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Chen W, Chen X, Zhang Y, Wu H, Zhao D. Variation on gut microbiota diversity of endangered red pandas ( Ailurus fulgens) living in captivity acrosss geographical latitudes. Front Microbiol 2024; 15:1420305. [PMID: 39165571 PMCID: PMC11333448 DOI: 10.3389/fmicb.2024.1420305] [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: 04/19/2024] [Accepted: 07/17/2024] [Indexed: 08/22/2024] Open
Abstract
The gut microbiome plays important roles in metabolic and immune system related to the health of host. This study applied non-invasive sampling and 16S rDNA high-throughput sequencing to study the gut microbiota structure of red pandas (Ailurus fulgens) for the first time under different geographical latitudes in captivity. The results showed that the two predominant phyla Firmicutes (59.30%) and Proteobacteria (38.58%) constituted 97.88% of the total microbiota in all the fecal samples from north group (red pandas from Tianjin Zoo and Jinan Zoo) and south group (red pandas from Nanjing Hongshan Forest Zoo). The relative abundance of Cyanobacteria in north group was significantly higher than that in south group. At the genus level, Escherichia-Shigella (24.82%) and Clostridium_sensu_stricto_1 (23.00%) were common dominant genera. The relative abundance of norank_f__norank_o__Chloroplast, Terrisporobacter and Anaeroplasma from south group was significantly higher than that of north group. Alpha and Beta analysis consistently showed significant differences between north group and south group, however, the main functions of intestinal microbiota were basically the same, which play an important role in metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in different environments, and amino acid biosynthesis. The variations in gut microbiota between the northern and southern populations of the same species, both kept in captivity, which are primarily driven by significant differences in climate and diet. These findings provide a deeper understanding of the gut microbiota in red pandas and have important implications for their conservation, particularly in optimizing diet and environmental conditions in captivity.
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Affiliation(s)
| | | | | | - Hong Wu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Dapeng Zhao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, Tianjin, China
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Dai W, Leng H, Li J, Li A, Li Z, Zhu Y, Li X, Jin L, Sun K, Feng J. The role of host traits and geography in shaping the gut microbiome of insectivorous bats. mSphere 2024; 9:e0008724. [PMID: 38509042 PMCID: PMC11036801 DOI: 10.1128/msphere.00087-24] [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: 02/06/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The gut microbiome is a symbiotic microbial community associated with the host and plays multiple important roles in host physiology, nutrition, and health. A number of factors have been shown to influence the gut microbiome, among which diet is considered to be one of the most important; however, the relationship between diet composition and gut microbiota in wild mammals is still not well recognized. Herein, we characterized the gut microbiota of bats and examined the effects of diet, host taxa, body size, gender, elevation, and latitude on the gut microbiota. The cytochrome C oxidase subunit I (COI) gene and 16S rRNA gene amplicons were sequenced from the feces of eight insectivorous bat species in southern China, including Miniopterus fuliginosus, Aselliscus stoliczkanus, Myotis laniger, Rhinolophus episcopus, Rhinolophus osgoodi, Rhinolophus ferrumequinum, Rhinolophus affinis, and Rhinolophus pusillus. The results showed that the composition of gut microbiome and diet exhibited significant differences among bat species. Diet composition and gut microbiota were significantly correlated at the order, family, genus, and operational taxonomic unit levels, while certain insects had a marked effect on the gut microbiome at specific taxonomic levels. In addition, elevation, latitude, body weight of bats, and host species had significant effects on the gut microbiome, but phylosymbiosis between host phylogeny and gut microbiome was lacking. These findings clarify the relationship between gut microbiome and diet and contribute to improving our understanding of host ecology and the evolution of the gut microbiome in wild mammals. IMPORTANCE The gut microbiome is critical for the adaptation of wildlife to the dynamic environment. Bats are the second-largest group of mammals with short intestinal tract, yet their gut microbiome is still poorly studied. Herein, we explored the relationships between gut microbiome and food composition, host taxa, body size, gender, elevation, and latitude. We found a significant association between diet composition and gut microbiome in insectivorous bats, with certain insect species having major impacts on gut microbiome. Factors like species taxa, body weight, elevation, and latitude also affected the gut microbiome, but we failed to detect phylosymbiosis between the host phylogeny and the gut microbiome. Overall, our study presents novel insights into how multiple factors shape the bat's gut microbiome together and provides a study case on host-microbe interactions in wildlife.
