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Xie K, Chang S, Ning J, Guo Y, Zhang C, Yan T, Hou F. Dietary supplementation of Allium mongolicum modulates rumen-hindgut microbial community structure in Simmental calves. Front Microbiol 2023; 14:1174740. [PMID: 37350783 PMCID: PMC10284144 DOI: 10.3389/fmicb.2023.1174740] [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: 02/27/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023] Open
Abstract
Compared to traditional herbage, functional native herbage is playing more important role in ruminant agriculture through improving digestion, metabolism and health of livestock; however, their effects on rumen microbial communities and hindgut fermentation are still not well understood. The objective of present study was to evaluate the effects of dietary addition of Allium mongolicum on bacterial communities in rumen and feces of claves. Sixteen 7-month-old male calves were randomly divided into four groups (n = 4). All calves were fed a basal ration containing roughage (alfalfa and oats) and mixed concentrate in a ratio of 60:40 on dry matter basis. In each group, the basal ration was supplemented with Allium mongolicum 0 (SL0), 200 (SL200), 400 (SL400), and 800 (SL800) mg/kg BW. The experiment lasted for 58 days. Rumen fluid and feces in rectum were collected, Rumen fluid and hindgut fecal were collected for analyzing bacterial community. In the rumen, Compared with SL0, there was a greater relative abundance of phylum Proteobacteria (p < 0.05) and genera Rikenellaceae_RC9_gut_group (p < 0.01) in SL800 treatment. In hindgut, compared with SL0, supplementation of A. mongolicum (SL200, SL400, or SL800) decreased in the relative abundances of Ruminococcaceae_UCG-014 (p < 0.01), Ruminiclostridium_5 (p < 0.01), Eubacterium_coprostanoligenes_group (p < 0.05), and Alistipes (p < 0.05) in feces; Whereas, the relative abundances of Christensenellaceae_R-7_group (p < 0.05), and Prevotella_1 (p < 0.01) in SL800 were higher in feces, to maintain hindgut stability. This study provided evidence that A. mongolicum affects the gastrointestinal of calves, by influencing microbiota in their rumen and feces.
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Affiliation(s)
- Kaili Xie
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shenghua Chang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Jiao Ning
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Yarong Guo
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Cheng Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Tianhai Yan
- Agri-Food and Biosciences Institute, Hillsborough, United Kingdom
| | - Fujiang Hou
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
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Thacher PR, Kendrick EL, Maslanka M, Muletz-Wolz CR, Bornbusch SL. Fecal microbiota transplants modulate the gut microbiome of a two-toed sloth (Choloepus didactylus). Zoo Biol 2023; 42:453-458. [PMID: 36629092 DOI: 10.1002/zoo.21751] [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: 08/11/2022] [Revised: 11/18/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
The microbes inhabiting an animal's gastrointestinal tracts, collectively known as the gut microbiome, are vital to animal health and wellbeing. For animals experiencing gut distress or infection, modulation of the gut microbiome, for example, via fecal microbiota transplant (FMT), provides a possible disease prevention and treatment method. The beneficial microbes present in the donor's transplanted feces can help combat pathogens, assist in digestion, and rebalance the recipient's microbiota. Investigating the efficacy of FMTs in animal health is a crucial step toward improving management strategies for species under human care. We present a case study of the use of FMTs in a two-toed sloth experiencing abnormally large, clumped, and frequent stools. We used 16 S rRNA amplicon sequencing of fecal samples to (a) compare the microbiomes of the FMT donor, a healthy, cohoused conspecific, and the FMT recipient and (b) assess the influence of multiple rounds of FMTs on the recipient's microbiome and stool consistency and frequency over time. In response to the FMTs, we found that the recipient's microbiome showed trends toward increased diversity, shifted community composition, and altered membership that more resembled the community of the donor. FMT treatment was also associated with marked, yet temporary, alleviation of the recipient's abnormal bowel movements, suggesting a broader impact on gut health. Our results provide valuable preliminary evidence that FMT treatments can augment the recipient's gut microbiome, with potential implications for animal health and management.
