiciplinares em Ecologia e Evolução (INCT IN-TREE), Salvador, Bahia, Brazil.,Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| |
Collapse
|
16
|
Ramos SC, Jeong CD, Mamuad LL, Kim SH, Kang SH, Kim ET, Cho YI, Lee SS, Lee SS. Diet Transition from High-Forage to High-Concentrate Alters Rumen Bacterial Community Composition, Epithelial Transcriptomes and Ruminal Fermentation Parameters in Dairy Cows. Animals (Basel) 2021; 11:838. [PMID: 33809588 PMCID: PMC8002347 DOI: 10.3390/ani11030838] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 02/07/2023] Open
Abstract
Effects of changing diet on rumen fermentation parameters, bacterial community composition, and transcriptome profiles were determined in three rumen-cannulated Holstein Friesian cows using a 3 × 4 cross-over design. Treatments include HF-1 (first high-forage diet), HC-1 (first high-concentrate diet), HC-2 (succeeding high-concentrate diet), and HF-2 (second high-forage diet as a recovery period). Animal diets contained Klein grass and concentrate at ratios of 8:2, 2:8, 2:8, and 8:2 (two weeks each), respectively. Ammonia-nitrogen and individual and total volatile fatty acid concentrations were increased significantly during HC-1 and HC-2. Rumen species richness significantly increased for HF-1 and HF-2. Bacteroidetes were dominant for all treatments, while phylum Firmicutes significantly increased during the HC period. Prevotella, Erysipelothrix, and Galbibacter significantly differed between HF and HC diet periods. Ruminococcus abundance was lower during HF feeding and tended to increase during successive HC feeding periods. Prevotellaruminicola was the predominant species for all diets. The RNA sequence analysis revealed the keratin gene as differentially expressed during the HF diet, while carbonic-anhydrase I and S100 calcium-binding protein were expressed in the HC diet. Most of these genes were highly expressed for HC-1 and HC-2. These results suggested that ruminal bacterial community composition, transcriptome profile, and rumen fermentation characteristics were altered by the diet transitions in dairy cows.
Collapse
Affiliation(s)
- Sonny C. Ramos
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (S.C.R.); (C.D.J.); (L.L.M.); (S.H.K.)
| | - Chang Dae Jeong
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (S.C.R.); (C.D.J.); (L.L.M.); (S.H.K.)
| | - Lovelia L. Mamuad
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (S.C.R.); (C.D.J.); (L.L.M.); (S.H.K.)
| | - Seon Ho Kim
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (S.C.R.); (C.D.J.); (L.L.M.); (S.H.K.)
| | - Seung Ha Kang
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Eun Tae Kim
- Dairy Science Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Korea;
| | - Yong Il Cho
- Animal Disease and Diagnostic Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea;
| | - Sung Sill Lee
- Institute of Agriculture and Life Science and University-Centered Labs, Gyeongsang National University, Jinju 52828, Korea;
| | - Sang Suk Lee
- Ruminant Nutrition and Anaerobe Laboratory, Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (S.C.R.); (C.D.J.); (L.L.M.); (S.H.K.)
| |
Collapse
|
17
|
Tang L, Li Y, Srivathsan A, Gao Y, Li K, Hu D, Zhang D. Gut Microbiomes of Endangered Przewalski's Horse Populations in Short- and Long-Term Captivity: Implication for Species Reintroduction Based on the Soft-Release Strategy. Front Microbiol 2020; 11:363. [PMID: 32226419 PMCID: PMC7081077 DOI: 10.3389/fmicb.2020.00363] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 02/18/2020] [Indexed: 12/16/2022] Open
Abstract
Captivity maybe the only choice for survival of many endangered vertebrates, and understanding its broad effects is important for animal management and conservation, including breeding endangered species for subsequent release. Extreme environmental changes during captivity may influence survival ability in the wild. Captivity decreases gut bacterial diversity in a wide range of animals. However, most studies directly compare animals living in captivity with those in the wild, and there is a lack of understanding of effects of gradient shift in lifestyle during species reintroduction based on the soft-release strategy, which involves a confinement period in a field enclosure. Here, we used 16S rRNA amplicon sequencing to analyze gut microbiomes of 11 captive and 12 semi-wild Przewalski’s horses (PH; Equus ferus przewalskii) under the same captivity environment, using fecal samples. A subset of samples with abundant extracted DNA (including 3 captive and 3 semi-wild individuals) was selected for whole-genome shotgun sequencing. We found that community diversity did not differ between the semi-wild PH and captive PH, but the semi-wild PH had significantly higher bacterial richness than those in captivity. Relative abundances of all dominant phyla were similar across the semi-wild or captive horses, while those of the non-dominant phyla Tenericutes and Proteobacteria were significantly higher in semi-wild PH than in captive PH. Beta diversity results indicated that bacterial communities of captives and semi-wild horses were clearly separated distinct when considering only composition. Functional profiling of the microbiomes revealed that the semi-wild and captive gut microbiomes were largely similar. However, semi-wild horse microbiomes had higher abundance of bacterial genes related to core metabolic processes, such as carbohydrates, amino acids, and nucleic acid metabolism. The study revealed that semi-wild PH could retain specific non-dominant bacteria and harbor a more diverse microbiome than the captive counterpart, and thus have higher metabolic potential to utilize the complex plants efficiently. These results indicate that change in host lifestyle may play a role in microbiome differentiation in the process of reintroduction, suggesting that a short period of time in captivity is acceptable for PH from the perspective of maintaining the richness of intestinal bacterial flora to some extent.
Collapse
Affiliation(s)
- Liping Tang
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yimeng Li
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yunyun Gao
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Kai Li
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Defu Hu
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Dong Zhang
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| |
Collapse
|
18
|
Microbial diversity within the digestive tract contents of Dezhou donkeys. PLoS One 2019; 14:e0226186. [PMID: 31834903 PMCID: PMC6910686 DOI: 10.1371/journal.pone.0226186] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 11/22/2019] [Indexed: 12/11/2022] Open
Abstract
Gastrointestinal microbiota has significant impact on the nutrition and health of monogastric herbivores animals including donkey. However, so far the microbiota in different gastrointestinal compartments of healthy donkey has not been described. Therefore, we investigated the abundance and function of microbiota at different sites of the gastrointestinal tract (GIT) (foregut: stomach, duodenum, jejunum and ileum; hindgut: cecum, ventral colon, dorsal colon, and rectum) of healthy adult donkeys mainly based on 16S rRNA gene sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis. Collectively, our results showed that donkey has a rich, diverse and multi-functional microbiota along the GIT. In general, the richness and diversity of the microbiota are much higher in the hindgut relative to that in the foregut; at phylum level, the Firmicutes is dominant in the foregut while both Firmicutes and Bacteroides are abundant in the hindgut; at the genus level, Lactobacillus was dominant in the foregut while Streptococcus was more dominant in the hindgut. Our further PICRUSt analysis showed that varying microbiota along the GIT is functionally compatible with the corresponding physiological function of different GIT sites. For example, the microbes in the foregut are more active at carbohydrate metabolism, and in the hindgut are more active at amino acid metabolism. This work at the first time characterized the donkey digestive system from the aspects of microbial composition and function, provided an important basic data about donkey healthy gastrointestinal microbiota, which may be utilized to evaluate donkey health and also offer clues to further investigate donkey digestive system, nutrition, even to develop the microbial supplements.
Collapse
|
19
|
Qian W, Ao W, Jia C, Li Z. Bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer (Cervus elaphus yarkandensis). Antonie van Leeuwenhoek 2019; 112:1283-1296. [PMID: 30941531 DOI: 10.1007/s10482-019-01260-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/26/2019] [Indexed: 12/18/2022]
Abstract
The rumen microbiome contributes greatly to the degradation of plant fibres to volatile fatty acids and microbial products, affecting the health and productivity of ruminants. In this study, we investigated the dynamics of colonisation by bacterial communities attached to reeds and cottonseed hulls in the rumen of Tarim red deer, a native species distributed in the desert of the Tarim Basin. The reed and cottonseed hull samples incubated in nylon bags for 1, 6, 12, and 48 h were collected and used to examine the bacterial communities by next-generation sequencing of the bacterial 16S rRNA gene. Prevotella1 and Rikenellaceae RC9 were the most abundant taxa in both the reed and cottonseed hull groups at various times, indicating a key role of these organisms in rumen fermentation in Tarim red deer. The relative abundances of cellulolytic bacteria, such as members of Fibrobacter, Treponema 2, Ruminococcaceae NK4A214 and Succiniclasticum increased, while that of the genus Prevotella 1 decreased, with increasing incubation time in both reeds and cottonseed hulls. Moreover, the temporal changes in bacterial diversity between reeds and cottonseed hulls were different, as demonstrated by the variations in the taxa Ruminococcaceae UCG 010 and Papillibacter in the reed group and Sphaerochaeta and Erysipelotrichaceae UCG 004 in the cottonseed hull group; the abundances of these bacteria first decreased and then increased. In conclusion, our results reveal the dynamics of bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer.