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Affiliation(s)
- Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jun Li
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
| | - Aoqiang Li
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zhongle Li
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Yue Zhu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Xiaolin Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
- College of Life Science, Jilin Agricultural University, Changchun, China
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3
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Zhang M, Zhou Y, Cui X, Zhu L. The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis. Microorganisms 2024; 12:713. [PMID: 38674657 PMCID: PMC11051890 DOI: 10.3390/microorganisms12040713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.
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Affiliation(s)
| | | | | | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210098, China; (M.Z.); (Y.Z.); (X.C.)
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4
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Bao Y, Zhao S, Wu N, Yuan Y, Ruan L, He J. Degradation of Atrazine by an Anaerobic Microbial Consortium Enriched from Soil of an Herbicide-Manufacturing Plant. Curr Microbiol 2024; 81:117. [PMID: 38492090 DOI: 10.1007/s00284-024-03624-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 01/23/2024] [Indexed: 03/18/2024]
Abstract
Atrazine is an important herbicide that has been widely used for weed control in recent decades. However, with the extensive use of atrazine, its residue seriously pollutes the environment. Therefore, the microbial degradation and detoxification of atrazine have received extensive attention. To date, the aerobic degradation pathway of atrazine has been well studied; however, little is known about its anaerobic degradation in the environment. In this study, an anaerobic microbial consortium capable of efficiently degrading atrazine was enriched from soil collected from an herbicide-manufacturing plant. Six metabolites including hydroxyatrazine, deethylatrazine, N-isopropylammelide, deisopropylatrazine, cyanuric acid, and the novel metabolite 4-ethylamino-6-isopropylamino-1,3,5-triazine (EIPAT) were identified, and two putative anaerobic degradation pathways of atrazine were proposed: a hydrolytic dechlorination pathway is similar to that seen in aerobic degradation, and a novel pathway initiated by reductive dechlorination. During enrichment, Denitratisoma, Thiobacillus, Rhodocyclaceae_unclassified, Azospirillum, and Anaerolinea abundances significantly increased, dominating the enriched consortium, indicating that they may be involved in atrazine degradation. These findings provide valuable evidence for elucidating the anaerobic catabolism of atrazine and facilitating anaerobic remediation of residual atrazine pollution.
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Affiliation(s)
- Yixuan Bao
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Shiyu Zhao
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Ningning Wu
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Ye Yuan
- Cuiying Honors College, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Luyao Ruan
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jian He
- Department of Microbiology, Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
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Tu W, Nie W, Yao X, Zhang J, Zhang H, Di D, Li Z. Growth performance, lipid metabolism, and systemic immunity of weaned piglets were altered by buckwheat protein through the modulation of gut microbiota. Mol Genet Genomics 2024; 299:15. [PMID: 38411753 DOI: 10.1007/s00438-024-02103-y] [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: 07/04/2023] [Accepted: 11/16/2023] [Indexed: 02/28/2024]
Abstract
Tartary buckwheat protein (BWP) is well known for the wide-spectrum antibacterial activity and the lipid metabolism- regulating property; therefore, BWP can be applied as feed additives to improve the animal's nutritional supply. With the aim to investigate the bioactive actions of the BWP, growth performance, lipid metabolism and systemic immunity of the weaned piglets were measured, and the alterations of pig gut microbiota were also analyzed. According to the results, the growth performances of the weaned piglets which were calculated as the average daily gain (ADG) and the average daily feed intake (ADFI) were significantly increased when compared to the control group. Simultaneously, the serum levels of the total cholesterol (TC), triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C) were decreased, while the levels of high-density lipoprotein cholesterol (HDL-C) were increased in the BWP group. Moreover, the relative abundances of Lactobacillus, Prevotella_9, Subdoligranulum, Blautia, and other potential probiotics in the gut microbiota of weaned piglets were obviously increased in the BWP group. However, the relative abundances of Escherichia-Shigella, Campylobacter, Rikenellaceae_RC9_gut_group and other opportunistic pathogens were obviously decreased in the BWP group. In all, BWP was proved to be able to significantly improve the growth performance, lipid metabolism, and systemic immunity of the weaned piglets, and the specific mechanism might relate to the alterations of the gut microbiota. Therefore, BWP could be explored as a prospective antibiotic alternative for pig feed additives.
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Affiliation(s)
- Weilong Tu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Engineering Research Center of Breeding Pig, Shanghai, 201302, China
| | - Wansen Nie
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, 200241, China
| | - Xiaohui Yao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, 200241, China
| | - Junjie Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, 200241, China
| | - Hailong Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, 200241, China
| | - Di Di
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, 200241, China
| | - Zongjie Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, 200241, China.