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Affiliation(s)
- Piper R Thacher
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, District of Columbia, USA.,Department of Environmental Science and Policy, Smithsonian Mason School of Conservation, George Mason University, Fairfax, Virginia, USA
| | - Erin L Kendrick
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, Washington, District of Columbia, USA
| | - Michael Maslanka
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, Washington, District of Columbia, USA
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, District of Columbia, USA
| | - Sally L Bornbusch
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, District of Columbia, USA.,Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, Washington, District of Columbia, USA
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Yang X, Li Y, Ma J, Wu F, Wang L, Sun L, Zhang P, Wang W, Xu J. Comparative physiological and soil microbial community structural analysis revealed that selenium alleviates cadmium stress in Perilla frutescens. FRONTIERS IN PLANT SCIENCE 2022; 13:1022935. [PMID: 36275509 PMCID: PMC9585217 DOI: 10.3389/fpls.2022.1022935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Cadmium (Cd) toxicity not only affects plant growth and development, but also affects human health through the food chain. Several studies have demonstrated that Selenium (Se) alleviates Cd stress in plants; however, whether and how Se-alleviated Cd stress by regulating the structure of soil microbial community remain largely unclear. Here, we investigated the alleviating effects of exogenous applied Se (foliar spraying or root application) on plant growth under Cd stress in perilla (Perilla frutescens L.) by measuring the biomass, photosynthetic fluorescence parameters, root cell wall components and soil microbial community structure and diversity. Under Cd stress, perilla seedlings supplemented with Se increased chlorophyll content. Foliar spraying Se increased the levels of relative chlorophyll content (ΦII), photosynthetic system II (ΦPSII) and electron transport rate (ETR) in perilla leaves under Cd stress; while, root application of Se increased the levels of photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), water use efficiency (WUE) and stomatal limitation value (Ls) under Cd stress. Compared with Cd toxicity alone, root application of Se increased the contents of hemicellulosic 1 and hemicellulosic 2 in the cell wall of perilla roots. Cd toxicity or root application of Se did not affect soil bacterial community diversity. Root application of Se increased the relative abundance of Proteobacteria, Bacteroidetes, Fibrobacteres, Sphingomonas and Nitrosospira in Cd-contaminated soil, and thereby improving soil microbial community structure, finally promoting the growth of perilla seedlings.
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Affiliation(s)
- Xiaohuan Yang
- College of Horticulture, Shanxi Agricultural University, Taigu, China
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Ying Li
- College of Horticulture, Shanxi Agricultural University, Taigu, China
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Jinhu Ma
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Fei Wu
- College of Horticulture, Shanxi Agricultural University, Taigu, China
| | - Liyin Wang
- College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Liangliang Sun
- College of Horticulture, Shanxi Agricultural University, Taigu, China
| | - Ping Zhang
- College of Horticulture, Shanxi Agricultural University, Taigu, China
| | - Wenying Wang
- College of Life Science, Qinghai Normal University, Xining, China
| | - Jin Xu
- College of Horticulture, Shanxi Agricultural University, Taigu, China
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Zhang J, Gao H, Jiang F, Liu D, Hou Y, Chi X, Qin W, Song P, Cai Z, Zhang T. Comparative Analysis of Gut Microbial Composition and Functions in Przewalski's Gazelle ( Procapra przewalskii) From Various Habitats. Front Microbiol 2022; 13:913358. [PMID: 35756029 PMCID: PMC9213746 DOI: 10.3389/fmicb.2022.913358] [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: 04/05/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Gut microbiota of mammals participates in host nutrient metabolism and plays an important role in host adaptation to the environment. Herein, to understand the relationship between environment differences and the composition and abundance of the gut microbiota of Przewalski's gazelle (Procapra przewalskii) in almost all its habitats, high throughput sequencing of the 16S rRNA gene was used to compared the characteristics of the gut microbiota based on total 120 fecal samples. The results showed that Przewalski's gazelle exhibited different characteristics of microbiota diversity in different habitats. The Jiangxigou Rescue Station (JX), Nongchang (NC), and Ganzihe and Haergai townships (GH) groups had a relatively high microbiota diversity, while the Niaodao scenic area (ND) group had the lowest diversity. This finding seemed to follow a similar pattern of change in the population of Przewalski's gazelle. Bacteroidetes and Actinobacteria were the phyla with significant differences, especially between the Wayu township (WY) and the other groups. The difference in the microbiota mainly included the Ruminococcaceae UCG-005, Christensenellaceae R-7 group, and Bacteroidaceae and was enriched in the ND, WY, and other regions. We speculated that the difference in the gut microbiota was due to a difference in environmental characteristics, particularly the food resources that the host can obtain. We speculated that a similar microbiome has important functions for species survival and represents the evolutionary commonality of Przewalski's gazelle, while a different microbiome plays an important role in the adaptation of Przewalski's gazelle to a different environment. The results of this study illustrate how the same species adapts to different environments from the perspective of gut microbiota plasticity and therefore are of great significance for the protection and restoration of the population of this species.