Collapse
Affiliation(s)
- Wenxi Qian
- College of Animal Science, Tarim University, Alar, 843300, China.,Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, Alar, 843300, China
| | - Weiping Ao
- College of Animal Science, Tarim University, Alar, 843300, China.,Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, Alar, 843300, China
| | - Cunhui Jia
- College of Animal Science, Tarim University, Alar, 843300, China.,Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, Alar, 843300, China
| | - Zhipeng Li
- Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, 130112, Changchun, China.
| |
Collapse
|
20
|
Ishaq SL, Page CM, Yeoman CJ, Murphy TW, Van Emon ML, Stewart WC. Zinc AA supplementation alters yearling ram rumen bacterial communities but zinc sulfate supplementation does not. J Anim Sci 2019; 97:687-697. [PMID: 30508094 PMCID: PMC6358250 DOI: 10.1093/jas/sky456] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/29/2018] [Indexed: 12/15/2022] Open
Abstract
Despite the body of research into Zn for human and animal health and productivity, very little work has been done to discern whether this benefit is exerted solely on the host organism, or whether there is some effect of dietary Zn upon the gastrointestinal microbiota, particularly in ruminants. We hypothesized that (i) supplementation with Zn would alter the rumen bacterial community in yearling rams, but that (ii) supplementation with either inorganically sourced ZnSO4, or a chelated Zn AA complex, which was more bioavailable, would affect the rumen bacterial community differently. Sixteen purebred Targhee yearling rams were utilized in an 84-d completely randomized design, and allocated to one of three pelleted dietary treatments: control diet without fortified Zn (~1 × NRC), a diet fortified with a Zn AA complex (~2 × NRC), and a diet fortified with ZnSO4 (~2 × NRC). Rumen bacterial community was assessed using Illumina MiSeq of the V4 to V6 region of the 16S rRNA gene. One hundred and eleven OTUs were found with > 1% abundance across all samples. The genera Prevotella, Solobacterium, Ruminococcus, Butyrivibrio, Olsenella, Atopobium, and the candidate genus Saccharimonas were abundant in all samples. Total rumen bacterial evenness and diversity in rams were reduced by supplementation with a Zn AA complex, but not in rams supplemented with an equal concentration of ZnSO4, likely due to differences in bioavailability between organic and inorganically sourced supplement formulations. A number of bacterial genera were altered by Zn supplementation, but only the phylum Tenericutes was significantly reduced by ZnSO4 supplementation, suggesting that either Zn supplementation formulation could be utilized without causing a high-level shift in the rumen bacterial community which could have negative consequences for digestion and animal health.
Collapse
Affiliation(s)
| | - Chad M Page
- Montana State University, Department of Animal and Range Sciences, Bozeman
| | - Carl J Yeoman
- Montana State University, Department of Animal and Range Sciences, Bozeman
| | - Thomas W Murphy
- Montana State University, Department of Animal and Range Sciences, Bozeman
| | - Megan L Van Emon
- Montana State University, Department of Animal and Range Sciences, Bozeman
| | - Whit C Stewart
- Montana State University, Department of Animal and Range Sciences, Bozeman
- University of Wyoming, Department of Animal Science, Laramie
| |
Collapse
|
21
|
Li JH, Yousif MH, Li ZQ, Wu ZH, Li SL, Yang HJ, Wang YJ, Cao ZJ. Effects of antibiotic residues in milk on growth, ruminal fermentation, and microbial community of preweaning dairy calves. J Dairy Sci 2019; 102:2298-2307. [PMID: 30692007 DOI: 10.3168/jds.2018-15506] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/30/2018] [Indexed: 01/05/2023]
Abstract
The aim of this study was to evaluate the effects of antibiotic residues in milk on growth, ruminal fermentation, and microbial community of dairy calves in their first 35 d of age. Twenty newborn Holstein bull calves were assigned to 1 of 2 treatments equally: milk replacer without antibiotics (control) and milk replacer plus 4 antibiotics: 0.024 mg/L of penicillin, 0.025 mg/L of streptomycin, 0.1 mg/L of tetracycline, and 0.33 mg/L of ceftiofur (ANT). Starter intake and fecal consistency scores of each calf were recorded on a daily basis. Body weight, withers height, body length, and heart girth were measured on d 1, 7, 14, 21, 28, and 35 before feeding in the morning. Rumen fluid was collected on d 15, 25, and 35 to determine ruminal pH, volatile fatty acids (VFA), and NH3-N concentrations. A total of 10 (5 per treatment) samples of rumen fluid taken on d 35 were analyzed for microbial community. Rumen tissues from the cranial ventral sac and cranial dorsal sac were collected from 8 calves of each group for morphology analysis on d 35 after being harvested. The results showed that calves in 2 treatments had similar starter intake, body weight, withers height, body length, heart girth, and average daily gain. The ANT group showed a lower diarrhea frequency in wk 4, and no differences were found for other weeks. Calves in the ANT group exhibited a greater concentration of acetic acid in the rumen and no differences for other VFA, total VFA, rumen pH, or NH3-N. As for rumen morphology, the length of papillae from cranial ventral sac of the ANT group was longer than that of the control group. The results of ruminal microbial community showed that antibiotic residues had minor effects on bacteria phyla and bacteria diversity. At the genus level, calves in the ANT group showed lower richness of Prevotella and higher richness of Acetitomaculum. In conclusion, antibiotic residues stimulated the development of ruminal papillae and increased the production of acetic acid in rumen, which might be caused by the influence of antibiotics on the ruminal microbial community.
Collapse
Affiliation(s)
- J H Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - M H Yousif
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Z Q Li
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan, 471003, China
| | - Z H Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - S L Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - H J Yang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Y J Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Z J Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
22
|
López-García A, Pineda-Quiroga C, Atxaerandio R, Pérez A, Hernández I, García-Rodríguez A, González-Recio O. Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences. Front Microbiol 2018; 9:3010. [PMID: 30619117 PMCID: PMC6300507 DOI: 10.3389/fmicb.2018.03010] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/21/2018] [Indexed: 01/16/2023] Open
Abstract
Background: Microbiome studies need to analyze massive sequencing data, which requires the use of sophisticated bioinformatics pipelines. Up to date, several tools are available, although the literature is scarce on studies that compare the performance of different bioinformatics pipelines on rumen microbiota when 16S rRNA amplicons are analyzed. The impact of the pipeline on the outcome of the results is also unknown, mainly in terms of the output from studies using these tools as an intermediate phenotype (pseudophenotypes). This study compares two commonly used software (Quantitative Insights Into Microbial Ecology) (QIIME) and mothur, and two microbial gene data bases (GreenGenes and SILVA) for 16S rRNA gene analysis, using metagenome read data collected from rumen content of a cohort of dairy cows. Results: We compared the relative abundance (RA) of the identified OTUs at the genus level. Both tools presented a high degree of agreement at identifying the most abundant genera: Bifidobacterium, Butyrivibrio, Methanobrevibacter, Prevotella, and Succiniclasticum (RA > 1%), regardless the database. There were no statistical differences between mothur and QIIME (P > 0.05) at estimating the overall RA of the most abundant (RA > 10%) genera, either using SILVA or GreenGenes. However, differences were found at RA < 10% (P < 0.05) when using GreenGenes as database, with mothur assigning OTUs to a larger number of genera and in larger RA for these less frequent microorganisms. With this database mothur resulted in larger richness (P < 0.05), more favorable rarefaction curves and a larger analytic sensitivity. These differences caused significant and relevant differences between tools at identifying the dissimilarity of microbiotas between pairs of animals. However, these differences were attenuated, but not erased, when SILVA was used as the reference database. Conclusion: The findings showed that the SILVA database seemed a preferred reference dataset for classifying OTUs from rumen microbiota. If this database was used, both QIIME and mothur produced comparable richness and diversity, and also in the RA of most common rumen microbes. However, important differences were found for less common microorganisms which impacted on the beta diversity calculated between pipelines. This may have relevant implications at studying global rumen microbiota.