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Chen L, Liu B, Ren L, Du H, Fei C, Qian C, Li B, Zhang R, Liu H, Li Z, Ma Z. High-fiber diet ameliorates gut microbiota, serum metabolism and emotional mood in type 2 diabetes patients. Front Cell Infect Microbiol 2023; 13:1069954. [PMID: 36794003 PMCID: PMC9922700 DOI: 10.3389/fcimb.2023.1069954] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/17/2023] [Indexed: 02/01/2023] Open
Abstract
Previous studies have demonstrated that patients with type 2 diabetes mellitus (T2DM) often had the problems of fecal microbiota dysbiosis, and were usually accompanied with psychiatric comorbidities (such as depression and anxiety). Here, we conducted a randomized clinical study to analyze the changes in gut microbiota, serum metabolism and emotional mood of patients with T2DM after consumption of a high-fiber diet. The glucose homeostasis of participants with T2DM was improved by the high-fiber diet, and the serum metabolome, systemic inflammation and psychiatric comorbidities were also altered. The increased abundances of Lactobacillus, Bifidobacterium and Akkermansias revealed that the proportions of beneficial gut microbes were enriched by the high-fiber diet, while the abundances of Desulfovibrio, Klebsiella and other opportunistic pathogens were decreased. Therefore, the current study demonstrated that the intestinal microbiota alterations which were influenced by the high-fiber diet could improve the serum metabolism and emotional mood of patients with T2DM.
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Affiliation(s)
- Lihua Chen
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
| | - Bo Liu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
| | - Lixia Ren
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China
| | - Hao Du
- Department of Gastroenterology, Mental Health Center of Fengxian District, Shanghai, China
| | - Chunhua Fei
- Department of Gastroenterology, Mental Health Center of Fengxian District, Shanghai, China
| | - Chang Qian
- Department of Gastroenterology, Mental Health Center of Fengxian District, Shanghai, China
| | - Bin Li
- Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruixia Zhang
- Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haixia Liu
- Safety & Quality Management Department, Sino-science Yikang (Beijing) Biotech Co., Ltd, Beijing, China
| | - Zongjie Li
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai, China,Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China,*Correspondence: Zongjie Li, ; Zhiyong Ma,
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, China,*Correspondence: Zongjie Li, ; Zhiyong Ma,
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7
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Lv S, Zhang Y, Zhang Z, Meng S, Pu Y, Liu X, Liu L, Ma Y, Liu W, Jiang L. Diversity of the fecal microbiota in Chinese ponies. Front Vet Sci 2023; 10:1102186. [PMID: 36777669 PMCID: PMC9909481 DOI: 10.3389/fvets.2023.1102186] [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: 11/18/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction The gut microbiomes of equine are plentiful and intricate, which plays an important part in the growth. However, there is a relative lack of information on the microbial diversity in the pony's gut. Methods In this article, 118 fecal samples from DeBa pony, NiQi pony and GuZh horse were studied by 16S rRNA amplicon sequencing. Results Diversity analysis was used to determine the difference of gut microbiota composition among different breeds. Alpha diversity analysis showed that the gut microbiota of NiQi ponies were abundant and various. Beta diversity analysis showed that the microorganisms constitution of DeBa ponies was more similar to that of NiQi ponies. LDA Effect Size (LEfSe) analysis result that the microorganism biomarkers for NiQi pony at the genus level were Phascolarctobacterium, Paludibacter, and Fibrobacter; the bacterial biomarker for DeBa pony was Streptococcus and Prevotella; and the bacterial biomarkers for GuZh horses was Treponema, Treponema Mogibacterium, Adlercreutzia, and Blautia. The correlation analysis between genera with >1% abundance and horse height found that Streptococcus (P < 0.01), Treponema (P < 0.01), Coprococcus (P < 0.01), Prevotella (P < 0.01), Phascolarctobacterium (P < 0.01), and Mogibacterium (P < 0.01) were significantly associated with horses' height. The functional prediction results indicated that DeBa pony have a microbiota functional more similar to NiQi pony. Discussion For the first time, our results announce the species composition and structure of the gut microbiota in Chinese ponies. At the same time, our results can provide theoretical reference for further understanding the healthy breeding, feeding management and disease prevention of horses.