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Affiliation(s)
- Jingjie Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Hongmei Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Feng Jiang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Daoxin Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuansheng Hou
- Qinghai Lake National Nature Reserve Bureau, Xining, China
| | | | - Wen Qin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhenyuan Cai
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
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Liu J, Wang X, Zhang W, Kulyar MFEA, Ullah K, Han Z, Qin J, Bi C, Wang Y, Li K. Comparative analysis of gut microbiota in healthy and diarrheic yaks. Microb Cell Fact 2022; 21:111. [PMID: 35659293 PMCID: PMC9164553 DOI: 10.1186/s12934-022-01836-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/25/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Yak (Bos grunniens) mainly inhabiting Tibet Plateau, displayed a high incidence of diarrhea due to harsh living environment and nutritional deficit. Gut microbial community has been reported to be closely related to many diseases including diabetes, obesity and inflammatory bowel disease, but information regarding diarrheic influence on gut microbiota in yaks remains scarce. Here, this study was performed to investigate the gut bacterial and fungal alternations of diarrheic yaks. RESULTS Results revealed that the gut bacterial and fungal communities of diarrheic yaks showed a distinct decline in alpha diversity, accompanied by significant shifts in taxonomic compositions. Specifically, diarrhea caused a distinct increase in the relative abundance of 1 phylum and 8 genera as well as a distinct decrease in 3 phyla and 30 genera. Fungal taxonomic analysis indicated that the relative richness of 1 phylum and 2 genera dramatically increased, whereas the relative richness of 2 phylum and 43 genera significantly decreased during diarrhea. Surprisingly, 2 bacterial genera and 5 fungal genera even cannot be detected in the gut microbiota of diarrheic yaks. CONCLUSIONS In summary, this study indicated that the gut bacterial and fungal compositions and diversities of yaks altered significantly during diarrhea. Moreover, these findings also contribute to understanding the gut microbial composition and diversity of yaks and developing strategies to alleviate and prevent diarrhea from gut microbial perspective.
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Affiliation(s)
- JunJun Liu
- College of Veterinary Medicine/Traditional Chinese Veterinary Medicine, Hebei Agriculture University, Baoding, 071001, People's Republic of China
| | - Xin Wang
- College of Agriculture and Forestry, Linyi University, Shuangling Road, Linyi, Shandong, 276005, People's Republic of China
| | - Wenqian Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Kalim Ullah
- Department of Zoology, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Zhaoqing Han
- College of Agriculture and Forestry, Linyi University, Shuangling Road, Linyi, Shandong, 276005, People's Republic of China
| | - Jianhua Qin
- College of Agriculture and Forestry, Linyi University, Shuangling Road, Linyi, Shandong, 276005, People's Republic of China
| | - Chongliang Bi
- College of Agriculture and Forestry, Linyi University, Shuangling Road, Linyi, Shandong, 276005, People's Republic of China.