Collapse
Affiliation(s)
- Adrian López-García
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | | | - Raquel Atxaerandio
- Departamento de Producción Animal, NEIKER-Tecnalia, Vitoria-Gasteiz, Spain
| | - Adrian Pérez
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain.,Departamento de Producción Agraria, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Itziar Hernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain.,Departamento de Producción Agraria, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain.,Departamento de Producción Agraria, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| |
Collapse
|
23
|
Li L, Qu M, Liu C, Xu L, Pan K, Song X, OuYang K, Li Y, Zhao X. Expression of a Recombinant Lentinula edodes Xylanase by Pichia pastoris and Its Effects on Ruminal Fermentation and Microbial Community in in vitro Incubation of Agricultural Straws. Front Microbiol 2018; 9:2944. [PMID: 30555451 PMCID: PMC6283887 DOI: 10.3389/fmicb.2018.02944] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022] Open
Abstract
Agricultural straws, such as rice straw, wheat straw, and corn straw, are produced abundantly every year but not utilized efficiently in China. An experiment was conducted to determine the effects of recombinant xylanase on ruminal fermentation and microbial community structure in in vitro incubation of these straws. The recombinant xylanase from Lentinula edodes (rLeXyn11A) was produced in Pichia pastoris. The optimal temperature and pH for rLeXyn11A were 40°C and 4.0, respectively. The rLeXyn11A featured resistance to high temperature and showed broad temperature adaptability (>50% of the maximum activity at 20-80°C). Supplemental rLeXyn11A enhanced the hydrolysis of three agricultural straws. After in vitro ruminal incubation, regardless of agricultural straws, the fiber digestibility, acetate concentration, total volatile fatty acids (VFAs) production, and fermentation liquid microbial protein were increased by rLeXyn11A. Supplemental rLeXyn11A increased the ammonia-N concentration for corn straw and rice straw. High throughput sequencing and real-time PCR data showed that the effects of rLeXyn11A on ruminal microbial community depended on the fermentation substrates. With rice straw, rLeXyn11A increased the relative abundance of fibrolytic bacteria including Firmicutes, Desulfovibrio, Ruminococcaceae and its some genus, and Fibrobacter succinogenes. With wheat straw, rLeXyn11A increased the relative abundance of Ruminococcus_1 and its three representative species F. succinogenes, Ruminococcus flavefaciens, Ruminococcus albus. With corn straw, the fibrolytic bacteria Firmicutes, Christensenellaceae_R_7_group, Saccharofermentans, and Desulfovibrio were increased by rLeXyn11A. This study demonstrates that rLeXyn11A could enhance in vitro ruminal digestion and fermentation of agricultural straws, showing the potential of rLeXyn11A for improving the utilization of agricultural straws in ruminants.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Xianghui Zhao
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, China
| |
Collapse
|
24
|
Characterisation of the bacterial community in the gastrointestinal tracts of elk (Cervus canadensis). Antonie van Leeuwenhoek 2018; 112:225-235. [PMID: 30155662 DOI: 10.1007/s10482-018-1150-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/21/2018] [Indexed: 02/07/2023]
Abstract
The resident bacteria of the gastrointestinal tract (GIT) and the behaviour of these microbes have been poorly characterised in elk as compared to other ruminant animal species such as sheep and cattle. In addition, most microbial community studies of deer gut have focused on rumen or faeces, while other parts of the GIT such as the small and large intestine have received little attention. To address this issue, the present study investigated the diversity of the GIT bacterial community in elk (Cervus canadensis) by 16S rRNA pyrosequencing analysis. Eight distinct GIT segments including the stomach (rumen, omasum, and abomasum), small intestine (duodenum and jejunum), and large intestine (cecum, colon, and rectum) obtained from four elks were examined. We found that bacterial richness and diversity were higher in the stomach and large intestine than in the small intestine (P < 0.05). A total of 733 genera belonging to 26 phyla were distributed throughout elk GITs, with Firmicutes, Bacteroidetes, and Proteobacteria identified as the predominant phyla. In addition, there was spatial heterogeneity in the composition, diversity, and species abundance of microbiota in the GIT (P < 0.0001). To the best of our knowledge, this is the first study to characterise bacterial communities from eight GIT regions of elk by 16S rRNA pyrosequencing.
Collapse
|
25
|
Hu X, Liu G, Li Y, Wei Y, Lin S, Liu S, Zheng Y, Hu D. High-Throughput Analysis Reveals Seasonal Variation of the Gut Microbiota Composition Within Forest Musk Deer ( Moschus berezovskii). Front Microbiol 2018; 9:1674. [PMID: 30093891 PMCID: PMC6070636 DOI: 10.3389/fmicb.2018.01674] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/04/2018] [Indexed: 01/08/2023] Open
Abstract
The gut microbiota plays a key role in the nutritional ecology of ruminants, and host diet has a significant effect on these microbial communities. Longitudinal studies assessing variation of seasonal microbiota in animals can provide a comparative context for interpreting the adaptive significance of such changes. However, few studies have investigated the effects of seasonally-related dietary shifts on the gut microbial communities of endangered forest musk deer (FMD), and the national breeding programs need this information to promote the growth of captive populations. The present study applied bacterial 16S rRNA genes based on high-throughput sequencing to profile the fecal microbial communities of FMD across four seasons. Microbial diversity was higher in seasons with dry leaf diets (winter and spring) compared to seasons with fresh leaf diets (summer and autumn). The dominant microbial phyla were Firmicutes and Bacteroidetes, and the core bacterial taxa also comprised mostly (94.40% of shared OTUs) Firmicutes (37 taxa) and Bacteroidetes (6 taxa), which were relatively stable across different seasons. The Firmicutes-Bacteroidetes ratio declined in seasons with fresh leaf diets relative to seasons with dry leaf diets, and the dominant genera among the four seasons showed no significant variation in abundance. This work explores the seasonal variation in the microbial communities of FMD for the first time, and reveals how gut microbial community dynamics vary seasonally in accordance with differences in dietary plants (fresh and dry leaf). These results indicate that the annual cyclic reconfiguration of FMD gut microbiota could be associated with shifts in dietary nutrients, which is important information to inform captive FMD management.
Collapse
Affiliation(s)
- Xiaolong Hu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Gang Liu
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
| | - Yimeng Li
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yuting Wei
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Shaobi Lin
- Zhangzhou Pien Tze Huang Pharmaceutical, Co., Ltd., Zhangzhou, China
| | - Shuqiang Liu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yunlin Zheng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Defu Hu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry University, Beijing, China
| |
Collapse
|
26
|
Huang J, Zhang Z, Zhang Y, Yang Y, Zhao J, Wang R, Jian F, Ning C, Zhang W, Zhang L. Prevalence and molecular characterization of Cryptosporidium spp. and Giardia duodenalis in deer in Henan and Jilin, China. Parasit Vectors 2018; 11:239. [PMID: 29650036 PMCID: PMC5898075 DOI: 10.1186/s13071-018-2813-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/25/2018] [Indexed: 11/10/2022] Open
Abstract
Background Little is known about the prevalence and zoonotic potential of Cryptosporidium spp. and Giardia duodenalis in deer in China. In this study, 662 fecal samples were collected from 11 farms in Henan and Jilin Provinces between July 2013 and August 2014, and were screened for the presence of Cryptosporidium and G. duodenalis with genotyping and subtyping methods. Results Cryptosporidium spp. and G. duodenalis were detected in 6.80% (45/662) and 1.21% (5/662) of samples, respectively. Six Cryptosporidium species/genotypes were identified based on the small subunit ribosomal ribonucleic acid (SSU rRNA) gene: C. parvum (n = 11); C. andersoni (n = 5); C. ubiquitum (n = 3); C. muris (n = 1); C. suis-like (n = 1); and Cryptosporidium deer genotype (n = 24). When five of the 11 C. parvum isolates were subtyped by sequencing the 60 kDa glycoprotein (gp60) gene, zoonotic subtypes IIaA15G2R2 (n = 4) and IIdA19G1 (n = 1) were found. According to a subtype analysis, three C. ubiquitum isolates belonged to XIIa subtype 2. In contrast, only assemblage E was detected in the five Giardia-positive samples with small subunit ribosomal ribonucleic acid (SSU rRNA) gene sequencing. Conclusions To our knowledge, this is the first study to report C. andersoni, as well as C. parvum zoonotic subtypes IIaA15G2R2 and IIdA19G1 in cervids. These data, though limited, suggest that cervids may be a source of zoonotic Cryptosporidium and Giardia. Cervids in the present study are likely to be of low zoonotic potential to humans, and more molecular epidemiological studies are required to clarify the prevalence and public health significance of Cryptosporidium and G. duodenalis in cervids throughout China.
Collapse
Affiliation(s)
- Jianying Huang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhenjie Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yiqi Zhang
- Zhengzhou Foreign Language School, Zhengzhou, 450001, China
| | - Yong Yang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jinfeng Zhao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Rongjun Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Fuchun Jian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Changshen Ning
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wanyu Zhang
- Basic Medicine College of the Zhengzhou University, Zhengzhou, 450001, China
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.
| |
Collapse
|
27
|
Qian W, Ao W, Hui X, Wu J. Lower dietary concentrate level increases bacterial diversity in the rumen of Cervus elaphus yarkandensis. Can J Microbiol 2018; 64:501-509. [PMID: 29562140 DOI: 10.1139/cjm-2018-0046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The ruminal microbiota plays major roles in feed digestion. The composition and fermentation of the bacterial communities in 3 important ruminant species have been studied previously. Here, we extended this research to the effect of concentrate-to-forage ratios on ruminal bacterial communities in Tarim red deer (Cervus elaphus yarkandensis). Different concentrate-to-forage ratios (2:8, 3:7, 4:6, and 5:5) were fed to Tarim red deer for 20 days. Ruminal bacterial communities were elucidated by 16S ribosomal RNA gene sequencing on an Illumina HiSeq 2500 platform. The microbial composition and biodiversity at the different concentrate-to-forage ratio levels were analyzed using clustering of operational taxonomic units based on 97% sequence identity, taxonomic classification at the phylum and genus levels, α diversity, and β diversity. Rumen microorganisms of deer fed a diet with a concentrate-to-forage ratio of 2:8 had the highest species diversity, followed by ratios of 3:7, 4:6, and 5:5. The community structure of the A1 and A2 samples and the A3 and A4 samples was similar. The bacterial composition appeared to be affected by diet, with a lower dietary concentrate level tending to increase the richness and diversity of ruminal bacteria in the rumen of Tarim red deer.