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Affiliation(s)
- Shipeng Lv
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China,Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yanli Zhang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Zhengkai Zhang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Sihan Meng
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yabin Pu
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xuexue Liu
- Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Lingling Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Yuehui Ma
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China,*Correspondence: Wujun Liu ✉
| | - Lin Jiang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,Lin Jiang ✉
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Zhuang T, Hu M, Wang J, Mei L, Zhu X, Zhang H, Jin F, Shao J, Wang T, Wang C, Niu X, Wu D. Sodium houttuyfonate effectively treats acute pulmonary infection of Pseudomonas aeruginosa by affecting immunity and intestinal flora in mice. Front Cell Infect Microbiol 2022; 12:1022511. [PMID: 36530439 PMCID: PMC9751016 DOI: 10.3389/fcimb.2022.1022511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/14/2022] [Indexed: 12/04/2022] Open
Abstract
Introduction Pseudomonas aeruginosa is a major nosocomial pathogen that frequently causes ventilator-associated pneumonia in specific populations. Sodium houttuyfonate (SH) has shown mild antibacterial activity against P. aeruginosa in vitro, but the mechanism of potent antimicrobial activity of SH against P. aeruginosa infection in vivo remains unclear. Methods Here, using the mouse pneumonia model induced by P. aeruginosa nasal drip to explore the therapeutic effects of SH. Results We found that SH exhibits dose-dependent therapeutic effects of reducing P. aeruginosa burden and systemic inflammation in pneumonia mice. SH ameliorates inflammatory gene expression and production of inflammatory proteins, such as interleukin-6 (IL-6), nuclear factor kappa-B (NF-κB) and toll-like receptor 4 (TLR4), associated with the TLR4/NF-κB pathway in mice with P. aeruginosa pneumonia. Furthermore, we analyzed the intestinal flora of mice and found that compared with the model group, the abundance and diversity of beneficial bacterial flora of SH treatment groups increased significantly, suggesting that SH can improve the intestinal flora disorder caused by inflammation. In addition, SH improves alpha and beta diversity index and reduces species abundance differences of intestinal flora in pneumonia mice. Discussion Taken together, our presented results indicate that SH may effectively alleviate the acute pulmonary infection induced by P. aeruginosa by reducing the disturbance of regulating immunity and intestinal flora in mice.
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Affiliation(s)
- Tian Zhuang
- Department of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China,Research Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, China
| | - Mengxue Hu
- Department of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China,Research Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, China
| | - Jian Wang
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China,Pathology Department, First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Longfei Mei
- Department of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China,Research Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, China
| | - Xiaoxiao Zhu
- Department of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China,Research Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, China
| | - Haitao Zhang
- Department of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China,Research Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, China
| | - Feng Jin
- Department of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China,Research Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, China
| | - Jing Shao
- Department of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China,Research Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, China,Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Tianming Wang
- Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Changzhong Wang
- Department of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China,Research Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, China,Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Xiaojia Niu
- Department of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China,Research Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, China,Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China,*Correspondence: Daqiang Wu, ; Xiaojia Niu,
| | - Daqiang Wu
- Department of Pathogenic Biology and Immunology, College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China,Key Laboratory of Xin’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, China,*Correspondence: Daqiang Wu, ; Xiaojia Niu,
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9
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Zhan M, Wang A, Yao Y, Zhou Y, Zhang S, Fu X, Zhou J, Pei E, Wang L. An amateur gut microbial configuration formed in giant panda for striving to digest cellulose in bamboo: Systematic evidence from intestinal digestive enzymes, functional genes and microbial structures. Front Microbiol 2022; 13:926515. [PMID: 35958139 PMCID: PMC9363027 DOI: 10.3389/fmicb.2022.926515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/04/2022] [Indexed: 11/14/2022] Open
Abstract
The giant panda has been considered to maximize nutritional intake including protein and soluble carbohydrates in bamboo, but it has spent almost entire life with the high-cellulose diet. Whether giant panda is still helpless about digesting bamboo cellulose or not is always contentious among many researchers around the world. The work has systematically clarified this issue from the perspectives of digestive enzymes, functional genes, and microbial structures in giant panda gut. The intestinal cellulase activities of panda increase with bamboo consumption, performing that the endoglucanase activity of adults reaches 10-fold that of pandas first consuming bamboo. More abundance and types of microbial endoglucanase genes occur in bamboo-diet giant panda gut, and the corresponding GH5 gene cluster is still efficiently transcribed. Gut microbes possessing cellulose-degrading genes, belong to the phylum Firmicutes and some Bacteroidetes, but their structural and functional configurations are insufficient to completely degrade cellulose. Therefore, giant panda is striving to digest cellulose in bamboo, but this adaptation is incomplete. This is probably related to the short straight carnivore-like gut structure of the giant panda, preventing the colonization of some efficient functional but anaerobic-preferred flora.