| | - Yaping Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China. .,MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Niu H, Feng XZ, Shi CW, Zhang D, Chen HL, Huang HB, Jiang YL, Wang JZ, Cao X, Wang N, Zeng Y, Yang GL, Yang WT, Wang CF. Gut Bacterial Composition and Functional Potential of Tibetan Pigs Under Semi-Grazing. Front Microbiol 2022; 13:850687. [PMID: 35464912 PMCID: PMC9023118 DOI: 10.3389/fmicb.2022.850687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/10/2022] [Indexed: 12/28/2022] Open
Abstract
Gut bacterial community plays a key role in maintaining host health. The Tibetan pig (Sus scrofa), an ancient breed in China, has been known for its high adaptability to harsh environments and for its meat quality. To understand the underlying mechanisms facilitating to shape these unique features, in this study, 16S rRNA sequencing using pigs feces and subsequent bacterial functional prediction were performed. Also, the gut bacteria of two other breeds of pigs, Barkshire and Landrace, were examined for comparison. It was revealed that the structure of bacterial community in Tibetan pigs appeared to be more complex; the relative abundances of dominant bacterial families varied inversely with those of the other pigs, and the proportion of Firmicutes in Tibetan pigs was lower, but Bacteroides, Fibrobacterota, Lachnospiraceae, Oscillospiraceae, and Ruminococcaceae were higher. Bacterial functional prediction revealed that the dominant flora in the Tibetan pigs was more correlated with functions regulating the hosts’ immune and inflammatory responses, such as NOD-like_receptor_signaling_pathway and vitamin metabolism. In addition, in Tibetan pigs, the taxonomic relationships in the gut bacteria on day 350 were closer than those on earlier stages. Furthermore, gender played a role in the composition and function of bacterial inhabitants in the gut; for boars, they were more correlated to drug resistance and xenobiotics metabolism of the host compared to the sows. In sum, our preliminary study on the gut bacterial composition of the Tibetan pigs provided an insight into the underlying host–microorganism interactions, emphasizing the role of intestinal bacteria in the context of modulating the host’s immune system and host development.
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Zhang Q, Xu J, Wang X, Zhu W, Pang X, Zhao J. Changes and distributions of antibiotic resistance genes in liquid and solid fractions in mesophilic and thermophilic anaerobic digestion of dairy manure. BIORESOURCE TECHNOLOGY 2021; 320:124372. [PMID: 33186839 DOI: 10.1016/j.biortech.2020.124372] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 06/11/2023]
Abstract
This study mainly explored the changes and distributions of antibiotic resistance genes (ARGs) in liquid fraction (LF) and solid fraction (SF) in anaerobic digestion (AD) of dairy manure. After mesophilic and thermophilic AD, the copy numbers of ARGs in LF decreased by 0.06-1.80 logs while those in SF increased by 0.08-7.85 logs, suggesting the enrichment of ARGs in SF. Statistical analysis elucidated that high total solids promoted the enrichment of ARGs in SF. The increased abundances of genera such as Ruminofilibacter, Treponema and Sphaerochaeta in SF were responsible for the enrichment of most ARGs. These insights demonstrated the digested solid had the potential risks to promote the spread of ARGs in the environment, and the digested solid of livestock manure should be post-treated before the application.
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Affiliation(s)
- Qiuping Zhang
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jifei Xu
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot, China.
| | - Xiujun Wang
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Wenbo Zhu
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Xiaoke Pang
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Ji Zhao
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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Wang K, Nan X, Tong J, Zhao G, Jiang L, Xiong B. Steam Explosion Pretreatment Changes Ruminal Fermentation in vitro of Corn Stover by Shifting Archaeal and Bacterial Community Structure. Front Microbiol 2020; 11:2027. [PMID: 32983029 PMCID: PMC7483759 DOI: 10.3389/fmicb.2020.02027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 07/31/2020] [Indexed: 01/09/2023] Open
Abstract
Steam explosion is an environment-friendly pretreatment method to improve the subsequent hydrolysis process of lignocellulosic biomass. Steam explosion pretreatment improved ruminal fermentation and changed fermentation pattern of corn stover during ruminal fermentation in vitro. The study gave a comprehensive insight into how stream explosion pretreatment shifted archaeal and bacterial community structure to change ruminal fermentation in vitro of corn stover. Results showed that steam explosion pretreatment dramatically improved the apparent disappearance of dry matter (DM), neutral detergent fiber (NDF), and acid detergent fiber (ADF). Steam explosion pretreatment significantly increased the molar proportion of propionate and decreased the ratio of acetate to propionate. At archaeal level, steam explosion pretreatment significantly increased the relative abundance of Methanobrevibacter, which can effectively remove metabolic hydrogen to keep the fermentation continuing. At bacterial level, the shift in fermentation was achieved by increasing the relative abundance of cellulolytic bacteria and propionate-related bacteria, including Spirochaetes, Elusimicrobia, Fibrobacteres, Prevotella, Treponema, Ruminococcus, and Fibrobacter.