Collapse
Affiliation(s)
- Wenxi Qian
- a College of Animal Science Tarim University, Alar Xinjiang 843300, China.,b Key Laboratory of Tarim Animal Husbandry Science & Technology Xinjiang Production & Construction Group, Alar Xinjiang 843300, China
| | - Weiping Ao
- a College of Animal Science Tarim University, Alar Xinjiang 843300, China.,b Key Laboratory of Tarim Animal Husbandry Science & Technology Xinjiang Production & Construction Group, Alar Xinjiang 843300, China
| | - Xiaohong Hui
- a College of Animal Science Tarim University, Alar Xinjiang 843300, China.,b Key Laboratory of Tarim Animal Husbandry Science & Technology Xinjiang Production & Construction Group, Alar Xinjiang 843300, China
| | - Jianping Wu
- c College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| |
Collapse
|
28
|
Comtet-Marre S, Chaucheyras-Durand F, Bouzid O, Mosoni P, Bayat AR, Peyret P, Forano E. FibroChip, a Functional DNA Microarray to Monitor Cellulolytic and Hemicellulolytic Activities of Rumen Microbiota. Front Microbiol 2018; 9:215. [PMID: 29487591 PMCID: PMC5816793 DOI: 10.3389/fmicb.2018.00215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/30/2018] [Indexed: 01/22/2023] Open
Abstract
Ruminants fulfill their energy needs for growth primarily through microbial breakdown of plant biomass in the rumen. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact animal productivity and health. To provide more insight into mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes encoding key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. Eight carbohydrate-active enzyme (CAZyme) families (GH5, GH9, GH10, GH11, GH43, GH48, CE1, and CE6) were selected which represented 392 genes from bacteria, protozoa, and fungi. The DNA microarray, designated as FibroChip, was validated using targets of increasing complexity and demonstrated sensitivity and specificity. In addition, FibroChip was evaluated for its explorative and semi-quantitative potential. Differential expression of CAZyme genes was evidenced in the rumen bacterium Fibrobacter succinogenes S85 grown on wheat straw or cellobiose. FibroChip was used to identify the expressed CAZyme genes from the targeted families in the rumen of a cow fed a mixed diet based on grass silage. Among expressed genes, those encoding GH43, GH5, and GH10 families were the most represented. Most of the F. succinogenes genes detected by the FibroChip were also detected following RNA-seq analysis of RNA transcripts obtained from the rumen fluid sample. Use of the FibroChip also indicated that transcripts of fiber degrading enzymes derived from eukaryotes (protozoa and anaerobic fungi) represented a significant proportion of the total microbial mRNA pool. FibroChip represents a reliable and high-throughput tool that enables researchers to monitor active members of fiber degradation in the rumen.
Collapse
Affiliation(s)
- Sophie Comtet-Marre
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France.,R&D Animal Nutrition, Lallemand, Blagnac, France
| | - Frédérique Chaucheyras-Durand
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France.,R&D Animal Nutrition, Lallemand, Blagnac, France
| | - Ourdia Bouzid
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pascale Mosoni
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ali R Bayat
- Milk Production Solutions, Green Technology, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Pierre Peyret
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Evelyne Forano
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| |
Collapse
|
29
|
Li Z, Wang X, Zhang T, Si H, Nan W, Xu C, Guan L, Wright ADG, Li G. The Development of Microbiota and Metabolome in Small Intestine of Sika Deer ( Cervus nippon) from Birth to Weaning. Front Microbiol 2018; 9:4. [PMID: 29410651 PMCID: PMC5787063 DOI: 10.3389/fmicb.2018.00004] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/03/2018] [Indexed: 02/05/2023] Open
Abstract
The dense and diverse community of microorganisms inhabiting the gastrointestinal tract of ruminant animals plays critical roles in the metabolism and absorption of nutrients, and gut associated immune function. Understanding microbial colonization in the small intestine of new born ruminants is a vital first step toward manipulating gut function through interventions during early life to produce long-term positive effects on host productivity and health. Yet the knowledge of microbiota colonization and its induced metabolites of small intestine during early life is still limited. In the present study, we examined the microbiota and metabolome in the jejunum and ileum of neonatal sika deer (Cervus nippon) from birth to weaning at days 1, 42, and 70. The microbial data showed that diversity and richness were increased with age, but a highly individual variation was observed at day 1. Principal coordinate analysis revealed significant differences in microbial community composition across three time points in the jejunum and ileum. The abundance of Halomonas spp., Lactobacillus spp., Escherichia–Shigella, and Bacteroides spp. tended to be decreased, while the proportion of Intestinibacter spp., Cellulosilyticum spp., Turicibacter spp., Clostridium sensu stricto 1 and Romboutsia spp. was significantly increased with age. For metabolome, metabolites separated from each other across the three time points in both jejunum and ileum. Moreover, the amounts of methionine, threonine, and putrescine were increased, while the amounts of myristic acid and pentadecanoic acid were decreased with age, respectively. The present study demonstrated that microbiota colonization and the metabolome becomes more developed in the small intestine with age. This may shed new light on the microbiota-metabolome-immune interaction during development.
Collapse
Affiliation(s)
- Zhipeng Li
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xiaoxu Wang
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Ting Zhang
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Huazhe Si
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Weixiao Nan
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Chao Xu
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Leluo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - André-Denis G Wright
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
| | - Guangyu Li
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| |
Collapse
|
30
|
Guan Y, Yang H, Han S, Feng L, Wang T, Ge J. Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing. AMB Express 2017; 7:212. [PMID: 29170893 PMCID: PMC5700909 DOI: 10.1186/s13568-017-0517-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022] Open
Abstract
The gut microbiota is characterized as a complex ecosystem that has effects on health and diseases of host with the interactions of many other factors together. Sika deer is the national level for the protection of wild animals in China. The available sequencing data of gut microbiota from feces of wild sika deer, especially for Cervus nippon hortulorum in Northeast China, are limited. Here, we characterized the gastrointestinal bacterial communities of wild (7 samples) and captive (12 samples) sika deer from feces, and compared their gut microbiota by analyzing the V4 region of 16S rRNA gene using high-throughput sequencing technology on the Illumina Hiseq platform [corrected]. Firmicutes (77.624%), Bacteroidetes (18.288%) and Tenericutes (1.342%) were the most predominant phyla in wild sika deer. While in captive sika deer, Firmicutes (50.710%) was the dominant phylum, followed by Bacteroidetes (31.996%) and Proteobacteria (4.806%). A total of 9 major phyla, 22 families and 30 genera among gastrointestinal bacterial communities showed significant differences between wild and captive sika deer. The specific function and mechanism of Tenericutes in wild sika deer need further study. Our results indicated that captive sika deer in farm had higher fecal bacterial diversity than the wild. Abundance and quantity of diet source for sika deer played crucial role in shaping the composition and structure of gut microbiota.
Collapse
|
31
|
Ishaq SL, AlZahal O, Walker N, McBride B. An Investigation into Rumen Fungal and Protozoal Diversity in Three Rumen Fractions, during High-Fiber or Grain-Induced Sub-Acute Ruminal Acidosis Conditions, with or without Active Dry Yeast Supplementation. Front Microbiol 2017; 8:1943. [PMID: 29067009 PMCID: PMC5641310 DOI: 10.3389/fmicb.2017.01943] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/21/2017] [Indexed: 01/08/2023] Open
Abstract
Sub-acute ruminal acidosis (SARA) is a gastrointestinal functional disorder in livestock characterized by low rumen pH, which reduces rumen function, microbial diversity, host performance, and host immune function. Dietary management is used to prevent SARA, often with yeast supplementation as a pH buffer. Almost nothing is known about the effect of SARA or yeast supplementation on ruminal protozoal and fungal diversity, despite their roles in fiber degradation. Dairy cows were switched from a high-fiber to high-grain diet abruptly to induce SARA, with and without active dry yeast (ADY, Saccharomyces cerevisiae) supplementation, and sampled from the rumen fluid, solids, and epimural fractions to determine microbial diversity using the protozoal 18S rRNA and the fungal ITS1 genes via Illumina MiSeq sequencing. Diet-induced SARA dramatically increased the number and abundance of rare fungal taxa, even in fluid fractions where total reads were very low, and reduced protozoal diversity. SARA selected for more lactic-acid utilizing taxa, and fewer fiber-degrading taxa. ADY treatment increased fungal richness (OTUs) but not diversity (Inverse Simpson, Shannon), but increased protozoal richness and diversity in some fractions. ADY treatment itself significantly (P < 0.05) affected the abundance of numerous fungal genera as seen in the high-fiber diet: Lewia, Neocallimastix, and Phoma were increased, while Alternaria, Candida Orpinomyces, and Piromyces spp. were decreased. Likewise, for protozoa, ADY itself increased Isotricha intestinalis but decreased Entodinium furca spp. Multivariate analyses showed diet type was most significant in driving diversity, followed by yeast treatment, for AMOVA, ANOSIM, and weighted UniFrac. Diet, ADY, and location were all significant factors for fungi (PERMANOVA, P = 0.0001, P = 0.0452, P = 0.0068, Monte Carlo correction, respectively, and location was a significant factor (P = 0.001, Monte Carlo correction) for protozoa. Diet-induced SARA shifts diversity of rumen fungi and protozoa and selects against fiber-degrading species. Supplementation with ADY mitigated this reduction in protozoa, presumptively by triggering microbial diversity shifts (as seen even in the high-fiber diet) that resulted in pH stabilization. ADY did not recover the initial community structure that was seen in pre-SARA conditions.