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Affiliation(s)
- Mingye Zhan
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | | | | | - Yingmin Zhou
- China Conservation and Research Center for the Giant Panda, Dujiangyan, China
| | | | - Xiaohua Fu
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | | | | | - Lei Wang
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
- *Correspondence: Lei Wang,
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Tang S, Li Y, Huang C, Yan S, Li Y, Chen Z, Wu Z. Comparison of Gut Microbiota Diversity Between Captive and Wild Tokay Gecko (Gekko gecko). Front Microbiol 2022; 13:897923. [PMID: 35783386 PMCID: PMC9248866 DOI: 10.3389/fmicb.2022.897923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/11/2022] [Indexed: 11/21/2022] Open
Abstract
Captive animals and wild animals may exhibit different characteristics due to the heterogeneity of their living environments. The gut microbiota play an important role in the digestion and absorption, energy metabolism, immune regulation, and physiological health of the host. However, information about the gut microbiota of captive and wild Gekko gecko is currently limited. To determine the difference in gut microbiota community composition, diversity, and structure between captive and wild geckos, we used the Illumina miseq platform to conduct high-throughput sequencing and bioinformatics analysis of the v3–v4 hypervariable region of 16S rRNA in 54 gecko samples. Our results showed that Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were the dominant gut microbiota phyla of the gecko. The dominant genera comprised mainly Pseudomonas, Burkholderia-caballeronia-paraburkholderia, Ralstonia, Romboutsia, and Bacteroides. Captive geckos had significantly higher alpha diversity and potential pathogenic bacteria than wild populations. Moreover, significant differences in beta diversity of gut microbiota were observed between two populations. Functional prediction analysis showed that the relative abundance of functional pathways of wild geckos was more higher in metabolism, genetic information processing and organismal system function than those in captive geckos. Total length significantly affected gut microbial community (R2 = 0.4527, p = 0.001) and explained 10.45% of the total variation for gut microbial community variance between two groups. These results may be related to differences in diet and living environment between two populations, suggesting that the management of captive populations should mimic wild environments to the greatest extent possible to reduce the impact on their gut microbiota.
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Affiliation(s)
- Sanqi Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Yuhui Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Chengming Huang
- Key Laboratory of Animal Ecology and Conservation, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shufa Yan
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Yongtai Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Zening Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- Zening Chen,
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
- *Correspondence: Zhengjun Wu,
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11
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de Jonge N, Carlsen B, Christensen MH, Pertoldi C, Nielsen JL. The Gut Microbiome of 54 Mammalian Species. Front Microbiol 2022; 13:886252. [PMID: 35783446 PMCID: PMC9246093 DOI: 10.3389/fmicb.2022.886252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiome plays a critical role in many aspects of host life, and the microbial community composition is heavily influenced by the prevailing conditions in the gut environment. Community composition has been suggested to have large implications for conservation efforts, and gut health has become of interest for optimizing animal care in captivity. In this study, we explore the gut microbiome of a wide range of animals in the context of conservation biology. The composition of the gut microbial community of 54 mammalian animal species was investigated using 16S rRNA gene amplicon sequencing. The composition of the gut microbiota clearly reflects diet and the structure of the gastrointestinal system, and it is to a certain degree more similar between closely related animals. Specific clusters of taxa were observed across animals of the same species, diet, and gut morphology. The microbiota retained regardless of captivity status is hypothesized to cover important symbiotic relationships with the host, while the remaining part reflects the artificial living conditions and can therefore be used as a future tool for conservation biologists. For five animal species (giraffes, horses, baboons, elephants, and zebras), it was possible to compare the microbiota of wild and captive individuals. Differences were observed in the proportion of microbiota detected between wild and captive specimens of the same animal species. We propose that the gut microbiota harbours important species, which can potentially serve as indicators for the well-being of the animal and the effect of living in captivity.