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Affiliation(s)
- Kun Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xuemei Nan
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinjin Tong
- Beijing Key Laboratory for Dairy Cow Nutrition, Beijing University of Agriculture, Beijing, China
| | - Guangyong Zhao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Linshu Jiang
- Beijing Key Laboratory for Dairy Cow Nutrition, Beijing University of Agriculture, Beijing, China
| | - Benhai Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Characteristics and Functions of the Rumen Microbial Community of Cattle-Yak at Different Ages. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3482692. [PMID: 32190661 PMCID: PMC7073488 DOI: 10.1155/2020/3482692] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/30/2020] [Accepted: 02/19/2020] [Indexed: 11/18/2022]
Abstract
A cattle-yak, which is a hybrid between a yak (Bos grunniens) and cattle (Bos taurus), is an important livestock animal, but basic questions regarding its physiology and environmental adaptation remain unanswered. To address this issue, the present study examined the species composition and functional characteristics of rumen microorganisms in the cattle-yak of different ages (2 and 3 years old) by metagenomic analysis. We found that rumen microbial community composition was similar at the two ages. Firmicutes, Fibrobacteres, Euryarchaeota, Bacteroidetes, and Proteobacteria were the predominant phyla, with Firmicutes accounting for the highest percentage of bacteria in 2-year-old (48%) and 3-year-old (46%) animals. Bacterial species involved in lignocellulose degradation were detected in the rumen of adult cattle-yaks including Ruminococcus flavefaciens, Ruminococcus albus, Fibrobacter succinogenes, and Prevotella ruminicola, with F. succinogenes being the most abundant. A total of 145,489 genes were annotated according to the Carbohydrate-active Enzyme database, which identified glycoside hydrolases as the most highly represented enzyme family. Further functional annotation revealed specific microflora and genes in the adult rumen that are potentially related to plateau adaptability. These results could explain the heterosis of the cattle-yak and provide insight into mechanisms of physiologic adaptation in plateau animals.
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Neumann AP, Suen G. The Phylogenomic Diversity of Herbivore-Associated Fibrobacter spp. Is Correlated to Lignocellulose-Degrading Potential. mSphere 2018; 3:e00593-18. [PMID: 30541780 PMCID: PMC6291624 DOI: 10.1128/msphere.00593-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 11/29/2018] [Indexed: 12/30/2022] Open
Abstract
Members of the genus Fibrobacter are cellulose-degrading bacteria and common constituents of the gastrointestinal microbiota of herbivores. Although considerable phylogenetic diversity is observed among members of this group, few functional differences explaining the distinct ecological distributions of specific phylotypes have been described. In this study, we sequenced and performed a comparative analysis of whole genomes from 38 novel Fibrobacter strains against the type strains for the two formally described Fibrobacter species F. succinogenes strain S85 and F. intestinalis strain NR9. Significant differences in the number of genes encoding carbohydrate-active enzyme families involved in plant cell wall polysaccharide degradation were observed among Fibrobacter phylotypes. F. succinogenes genomes were consistently enriched in genes encoding carbohydrate-active enzymes compared to those of F. intestinalis strains. Moreover, genomes of F. succinogenes phylotypes that are dominant in the rumen had significantly more genes annotated to major families involved in hemicellulose degradation (e.g., CE6, GH10, and GH43) than did the genomes of F. succinogenes phylotypes typically observed in the lower gut of large hindgut-fermenting herbivores such as horses. Genes encoding a putative urease were also identified in 12 of the Fibrobacter genomes, which were primarily isolated from hindgut-fermenting hosts. Screening for growth on urea as the sole source of nitrogen provided strong evidence that the urease was active in these strains. These results represent the strongest evidence reported to date for specific functional differences contributing to the ecology of Fibrobacter spp. in the herbivore gut.IMPORTANCE The herbivore gut microbiome is incredibly diverse, and a functional understanding of this diversity is needed to more reliably manipulate this community for specific gain, such as increased production in ruminant livestock. Microbial degraders of plant cell wall polysaccharides in the herbivore gut, particularly Fibrobacter spp., are of fundamental importance to their hosts for digestion of a diet consisting primarily of recalcitrant plant fibers. Considerable phylogenetic diversity exists among members of the genus Fibrobacter, but much of this diversity remains cryptic. Here, we used comparative genomics, applied to a diverse collection of recently isolated Fibrobacter strains, to identify a robust association between carbohydrate-active enzyme gene content and the Fibrobacter phylogeny. Our results provide the strongest evidence reported to date for functional differences among Fibrobacter phylotypes associated with either the rumen or the hindgut and emphasize the general significance of carbohydrate-active enzymes in the evolution of fiber-degrading bacteria.