Collapse
Affiliation(s)
| | | | | | - Brian McBride
- Animal Biosciences, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
32
|
O’ Donnell MM, Harris HMB, Ross RP, O'Toole PW. Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals. Microbiologyopen 2017; 6:e00509. [PMID: 28834331 PMCID: PMC5635170 DOI: 10.1002/mbo3.509] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 12/21/2022] Open
Abstract
In this pilot study, we determined the core fecal microbiota composition and overall microbiota diversity of domesticated herbivorous animals of three digestion types: hindgut fermenters, ruminants, and monogastrics. The 42 animals representing 10 animal species were housed on a single farm in Ireland and all the large herbivores consumed similar feed, harmonizing two of the environmental factors that influence the microbiota. Similar to other mammals, the fecal microbiota of all these animals was dominated by the Firmicutes and Bacteroidetes phyla. The fecal microbiota spanning all digestion types comprised 42% of the genera identified. Host phylogeny and, to a lesser extent, digestion type determined the microbiota diversity in these domesticated herbivores. This pilot study forms a platform for future studies into the microbiota of nonbovine and nonequine domesticated herbivorous animals.
Collapse
Affiliation(s)
- Michelle M. O’ Donnell
- Food Biosciences DepartmentTeagasc Food Research CentreCorkIreland
- Department of MicrobiologyUniversity College CorkCorkIreland
| | | | - R. Paul Ross
- Food Biosciences DepartmentTeagasc Food Research CentreCorkIreland
- Department of MicrobiologyUniversity College CorkCorkIreland
| | - Paul W. O'Toole
- Department of MicrobiologyUniversity College CorkCorkIreland
| |
Collapse
|
33
|
The Gut Bacterial Community Composition of Wild Cervus albirostris (White-Lipped Deer) Detected by the 16S Ribosomal RNA Gene Sequencing. Curr Microbiol 2017; 74:1100-1107. [PMID: 28667467 DOI: 10.1007/s00284-017-1288-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/20/2017] [Indexed: 12/18/2022]
Abstract
Cervus albirostris (white-lipped deer) is an endemic species in China. As the name implies, C. albirostris has a characteristic pure white marking around their mouth and on the underside of the throat. The animal is a typical alpine species normally living at the height of 3500-4300 m. In this study, by pyrosequencing the 16S rRNA gene sequences, we for the first time analyzed the gut bacterial community composition in eight feces samples of wild C. albirostris. From a total of 243,634 high-quality sequences, we identified 186 genera, included in 17 prokaryotic phyla in the feces. The relative proportions of Firmicutes and Bacteroidetes were highly consistent in each individual sample. The most frequently detected genus was Ruminococcaceae UCG-005, ranging from 6.70 to 21.00%, displaying positively connections with the Rikenellaceae RC9 gut group. The bacterial communities associated with C. albirostris provide the basic knowledge for further microbiological studies and facilitates the conservation efforts of this vulnerable deer species.
Collapse
|
34
|
Huang J, Zhang Z, Yang Y, Wang R, Zhao J, Jian F, Ning C, Zhang L. New Genotypes of Enterocytozoon bieneusi Isolated from Sika Deer and Red Deer in China. Front Microbiol 2017; 8:879. [PMID: 28572794 PMCID: PMC5435827 DOI: 10.3389/fmicb.2017.00879] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 05/02/2017] [Indexed: 11/18/2022] Open
Abstract
To examine the occurrence and genotype distribution of Enterocytozoon bieneusi in cervids, 615 fecal samples were collected from red deer (Cervus elaphus) and sika deer (Cervus nippon) on 10 different farms in Henan and Jilin Province. Enterocytozoon bieneusi was identified and genotyped with a nested PCR analysis of the internal transcribed spacer (ITS) region of the rRNA genes, showing an average infection rate of 35.9% (221/615). In this study, 25 ITS genotypes were identified including seven known genotypes (BEB6, EbpC, EbpA, D, HLJDI, HLJD-IV, and COS-I) and 18 novel genotypes (designated JLD-I to JLD-XIV, HND-I to HND-IV). Among these, BEB6 (131/221, 59.3%) was the predominant genotype (P < 0.01), followed by HLJDI (18/221, 8.1%) and JLD-VIII (16/221, 7.2%). BEB6 has recently been detected in humans and nonhuman primates in China. The phylogenetic analysis showed that BEB6, HLJDI, HLJD-IV, COS-I, and 10 novel genotypes (JLD-VII to JLD-XIV, HND-III to HND-IV) clustered in group 2. Genotype D, EbpC, and EbpA, known to cause human microsporidiosis worldwide, clustered in group 1, the members of which have zoonotic potential, together with eight novel genotypes (JLD-I to JLD-VI, HND-I to HND-II). Therefore, deer may play a role in the transmission of E. bieneusi to humans.
Collapse
Affiliation(s)
- Jianying Huang
- College of Animal Science and Veterinary Medicine, Henan Agricultural UniversityZhengzhou, China
| | - Zhenjie Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural UniversityZhengzhou, China
| | - Yong Yang
- Wu Xi Medical School, Jiangnan UniversityWuxi, China.,State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Science, Chinese Academy of Agricultural SciencesChangchun, China
| | - Rongjun Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural UniversityZhengzhou, China
| | - Jinfeng Zhao
- College of Animal Science and Veterinary Medicine, Henan Agricultural UniversityZhengzhou, China
| | - Fuchun Jian
- College of Animal Science and Veterinary Medicine, Henan Agricultural UniversityZhengzhou, China
| | - Changshen Ning
- College of Animal Science and Veterinary Medicine, Henan Agricultural UniversityZhengzhou, China
| | - Longxian Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural UniversityZhengzhou, China
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Hu X, Liu G, Shafer ABA, Wei Y, Zhou J, Lin S, Wu H, Zhou M, Hu D, Liu S. Comparative Analysis of the Gut Microbial Communities in Forest and Alpine Musk Deer Using High-Throughput Sequencing. Front Microbiol 2017; 8:572. [PMID: 28421061 PMCID: PMC5376572 DOI: 10.3389/fmicb.2017.00572] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/20/2017] [Indexed: 12/31/2022] Open
Abstract
The gut ecosystem is characterized by dynamic and reciprocal interactions between the host and bacteria. Although characterizing microbiota for herbivores has become recognized as important tool for gauging species health, no study to date has investigated the bacterial communities and evaluated the age-related bacterial dynamics of musk deer. Moreover, gastrointestinal diseases have been hypothesized to be a limiting factor of population growth in captive musk deer. Here, high-throughput sequencing of the bacterial 16S rRNA gene was used to profile the fecal bacterial communities in juvenile and adult alpine and forest musk deer. The two musk deer species harbored similar bacterial communities at the phylum level, whereas the key genera for the two species were distinct. The bacterial communities were dominated by Firmicutes and Bacteroidetes, with the bacterial diversity being higher in forest musk deer. The Firmicutes to Bacteroidetes ratio also increased from juvenile to adult, while the bacterial diversity, within-group and between-group similarity, all increased with age. This work serves as the first sequence-based analysis of variation in bacterial communities within and between musk deer species, and demonstrates how the gut microbial community dynamics vary among closely related species and shift with age. As gastrointestinal diseases have been observed in captive populations, this study provides valuable data that might benefit captive management and future reintroduction programs.
Collapse
Affiliation(s)
- Xiaolong Hu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry UniversityBeijing, China
| | - Gang Liu
- Institute of Wetland Research – Chinese Academy of ForestryBeijing, China
| | - Aaron B. A. Shafer
- Forensic Science and Environmental & Life Sciences, Trent University, PeterboroughON, Canada
| | - Yuting Wei
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry UniversityBeijing, China
| | - Juntong Zhou
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry UniversityBeijing, China
| | - Shaobi Lin
- Zhangzhou Pien Tze Huang Pharmaceutical Co., LtdZhangzhou, China
| | - Haibin Wu
- Zhangzhou Pien Tze Huang Pharmaceutical Co., LtdZhangzhou, China
| | - Mi Zhou
- Breeding Centre of Alpine Musk Deer in FengchunLanzhou, China
| | - Defu Hu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry UniversityBeijing, China
| | - Shuqiang Liu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry UniversityBeijing, China
| |
Collapse
|
37
|
Qian W, Li Z, Ao W, Zhao G, Wu J, Li G. Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries). Can J Microbiol 2017; 63:375-383. [PMID: 28177790 DOI: 10.1139/cjm-2016-0596] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The rumen microbiota plays a major role in the metabolism and absorption of indigestible food sources. Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries) are important ruminant species for animal husbandry in the Tarim Basin. However, the microbiota and rumen fermentation of these animals are poorly understood. Here, we apply high-throughput sequencing to examine the bacterial community in the rumen of cattle, red deer, and sheep and measured rumen fermentation products. Overall, 548 218 high-quality sequences were obtained and then classified into 6034 operational taxonomic units. Prevotella spp., Succiniclasticum spp., and unclassified bacteria within the families Succinivibrionaceae, Lachnospiraceae, and Veillonellaceae were the dominant bacteria in the rumen across the 3 hosts. Principal coordinate analysis identified significant differences in the bacterial communities across the 3 hosts. Pseudobutyrivibrio spp., Oscillospira spp., and Prevotella spp. were more prevalent in the rumen of the cattle, red deer, and sheep, respectively. Among the 3 hosts, the red deer rumen had the greatest amounts of acetate and butyrate and the lowest pH value. These results showed that Prevotella spp. are the dominant bacteria in the rumen of the cattle, red deer, and sheep, providing new insight into the rumen fermentation of ruminants distributed in the Tarim Basin.