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Affiliation(s)
- Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Benjamin Carlsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Cino Pertoldi
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Aalborg Zoo, Aalborg, Denmark
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- *Correspondence: Jeppe Lund Nielsen
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12
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Mink (Neovison vison) fecal microbiomes are influenced by sex, temperature, and time postdefecation. J Mammal 2022. [DOI: 10.1093/jmammal/gyab140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Gut microbiomes encode myriad metabolic functions critical to mammalian ecology and evolution. While fresh fecal samples provide an efficient, noninvasive method of sampling gut microbiomes, collecting fresh feces from elusive species is logistically challenging. Nonfresh feces, however, may not accurately represent the gut microbiome of the host due to succession of gut microbial consortia postdefecation as well as colonization by microbes from the surrounding environment. Using American mink (Neovison vison) as a model species, we examined postdefecation microbial community succession to learn how ambient temperature and temporal sampling constraints influence the reliability of nonfresh feces to represent host gut microbiomes. To achieve our goal, we analyzed fresh mink feces (n = 5 females; n = 5 males) collected at the time of defecation from captive mink at a farm in the Upper Peninsula of Michigan and we subsequently subsampled each fecal specimen to investigate microbial community succession over five days, under both warm (21°C) and cold (–17°C to –1°C) temperature treatments. We found that both temperature and time influenced fecal microbiome composition; and we also detected significant sexual dimorphism in microbial community structures, with female mink microbiomes exhibiting significantly greater variation than males’ when exposed to the warm temperature treatment. Our results demonstrate that feces from unknown individuals can be a powerful tool for examining carnivore gut microbiomes, though rigorous study design is required because sex, ambient temperature, and time since defecation drive significant microbial variation and the sample size requirements necessary for detecting statistically significant differences between target populations is an important consideration for future ecologically meaningful research.
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13
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The diagnostic potential of gut microbiome for early hepatitis B virus-related hepatocellular carcinoma. Eur J Gastroenterol Hepatol 2021; 33:e167-e175. [PMID: 33208683 DOI: 10.1097/meg.0000000000001978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS Gut microbiota is related with hepatocellular carcinoma (HCC). However, the relationship between the gut microbiota and the hepatitis B virus (HBV)-related HCC remains unclear. We aimed to characterize gut microbiome in HBV-related HCC patients and estimate the clinical potential of gut microbiome as biomarkers for HBV-related HCC. METHODS We collected fecal and plasma samples from 20 health controls, 20 HBV-related cirrhosis and 20 HBV-related HCC in the First Affiliated Hospital of Chongqing Medical University. The fecal samples were subjected to the V3-V4 region of 16S rRNA Miseq sequencing. Plasma samples were calculated for interleukin-6 (IL-6), IL-2, IL-8, IL-10, tumor necrosis factor α (TNF-α), aspartate aminotransferase (AST) and alanine aminotransferase (ALT). Then, we analyzed the correlation between the index and the gut microbiota. RESULTS We have found that the bacterial richness of the liver cirrhosis group was lower than the HCC group. The bacterial diversities were in consistent with IL-2. The pro-inflammatory bacteria (Veillonella, Escherichia-shigella) have increased in the liver cirrhosis group. The random forest model has achieved an area under the curve value was 94% with 95% CI, 88-100% between the HCC group and the non-HCC group. The results revealed that IL-2 was highly associated with the whole gut bacterial communities of HCC and liver cirrhosis groups. ALT, AST and glutamyl transpeptidase have strongly elevated in liver cirrhosis and HCC groups, which were associated with gut microbiome. CONCLUSIONS It could be helpful to define the potential bacteria linking to pathological mechanisms of HBV-related HCC. The diagnosis potential of gut microbiome for early HBV-related HCC has been estimated.
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14
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Pan Y, Kang P, Hu J, Song N. Bacterial community demonstrates stronger network connectivity than fungal community in desert-grassland salt marsh. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149118. [PMID: 34332392 DOI: 10.1016/j.scitotenv.2021.149118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
The diversity of soil bacterial and fungal communities is closely related to the soil characteristics and vegetation types in salt marsh ecosystems, but the biogeographic patterns and driving factors in desert-grassland salt marsh (DGSM) are still unclear. In this study, we divided sample plots according to the dominant species in Jiantan Lake wetland of a typical DGSM in Northwestern China. The effects of different environmental factors and halophytes on the structure of soil bacterial and fungal communities were investigated using soil physicochemical characterization and high-throughput sequencing analysis. The diversity of bacterial communities in bulk soil and three dominant halophytes (Kalidium cuspidatum, Nitraria tangutorum and Sophora alopecuroides) were the main factors affecting soil physicochemical properties and halophyte vegetation coverage. Proteobacteria, Bacteroides and Gemmatimonadetes had the highest abundance in bulk soil and the lowest in Sophora alopecuroides sample soil; the opposite was true for Acidobacteria and Chloroflexi. The abundance of Ascomycota in bulk soil and Sophora alopecuroides sample soil was higher than Kalidium cuspidatum and Nitraria tangutorum sample soils, whereas the Mortierellomycota was the highest in Nitraria tangutorum sample soil. Co-occurrence network analysis showed that halophyte cover increased the connectivity and complexity of the bacterial-fungal interaction network, and the halophytic shrub sample soil had a more stable network relationship than the halophytic herb soil. The key taxa of each plot were identified through network relationships. It was found that the keystone taxa of Proteobacteria, Firmicutes, Ascomycota and Chytridiomycota played important roles in maintaining community functions, and most of them were not significantly influenced by soil physicochemical properties. The results of this study provide new insights for a deeper understanding of the halophytes that drive the multifunctionality and stability of soil ecosystems in DGSM.