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Affiliation(s)
- Anthony P Neumann
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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11
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Tang Y, Li M, Xu D, Huang J, Sun J. Application potential of aerobic denitrifiers coupled with a biostimulant for nitrogen removal from urban river sediment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:5980-5993. [PMID: 29236243 DOI: 10.1007/s11356-017-0903-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 12/01/2017] [Indexed: 06/07/2023]
Abstract
Aerobic denitrifiers coupled with a denitrification agent were applied in the sediment of an urban river for the bioremediation of nitrogen pollution. The results revealed that 14.7% of the total nitrogen in the sediment was removed after 115 days of treatment and the nitrate nitrogen concentration removal rate was enhanced in the overlying water. Compared with the control, the total transferable nitrogen in the sediment increased from 0.097 to 0.166 mg/g, indicating that more nitrogen is likely to be involved in the biogeochemical cycling of nitrogen. Increased urease activity indicated the possible further potential of nitrogen biodegradation, while the decreased protease pointed to the low concentration of protein remaining in the sediment. Sequencing revealed that the bacterial community diversity in the sediment increased significantly after 43 days of treatment and that the effect persisted. Compared with other microcosms, the dominant phyla in the sediment after 43 days were Firmicutes, Elusimicrobia, Spirochaetae and Fibrobacteres; whereas, after 115 of treatment, the dominant bacteria were Nitrospirae, Deferribacteres and Chloroflexi. The dominant bacteria in the sediment are mainly associated with nitrogen cycling and thus contributed considerably to nitrogen removal in the sediment. Overall, the direction of species succession was similar to natural succession; namely, there were no undesirable ecological risks involved. This study highlights the possible benefits and feasibility of using bioaugmentation technology coupled with biostimulation to remediate nitrogen-polluted sediments.
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Affiliation(s)
- Yinqi Tang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, People's Republic of China
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Meng Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, People's Republic of China
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Danning Xu
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, People's Republic of China
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Jianjun Huang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Jingmei Sun
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, People's Republic of China.
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, 300350, People's Republic of China.
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12
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Neumann AP, McCormick CA, Suen G. Fibrobacter communities in the gastrointestinal tracts of diverse hindgut-fermenting herbivores are distinct from those of the rumen. Environ Microbiol 2017; 19:3768-3783. [PMID: 28752955 PMCID: PMC5599356 DOI: 10.1111/1462-2920.13878] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/20/2017] [Accepted: 07/25/2017] [Indexed: 12/31/2022]
Abstract
The genus Fibrobacter contains cellulolytic bacteria originally isolated from the rumen. Culture-independent investigations have since identified Fibrobacter populations in the gastrointestinal tracts of numerous hindgut-fermenting herbivores, but their physiology is poorly characterized due to few representative axenic cultures. To test the hypothesis that novel Fibrobacter diversity exists in hindgut fermenters, we performed culturing and 16S rRNA gene amplicon sequencing on samples collected from phylogenetically diverse herbivorous hosts. Using a unique approach for recovering axenic Fibrobacter cultures, we isolated 45 novel strains from 11 different hosts. Full-length 16S rRNA gene sequencing of these isolates identified nine discrete phylotypes (cutoff = 0.03%) among them, including several that were only isolated from hindgut-fermenting hosts, and four previously unrepresented by axenic cultures. Our phylogenetic analysis indicated that six of the phylotypes are more closely related to previously described subspecies of Fibrobacter succinogenes, while the remaining three were more closely related to F. intestinalis. Culture-independent bacterial community profiling confirmed that most isolates were representative of numerically dominant phylotypes in their respective samples and strengthened the association of certain phylotypes with either ruminants or hindgut-fermenters. Despite considerable phylogenetic diversity observed among the Fibrobacter strains isolated here, phenotypic characterization suggests a conserved specialization for growth on cellulose.