Collapse
Affiliation(s)
- Wenxi Qian
- a College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, People's Republic of China.,b College of Animal Science, Tarim University, Alar 843300, People's Republic of China
| | - ZhiPeng Li
- c Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, People's Republic of China
| | - Weiping Ao
- b College of Animal Science, Tarim University, Alar 843300, People's Republic of China
| | - Guangyong Zhao
- d College of Animal Science and Technology, China Agricultural University, Beijing 100083, People's Republic of China
| | - JianPing Wu
- a College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, People's Republic of China
| | - Guangyu Li
- c Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, People's Republic of China
| |
Collapse
|
38
|
Salgado-Flores A, Hagen LH, Ishaq SL, Zamanzadeh M, Wright ADG, Pope PB, Sundset MA. Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions. PLoS One 2016; 11:e0155213. [PMID: 27159387 PMCID: PMC4861291 DOI: 10.1371/journal.pone.0155213] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/26/2016] [Indexed: 02/01/2023] Open
Abstract
Reindeer (Rangifer tarandus tarandus) are large Holarctic herbivores whose heterogeneous diet has led to the development of a unique gastrointestinal microbiota, essential for the digestion of arctic flora, which may include a large proportion of lichens during winter. Lichens are rich in plant secondary metabolites, which may affect members of the gut microbial consortium, such as the methane-producing methanogenic archaea. Little is known about the effect of lichen consumption on the rumen and cecum microbiotas and how this may affect methanogenesis in reindeer. Here, we examined the effects of dietary lichens on the reindeer gut microbiota, especially methanogens. Samples from the rumen and cecum were collected from two groups of reindeer, fed either lichens (Ld: n = 4), or a standard pelleted feed (Pd: n = 3). Microbial densities (methanogens, bacteria and protozoa) were quantified using quantitative real-time PCR and methanogen and bacterial diversities were determined by 454 pyrosequencing of the 16S rRNA genes. In general, the density of methanogens were not significantly affected (p>0.05) by the intake of lichens. Methanobrevibacter constituted the main archaeal genus (>95% of reads), with Mbr. thaueri CW as the dominant species in both groups of reindeer. Bacteria belonging to the uncharacterized Ruminococcaceae and the genus Prevotella were the dominant phylotypes in the rumen and cecum, in both diets (ranging between 16–38% total sequences). Bacteria belonging to the genus Ruminococcus (3.5% to 0.6%; p = 0.001) and uncharacterized phylotypes within the order Bacteroidales (8.4% to 1.3%; p = 0.027), were significantly decreased in the rumen of lichen-fed reindeer, but not in the cecum (p = 0.2 and p = 0.087, respectively). UniFrac-based analyses showed archaeal and bacterial libraries were significantly different between diets, in both the cecum and the rumen (vegan::Adonis: pseudo-F<0.05). Based upon previous literature, we suggest that the altered methanogen and bacterial profiles may account for expected lower methane emissions from lichen-fed reindeer.
Collapse
Affiliation(s)
- Alejandro Salgado-Flores
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway
- * E-mail:
| | - Live H. Hagen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Suzanne L. Ishaq
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, United States of America
| | | | - André-Denis G. Wright
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Phillip B. Pope
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Monica A. Sundset
- Department of Arctic and Marine Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
39
|
Kim KH, Arokiyaraj S, Lee J, Oh YK, Chung HY, Jin GD, Kim EB, Kim EK, Lee Y, Baik M. Effect of rhubarb (Rheum spp.) root on in vitro and in vivo ruminal methane production and a bacterial community analysis based on 16S rRNA sequence. ANIMAL PRODUCTION SCIENCE 2016. [DOI: 10.1071/an15585] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The objective of this study was to evaluate the anti-methanogenic effect of rhubarb (Rheum spp.) on in vitro, in vivo, and bacterial community composition using Quantitative Insights into Microbial Ecology sequencing. Rhubarb root powder was tested at different concentrations (0, 0.33, 0.67, and 1.33 g/L) in vitro, and all incubations were carried out in triplicate two runs on separate days. Concentrations of 0.67 and 1.33 g/L rhubarb significantly (P < 0.05) reduced methane production and the acetate : propionate ratio compared with those of the Control, without adverse effects on total volatile fatty acids and total gas production. In the second in vivo trial, four Hanwoo (Korean native) steers (live bodyweight, 556 ± 46 kg) with a ruminal cannula were housed individually in metabolic stalls and fed a basal diet twice daily in equal amounts at 0900 hours and 2100 hours. The before rhubarb treatment (before treatment) duration was 24 days for all steers; 14 days were used for diet adaptation and 10 days were used for gas samples collected 1, 2, and 3 h after the morning feeding on Days 3, 5, 7, and 9. We used three syringe needles passed through the ruminal cannula stopper at different time points as a simple and rapid method to sample rumen gas. Thereafter, three mesh bags containing 30 g of sliced rhubarb root each were placed at different depths in the rumen of each steer for 14 days (after treatment), and gas samples were collected on Days 4, 7, 10, 12, and 13. The results showed a significant (P < 0.05) decrease in methane concentration from the rhubarb-treated steers and provide the evidence that this method would be useful for in vivo screening of anti-methanogenic feed additives or plant material. Furthermore, 16s RNA sequencing after treatment showed increases in the numbers of Prevotella, and Lactobacillus, but decreases in Methanobrevibacter. In conclusion, rhubarb had an anti-methanogenic effect in vitro and in vivo, and the increase in the number of Prevotella shifted ruminal fermentation towards propionate production.
Collapse
|
40
|
Wan X, Ruan R, McLaughlin RW, Hao Y, Zheng J, Wang D. Fecal Bacterial Composition of the Endangered Yangtze Finless Porpoises Living Under Captive and Semi-natural Conditions. Curr Microbiol 2015; 72:306-14. [PMID: 26620537 DOI: 10.1007/s00284-015-0954-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/22/2015] [Indexed: 11/25/2022]
Abstract
Intestinal microbiota is essential to the health and physiology of host animals. We undertook the first microbiological study of the fecal bacterial composition from critically endangered (CR) Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis; YFPs) living under captive and semi-natural conditions using both high-throughput sequencing method and 16S rRNA gene clone library method. As determined by high-throughput sequencing of V3-V4 regions of the 16S rRNA gene, semi-natural samples harbored 30 and 36 operational taxonomic units (OTUs), which was more than the 22 and 27 OTUs detected from YFPs living in captivity. In captive YFPs Firmicutes was the predominant phylum, whereas this was Proteobacteria for YFPs living in semi-nature conditions. This suggests habitat-specific fecal bacterial composition of YFPs. Plesiomonas spp. and Aeromonas spp., which are potentially pathogenic, were identified in all the feces. Bacterial diversity from one porpoise living in captivity was also determined by constructing a 16S rRNA gene clone library and only 1 phylum was identified. High-throughput sequencing was more effective at determining the bacterial diversity compared to the 16S rRNA gene clone library. This study provides important information for the management and conservation of the CR YFPs.
Collapse
Affiliation(s)
- Xiaoling Wan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Rui Ruan
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Richard William McLaughlin
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuhan, 430072, China.,Biology Department, Saint Mary's University of Minnesota, 700 Terrace, Winona, MN, 55987-1399, USA
| | - Yujiang Hao
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuhan, 430072, China
| | - Jinsong Zheng
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuhan, 430072, China.
| | - Ding Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuhan, 430072, China.
| |
Collapse
|
41
|
Ghali I, Shinkai T, Mitsumori M. Mining of luxS genes from rumen microbial consortia by metagenomic and metatranscriptomic approaches. Anim Sci J 2015; 87:666-73. [PMID: 26277986 DOI: 10.1111/asj.12476] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/27/2015] [Indexed: 11/27/2022]
Abstract
Although rumen bacterial communities vary depending on many factors such as diet, age and physiological conditions, a core microbiota exists within the rumen. In many natural environments, some bacteria use a quorum-sensing (QS) system to regulate their physiological activities. However, very limited information is available about QS systems in rumen. To investigate the autoinducer 2 (AI-2)-mediated QS system in rumen, we detected genes (luxS) encoding the AI-2 synthase (LuxS), from three datasets embedded in metagenomics RAST server (MG-RAST) and from a metatranscriptome dataset. We collected 135 luxS genes from the metagenomic datasets, which were presumed to originate from Bacteroidetes, Firmicutes, Fusobacteria and Actinobacteria, and 34 luxS genes from the metatranscriptome dataset, which probably originated from Bacteroidetes, Firmicutes and Spirochaetes. Because the essential amino acids for LuxS activity were conserved in the LuxS homologues predicted from luxS gene sequences from both datasets, the LuxS homologues probably function in the rumen. Since the largest number of sequences of luxS genes were collected from the genera Prevotella, Ruminococcus and Eubacterium, which include many fibrolytic bacteria and constituent members of biofilm on feed particles, an AI-2-mediated QS system is likely involved in biofilm formation and fibrolytic activity in the rumen.