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Affiliation(s)
- Yaqing Pan
- College of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan 750021, Ningxia, China; Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ministry of Education, Ningxia University, Yinchuan 750021, China
| | - Peng Kang
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan 750021, China; Ningxia Key Laboratory for the Development and Application of Microbial Resources in Extreme Environments, North Minzu University, Yinchuan 750021, China
| | - Jinpeng Hu
- College of Biological Sciences and Engineering, North Minzu University, Yinchuan 750021, China
| | - Naiping Song
- College of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan 750021, Ningxia, China; Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ministry of Education, Ningxia University, Yinchuan 750021, China.
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15
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Zhang W, Liu F, Zhu Y, Han R, Xu L, Liu J. Differing Dietary Nutrients and Diet-Associated Bacteria Has Limited Impact on Spider Gut Microbiota Composition. Microorganisms 2021; 9:2358. [PMID: 34835483 PMCID: PMC8618231 DOI: 10.3390/microorganisms9112358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/18/2022] Open
Abstract
Spiders are a key predator of insects across ecosystems and possess great potential as pest control agents. Unfortunately, it is difficult to artificially cultivate multiple generations of most spider species. Since gut bacterial flora has been shown to significantly alter nutrient availability, it is plausible that the spiders' microbial community plays a key role in their unsuccessful breeding. However, both the gut microbial composition and its influencing factors in many spiders remain a mystery. In this study, the gut microbiota of Campanicola campanulata, specialists who prey on ants and are widely distributed across China, was characterized. After, the impact of diet and diet-associated bacteria on gut bacterial composition was evaluated. First, two species of prey ants (Lasius niger and Tetramorium caespitum) were collected from different locations and fed to C. campanulata. For each diet, we then profiled the nutritional content of the ants, as well as the bacterial communities of both the ants and spiders. Results showed that the protein and carbohydrate content varied between the two prey ant species. We isolated 682 genera from 356 families in the ants (dominant genera including Pseudomonas, Acinetobacter, Paraburkholderia, Staphylococcus, and Novosphingobium), and 456 genera from 258 families in the spiders (dominated by Pseudomonas). However, no significant differences were found in the gut microbiota of spiders that were fed the differing ants. Together, these results indicate that nutritional variation and diet-associated bacterial differences have a limited impact on the microbial composition of spider guts, highlighting that spiders may have a potentially stable internal environment and lay the foundation for future investigations into gut microbiota.
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Affiliation(s)
- Wang Zhang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, Hubei University, Wuhan 430062, China;
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, College of Life Sciences, Hubei University, Wuhan 430062, China; (F.L.); (Y.Z.)
| | - Fengjie Liu
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, College of Life Sciences, Hubei University, Wuhan 430062, China; (F.L.); (Y.Z.)
| | - Yang Zhu
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, College of Life Sciences, Hubei University, Wuhan 430062, China; (F.L.); (Y.Z.)
| | - Runhua Han
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA;
| | - Letian Xu
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, College of Life Sciences, Hubei University, Wuhan 430062, China; (F.L.); (Y.Z.)
| | - Jie Liu
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, Hubei University, Wuhan 430062, China;
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, College of Life Sciences, Hubei University, Wuhan 430062, China; (F.L.); (Y.Z.)