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Affiliation(s)
- Anthony P. Neumann
- Department of Bacteriology, University of Wisconsin – Madison, Madison, Wisconsin, USA
| | - Caroline A. McCormick
- Department of Bacteriology, University of Wisconsin – Madison, Madison, Wisconsin, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin – Madison, Madison, Wisconsin, USA
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13
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Svartström O, Alneberg J, Terrapon N, Lombard V, de Bruijn I, Malmsten J, Dalin AM, El Muller E, Shah P, Wilmes P, Henrissat B, Aspeborg H, Andersson AF. Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation. ISME JOURNAL 2017; 11:2538-2551. [PMID: 28731473 DOI: 10.1038/ismej.2017.108] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/05/2017] [Accepted: 05/30/2017] [Indexed: 12/25/2022]
Abstract
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.
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Affiliation(s)
- Olov Svartström
- School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Alneberg
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Nicolas Terrapon
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Vincent Lombard
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Ino de Bruijn
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Jonas Malmsten
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden.,Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ann-Marie Dalin
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emilie El Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pranjul Shah
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, 13288 Marseille, France.,INRA, USC 1408 AFMB, 13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Henrik Aspeborg
- School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders F Andersson
- School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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14
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Li W, Han Y, Yuan X, Wang G, Wang Z, Pan Q, Gao Y, Qu Y. Metagenomic analysis reveals the influences of milk containing antibiotics on the rumen microbes of calves. Arch Microbiol 2016; 199:433-443. [DOI: 10.1007/s00203-016-1311-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/11/2016] [Accepted: 10/21/2016] [Indexed: 11/24/2022]
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15
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Abdul Rahman N, Parks DH, Vanwonterghem I, Morrison M, Tyson GW, Hugenholtz P. A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres. Front Microbiol 2016; 6:1469. [PMID: 26779135 PMCID: PMC4704652 DOI: 10.3389/fmicb.2015.01469] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/07/2015] [Indexed: 12/13/2022] Open
Abstract
The Fibrobacteres has been recognized as a bacterial phylum for over a decade, but little is known about the group beyond its environmental distribution, and characterization of its sole cultured representative genus, Fibrobacter, after which the phylum was named. Based on these incomplete data, it is thought that cellulose hydrolysis, anaerobic metabolism, and lack of motility are unifying features of the phylum. There are also contradicting views as to whether an uncultured sister lineage, candidate phylum TG3, should be included in the Fibrobacteres. Recently, chitin-degrading cultured representatives of TG3 were isolated from a hypersaline soda lake, and the genome of one species, Chitinivibrio alkaliphilus, sequenced and described in detail. Here, we performed a comparative analysis of Fibrobacter succinogenes, C. alkaliphilus and eight near or substantially complete Fibrobacteres/TG3 genomes of environmental populations recovered from termite gut, anaerobic digester, and sheep rumen metagenomes. We propose that TG3 should be amalgamated with the Fibrobacteres phylum based on robust monophyly of the two lineages and shared character traits. Polymer hydrolysis, using a distinctive set of glycoside hydrolases and binding domains, appears to be a prominent feature of members of the Fibrobacteres. Not all members of this phylum are strictly anaerobic as some termite gut Fibrobacteres have respiratory chains adapted to the microaerophilic conditions found in this habitat. Contrary to expectations, flagella-based motility is predicted to be an ancestral and common trait in this phylum and has only recently been lost in F. succinogenes and its relatives based on phylogenetic distribution of flagellar genes. Our findings extend current understanding of the Fibrobacteres and provide an improved basis for further investigation of this phylum.
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Affiliation(s)
- Nurdyana Abdul Rahman
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia; Advanced Water Management Center, The University of QueenslandBrisbane, QLD, Australia
| | - Mark Morrison
- Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Translational Research Institute Brisbane, QLD, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia; Genomics and Computational Biology, Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia
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