Collapse
Affiliation(s)
- Ines Ghali
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Takumi Shinkai
- NARO Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Makoto Mitsumori
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,NARO Institute of Livestock and Grassland Science, Tsukuba, Japan
| |
Collapse
|
42
|
Li Z, Wright ADG, Liu H, Fan Z, Yang F, Zhang Z, Li G. Response of the Rumen Microbiota of Sika Deer (Cervus nippon) Fed Different Concentrations of Tannin Rich Plants. PLoS One 2015; 10:e0123481. [PMID: 25955033 PMCID: PMC4425498 DOI: 10.1371/journal.pone.0123481] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/25/2015] [Indexed: 02/01/2023] Open
Abstract
High throughput sequencing was used to examine the rumen microbiota of sika deer fed high (OLH) and low concentration (OLL) of tannin rich oak leaves. The results showed that Prevotella spp. were the most dominant bacteria. The most predominant methanogens were the members of the order Methanoplasmatales. The dominant rumen protozoa were Entodinium longinucleatum, Eudiplodinium maggii, and Epidinium caudatum, and the fungal communities were mostly represented by Piromyces spp. Moreover, the relative abundance of Pseudobutyrivibrio spp. (P=0.026), unidentified bacteria (P=0.028), and Prevotella spp. (P=0.022) was lower in the OLH group than in the OLL group. The concentration of propionate in the OLH group was greater than in the OLL group (P=0.006). Patterns of relationships showed that methanogens belonging to the order Methanoplasmatales were negatively correlated with Treponema spp., Ent. Longinucleatum, and acetate. Methanosphaera stadtmanae was positively correlated to propionate, while Methanobrevibacter ruminantium was negatively associated with Methanobrevibacter thaueri and Methanobrevibacter millerae. Tannins altered the rumen microbes and fermentation patterns. However, the response of the entire rumen microbiota and the relationship between rumen microorganisms and the fermentation parameters were not fully understood.
Collapse
Affiliation(s)
- Zhipeng Li
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| | - André-Denis G Wright
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Hanlu Liu
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Zhongyuan Fan
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Fuhe Yang
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Zhigang Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Guangyu Li
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| |
Collapse
|
43
|
Cersosimo LM, Lachance H, St-Pierre B, van Hoven W, Wright ADG. Examination of the rumen bacteria and methanogenic archaea of wild impalas (Aepyceros melampus melampus) from Pongola, South Africa. MICROBIAL ECOLOGY 2015; 69:577-585. [PMID: 25351144 DOI: 10.1007/s00248-014-0521-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 10/15/2014] [Indexed: 06/04/2023]
Abstract
Although the rumen microbiome of domesticated ruminants has been evaluated, few studies have explored the rumen microbiome of wild ruminants, and no studies have identified the rumen microbiome in the impala (Aepyceros melampus melampus). In the present study, next-generation sequencing and real-time polymerase chain reaction were used to investigate the diversity and density of the bacteria and methanogenic archaea residing in the rumen of five adult male impalas, culled during the winter dry season in Pongola, South Africa. A total of 15,323 bacterial 16S rRNA gene sequences (from five impala), representing 3,892 different phylotypes, were assigned to 1,902 operational taxonomic units (OTUs). A total of 20,124 methanogen 16S rRNA gene sequence reads (from four impala), of which 5,028 were unique, were assigned to 344 OTUs. From the total sequence reads, Bacteroidetes, Proteobacteria, and Firmicutes were the most abundant bacterial phyla. While the majority of the bacterial genera found were unclassified, Prevotella and Cupriavidus were the most abundant classified genera. For methanogens, the genera Methanobrevibacter and Methanosphaera represented 94.3% and 4.0% of the classified sequences, respectively. Most notable was the identification of Methanobrevibacter thaueri-like 16S rRNA gene sequence reads in all four impala samples, representing greater than 30% of each individual's total sequences. Both data sets are accessible through NCBI's Sequence Read Archive (SRA), under study accession number SRP [048619]. The densities of bacteria (1.26 × 10(10)-3.82 × 10(10) cells/ml whole rumen contents) and methanogens (4.48 × 10(8)-7.2 × 10(9) cells/ml of whole rumen contents) from five individual impala were similar to those typically observed in domesticated ruminants.
Collapse
Affiliation(s)
- Laura M Cersosimo
- Department of Animal Science, The University of Vermont, 570 Main Street, Burlington, VT, 05405, USA
| | | | | | | | | |
Collapse
|
44
|
Singh KM, Patel AK, Shah RK, Reddy B, Joshi CG. Potential functional gene diversity involved in methanogenesis and methanogenic community structure in Indian buffalo (Bubalus bubalis) rumen. J Appl Genet 2015; 56:411-26. [PMID: 25663664 DOI: 10.1007/s13353-015-0270-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/26/2014] [Accepted: 01/06/2015] [Indexed: 11/26/2022]
Abstract
Understanding the methanogen community structure and methanogenesis from Bubalus bubalis in India may be beneficial to methane mitigation. Our current understanding of the microbial processes leading to methane production is incomplete, and further advancement in the knowledge of methanogenesis pathways would provide means to manipulate its emission in the future. In the present study, we evaluated the methanogenic community structure in the rumen as well as their potential genes involved in methanogenesis. The taxonomic and metabolic profiles of methanogens were assessed by shotgun sequencing of rumen metagenome by Ion Torrent semiconductor sequencing. The buffalo rumen contained representative genera of all the families of methanogens. Members of Methanobacteriaceae were found to be dominant, followed by Methanosarcinaceae, Methanococcaceae, Methanocorpusculaceae, and Thermococcaceae. A total of 60 methanogenic genera were detected in buffalo rumen. Methanogens related to the genera Methanobrevibacter, Methanosarcina, Methanococcus, Methanocorpusculum, Methanothermobacter, and Methanosphaera were predominant, representing >70 % of total archaeal sequences. The metagenomic dataset indicated the presence of genes involved in the methanogenesis and acetogenesis pathways, and the main functional genes were those of key enzymes in the methanogenesis. Sequences related to CoB--CoM heterodisulfide reductase, methyl coenzyme M reductase, f420-dependent methylenetetrahydromethanopterin reductase, and formylmethanofuran dehydrogenase were predominant in rumen. In addition, methenyltetrahydrofolate cyclohydrolase, methylenetetrahydrofolate dehydrogenase, 5,10-methylenetetrahydrofolate reductase, and acetyl-coenzyme A synthetase were also recovered.
Collapse
Affiliation(s)
- Krishna M Singh
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India,
| | | | | | | | | |
Collapse
|
45
|
Li Z, Wright ADG, Liu H, Bao K, Zhang T, Wang K, Cui X, Yang F, Zhang Z, Li G. Bacterial community composition and fermentation patterns in the rumen of sika deer (Cervus nippon) fed three different diets. MICROBIAL ECOLOGY 2015; 69:307-318. [PMID: 25252928 DOI: 10.1007/s00248-014-0497-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/08/2014] [Indexed: 06/03/2023]
Abstract
Sika deer (Cervus nippon) rely on microorganisms living in the rumen to convert plant materials into chemical compounds, such as volatile fatty acids (VFAs), but how the rumen bacterial community is affected by different forages and adapt to altered diets remains poorly understood. The present study used 454-pyrosequencing of bacterial 16S ribosomal RNA (rRNA) genes to examine the relationship between rumen bacterial diversity and metabolic phenotypes using three sika deer in a 3 × 3 latin square design. Three sika deer were fed oak leaves (OL), corn stover (CS), or corn silage (CI), respectively. After a 7-day feeding period, when compared to the CS and CI groups, the OL group had a lower proportion of Prevotella spp. and a higher proportion of unclassified bacteria belonging to the families Succinivibrionaceae and Paraprevotellaceae (P<0.05). Meanwhile, the concentration of isobutyrate was significantly lower (P<0.05) in the OL group than in the CS and CI groups. There was no significant change of dominant bacterial genera in the OL group after 28 days of feeding. Conversely, total volatile fatty acids (TVFAs) showed an increase after 28 days of feeding, mainly due to the increasing of acetate, propionate, and valerate (P<0.05). The interplay between bacteria and metabolism in the OL group differed from that in the CS and CI groups, especially for the interaction of TVFAs and acetate/propionate. Overall, the current study suggested that Prevotella spp. played critical roles in the fermentation of feed in the rumen of sika deer. However, the differences in interplay patterns between rumen bacterial community composition and metabolic phenotypes were altered in the native and domesticated diets indicating the changed fermentation patterns in the rumen of sika deer.
Collapse
Affiliation(s)
- Zhipeng Li
- Jilin Provincial Key Labororary for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Bacteria and methanogens differ along the gastrointestinal tract of Chinese roe deer (Capreolus pygargus). PLoS One 2014; 9:e114513. [PMID: 25490208 PMCID: PMC4260832 DOI: 10.1371/journal.pone.0114513] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 11/10/2014] [Indexed: 02/01/2023] Open
Abstract
The current study provides the insight into the bacteria in the gastrointestinal tract (GIT) and methanogens presented in the rumen and cecum of the Chinese roe deer (Capreolus pygargus). The ruminal, ileal, cecal, and colonic contents, as well as feces, were obtained from each of the three, free-range, roe deer ingesting natural pasture after euthanasia. For the bacterial community, a total of 697,031 high-quality 16S rRNA gene sequences were generated using high-throughput sequencing, and assigned to 2,223 core operational taxonomic units (OTUs) (12 bacterial phyla and 87 genera). The phyla Firmicutes (51.2%) and Bacteroidetes (39.4%) were the dominant bacteria in the GIT of roe deer. However, the bacterial community in the rumen was significantly (P<0.01) different from the other sampled regions along the GIT. Secondly, Prevotella spp., Anaerovibrio spp., and unidentified bacteria within the families Veillonellaceae and Paraprevotellaceae were more abundant in the rumen than in the other regions. Unidentified bacteria within the family Enterobacteriaceae, Succinivibrio spp., and Desulfovibrio spp. were more predominant in the colon than in other regions. Unidentified bacteria within the family Ruminococcaceae, and Bacteroides spp. were more prevalent in the ileum, cecum and fecal pellets. For methanogens in the rumen and cecum, a total of 375,647 high quality 16S rRNA gene sequences were obtained and assigned to 113 core OTUs. Methanobrevibacter millerae was the dominant species accounting for 77.3±7.4 (S.E) % and 68.9±4.4 (S.E) % of total sequences in the rumen and cecum of roe deer, respectively. However, the abundance of Methanobrevibacter smithii was higher in the rumen than in the cecum (P = 0.004). These results revealed that there was intra variation in the bacterial community composition across the GIT of roe deer, and also showed that the methanogen community in the rumen differed from that in the cecum.
Collapse
|
47
|
Qin SY, Zhang XX, Cong W, Zhou DH, Wang JL, Yin MY, Tan QD, Zhao Q, Zhu XQ. Seroprevalence and risk factors of Toxoplasma gondii infection in domestic sika deer (Cervus nippon) in northeastern China. Acta Trop 2014; 140:184-7. [PMID: 25201489 DOI: 10.1016/j.actatropica.2014.08.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/21/2014] [Accepted: 08/27/2014] [Indexed: 12/11/2022]
Abstract
Toxoplasmosis is a worldwide zoonosis caused by Toxoplasma gondii, which can infect warm-blooded animals and humans. A serological survey was undertaken to examine the seroprevalence and risk factors associated with T. gondii infection in sika deer in northeastern China. 114 (13.46%, 95% CI 11.16-15.76) out of 847 serum samples were positive to T. gondii by modified agglutination test (MAT) at a 1:25 cut-off, with titers of 1:25 in 44, 1:50 in 32, 1:100 in 17, 1:500 in 11, 1:1500 or higher in 10. These samples were collected between November 2012 and October 2013 from Inner Mongolia, Jilin and Heilongjiang provinces in China. However, statistically significant differences were not observed between T. gondii seroprevalence and genders or regions of sika deer in the logistic regression analysis (P>0.05) and left out of the final model. Seroprevalence of T. gondii infection in male sika deer was 14.07% (95% CI 11.14-17.01), slightly higher than that in the female (12.38%) (95% CI 8.69-16.06) and seroprevalence of T. gondii infection in Harbin, Changchun city, Jilin city and Chifeng city were 12.02% (95% CI 7.60-16.44), 15.51% (95% CI 11.52-19.50), 12.27% (95% CI 7.23-17.31) and 12.50% (95% CI 7.38-17.63), respectively. Seasons of sampling were considered as main risk factors associated with T. gondii infection, autumn (15.32%) were more than two times (OR=1.98, 95% CI=1.18-3.33, P=0.01) at risk of acquiring T. gondii infection compared to winter (8.37%). Our results indicated a widespread exposure to T. gondii among sika deer in China. To our knowledge, this is the first report of T. gondii seroprevalence in sika deer in China.
Collapse
|
48
|
Pitta DW, Parmar N, Patel AK, Indugu N, Kumar S, Prajapathi KB, Patel AB, Reddy B, Joshi C. Bacterial diversity dynamics associated with different diets and different primer pairs in the rumen of Kankrej cattle. PLoS One 2014; 9:e111710. [PMID: 25365522 PMCID: PMC4218807 DOI: 10.1371/journal.pone.0111710] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 09/29/2014] [Indexed: 11/18/2022] Open
Abstract
The ruminal microbiome in herbivores plays a dominant role in the digestion of lignocellulose and has potential to improve animal productivity. Kankrej cattle, a popular native breed of the Indian subcontinent, were used to investigate the effect of different dietary treatments on the bacterial diversity in ruminal fractions using different primer pairs. Two groups of four cows were assigned to two primary diets of either dry or green forages. Each group was fed one of three dietary treatments for six weeks each. Dietary treatments were; K1 (50% dry/green roughage: 50% concentrate), K2 (75% dry/green roughage: 25% concentrate) and K3 (100% dry/green roughage). Rumen samples were collected using stomach tube at the end of each dietary period and separated into solid and liquid fractions. The DNA was extracted and amplified for V1–V3, V4–V5 and V6–V8 hypervariable regions using P1, P2 and P3 primer pairs, sequenced on a 454 Roche platform and analyzed using QIIME. Community compositions and the abundance of most bacterial lineages were driven by interactions between primer pair, dietary treatment and fraction. The most abundant bacterial phyla identified were Bacteroidetes and Firmicutes however, the abundance of these phyla varied between different primer pairs; in each primer pair the abundance was dependent on the dietary treatment and fraction. The abundance of Bacteroidetes in cattle receiving K1 treatment indicate their diverse functional capabilities in the digestion of both carbohydrate and protein while the predominance of Firmicutes in the K2 and K3 treatments signifies their metabolic role in fibre digestion. It is apparent that both liquid and solid fractions had distinct bacterial community patterns (P<0.001) congruent to changes in the dietary treatments. It can be concluded that the P1 primer pair flanking the V1–V3 hyper-variable region provided greater species richness and diversity of bacterial populations in the rumen of Kankrej cattle.
Collapse
Affiliation(s)
- Dipti W. Pitta
- Center for Animal Health and Productivity, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| | - Nidhi Parmar
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Amrut K. Patel
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Nagaraju Indugu
- Center for Animal Health and Productivity, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sanjay Kumar
- Center for Animal Health and Productivity, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Karsanbhai B. Prajapathi
- Livestock Production and Management Department, College of Veterinary Science and Animal Husbandry, Sardar Krushi Nagar Dantiwada Agricultural University, Sardar Krushi Nagar, Gujarat, India
| | - Anand B. Patel
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Bhaskar Reddy
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Chaitanya Joshi
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| |
Collapse
|
49
|
Parmar NR, Solanki JV, Patel AB, Shah TM, Patel AK, Parnerkar S, Kumar JIN, Joshi CG. Metagenome of Mehsani buffalo rumen microbiota: an assessment of variation in feed-dependent phylogenetic and functional classification. J Mol Microbiol Biotechnol 2014; 24:249-61. [PMID: 25228469 DOI: 10.1159/000365054] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
AIM To gain a greater understanding of the ecology and metabolic potential of the rumen microbiome with the changes in the animal diet. METHODS Diet composed of varying proportion of green and dry roughages along with grains was given to 8 Mehsani buffaloes, and rumen metagenome was sketched using shotgun semiconductor sequencing. RESULTS In the present study, the Bacteroidetes were found to be dominant at the phyla level and Prevotella at the genus level. The ratio of Firmicutes to Bacteroidetes was found to be higher in the solid fraction as compared to the liquid fraction. In the solid fraction of the dry roughage group, the significant increment (p < 0.05) in Bacteroidetes abundance was observed with increment of roughage concentration. At the genus level, Clostridium significantly increased with the increment in roughage concentration. A comparison of glycoside hydrolase and cellulosome functional genes revealed more glycoside hydrolase 3 encoding genes with higher fiber diet and significant difference in carbohydrate-active enzymes family composition between green and dry roughage groups of the liquid fraction. CONCLUSION The present study provides a base to understand the modulating behavior of microbiota which can be manipulated to improve livestock nutrient utilization efficiency and for targeting the efficient catabolism of complex carbohydrate molecules as well.
Collapse
Affiliation(s)
- Nidhi R Parmar
- Institute of Science and Technology for Advanced Studies and Research, V.V. Nagar, India
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Li ZP, Liu HL, Jin CA, Cui XZ, Jing Y, Yang FH, Li GY, Wright ADG. Differences in the methanogen population exist in sika deer (Cervus nippon) fed different diets in China. MICROBIAL ECOLOGY 2013; 66:879-888. [PMID: 24061342 DOI: 10.1007/s00248-013-0282-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 08/21/2013] [Indexed: 06/02/2023]
Abstract
Understanding the methanogen structure from sika deer (Cervus nippon) in China may be beneficial to methane mitigation. In the present preliminary study, we investigated the methanogen community in the rumen of domesticated sika deer fed either tannin-rich plants (oak leaf, OL group) or corn stalk (CS group) using 16S rRNA gene clone libraries. Overall, we obtained 197 clone sequences, revealing 146 unique phylotypes, which were assigned to 36 operational taxonomic units at the species level (98 % identity). Methanogens related to the genus Methanobrevibacter were the predominant phylotypes representing 83.9 % (OL library) and 85.9 % (CS library) of the clones. Methanobrevibacter millerae was the most abundant species in both libraries, but the proportion of M. millerae-related clones in the CS library was higher than in the OL library (69.5 and 51.4 %, respectively). Moreover, Methanobrevibacter wolinii-related clones (32.5 %) were predominant in the OL library. Methanobrevibacter smithii-related clones and Methanobrevibacter ruminantium-related clones accounted for 6.5 and 6.6 % in the CS library, respectively. However, these clones were absent from the OL library. The concentrations of butyrate and total short-chain fatty acids (SCFAs) were significantly higher in the OL group, but the concentrations of acetate, propionate, and valerate and the acetate to propionate ratio in the OL group were not significantly different between the two groups. Tannin-rich plants may have affected the distribution of genus Methanobrevibacter phylotypes at the species level and the concentration and composition of SCFAs.
Collapse
Affiliation(s)
- Zhi Peng Li
- Department of Economical Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin, China
| | | | | | | | | | | | | | | |
Collapse
|