- School of Nuclear Technology and Chemistry, Biology University of Science and Technology, Xianning 437100, China
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16
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Liu R, Shi J, Shultz S, Guo D, Liu D. Fecal Bacterial Community of Allopatric Przewalski's Gazelles and Their Sympatric Relatives. Front Microbiol 2021; 12:737042. [PMID: 34630362 PMCID: PMC8499116 DOI: 10.3389/fmicb.2021.737042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/26/2021] [Indexed: 01/07/2023] Open
Abstract
Mammal gastrointestinal tracts harbor diverse bacterial communities that play important roles in digestion, development, behavior, and immune function. Although, there is an increasing understanding of the factors that affect microbial community composition in laboratory populations, the impact of environment and host community composition on microbiomes in wild populations is less understood. Given that the composition of bacterial communities can be shaped by ecological factors, particularly exposure to the microbiome of other individuals, inter-specific interactions should impact on microbiome community composition. Here, we evaluated inter-population and inter-specific similarity in the fecal microbiota of Przewalski's gazelle (Procapra przewalskii), an endangered endemic ruminant around Qinghai Lake in China. We compared the fecal bacterial communities of three Przewalski's gazelle populations, with those of two sympatric ruminants, Tibetan gazelle (Procapra picticaudata) and Tibetan sheep (Ovis aries). The fecal bacterial community richness (Chao1, ACE) did not vary across the three Przewalski's gazelle populations, nor did the composition vary between species. In contrast, the managed Przewalski's gazelle population had higher bacterial diversity (Shannon and Simpson) and was more similar to its sympatric Tibetan sheep in beta diversity than the wild Przewalski's gazelle populations. These results suggest that ecological factors like host community composition or diet affect Przewalski's gazelle's gastrointestinal bacterial community. The role of bacterial community composition in maintaining gastrointestinal health should be assessed to improve conservation management of endangered Przewalski's gazelle. More broadly, captive breeding and reintroduction efforts may be impeded, where captive management results in dysbiosis and introduction of pathogenic bacteria. In free ranging populations, where wildlife and livestock co-occur, infection by domestic pathogens and diseases may be an underappreciated threat to wild animals.
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Affiliation(s)
- Ruoshuang Liu
- School of Environment, Beijing Normal University, Beijing, China
| | - Jianbin Shi
- School of Environment, Beijing Normal University, Beijing, China
| | - Susanne Shultz
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, United Kingdom
| | - Dongsheng Guo
- Key Laboratory of Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Dingzhen Liu
- Key Laboratory of Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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17
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Yao R, Dai Q, Wu T, Yang Z, Chen H, Liu G, Zhu Y, Qi D, Yang X, Luo W, Gu X, Yang X, Zhu L. Fly-over phylogeny across invertebrate to vertebrate: The giant panda and insects share a highly similar gut microbiota. Comput Struct Biotechnol J 2021; 19:4676-4683. [PMID: 34504662 PMCID: PMC8390952 DOI: 10.1016/j.csbj.2021.08.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/30/2021] [Accepted: 08/16/2021] [Indexed: 01/19/2023] Open
Abstract
Many studies highlight that host phylogeny and diet are the two main factors influencing the animal gut microbiota. However, the internal mechanisms driving the evolution of animal gut microbiota may be more complex and complicated than we previously realized. Here, based on a large-scale meta-analysis of animal gut microbiota (16 s RNA gene data from approximately 1,800 samples; 108 metagenomes) across a wide taxonomic range of hosts, from invertebrate to vertebrate, we found high similarity in the gut microbial community (high proportion of Gammaproteobacteria (Pseudomonas)) of invertebrate insects and vertebrate bamboo-eating pandas (giant panda and red panda), which might be associated their plant-eating behavior and the presence of oxygen in the intestinal tract. A Pseudomonas strain-level analysis using 108 metagenomes further revealed that the response to either host niches or selection by the host might further lead to host-specific strains (or sub-strains) among the different hosts congruent with their evolutionary history. In this study, we uncovered new insights into the current understanding of the evolution of animals and their gut microbiota.
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Affiliation(s)
- Ran Yao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qinlong Dai
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Tonggui Wu
- East China Coastal Forest Ecosystem Long-term Research Station, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou Zhejiang, China
| | | | - Hua Chen
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Guoqi Liu
- Mingke Biotechnology Co., Ltd., Hangzhou, China
| | - Yudong Zhu
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Dunwu Qi
- Chengdu Giant Panda Breeding Center, Chengdu, China
| | - Xu Yang
- Chengdu Xinagai Information Technology Co., Ltd., Chengdu, China
| | - Wei Luo
- Sichuan Liziping National Nature Reserve, Shimian, China
- Shimian Research Center of Giant Panda Small Population Conservation and Rejuvenation, Shimian, China
| | - Xiaodong Gu
- Sichuan Station of Wildlife Survey and Management, Chengdu, China
| | - Xuyu Yang
- Sichuan Station of Wildlife Survey and Management, Chengdu, China
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Corresponding author.
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18
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Song X, Wang H, Xu X. Investigation of microbial contamination in a chicken slaughterhouse environment. J Food Sci 2021; 86:3598-3610. [PMID: 34287883 DOI: 10.1111/1750-3841.15842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 06/04/2021] [Accepted: 06/13/2021] [Indexed: 12/01/2022]
Abstract
The environment in poultry abattoirs is the primary potential source of bacterial contamination and cross-contamination of broiler carcasses. In this context, we explored the influence of chilling water and contact surfaces on the microbial diversity of broiler carcasses in warm and cold seasons. High-throughput sequencing was used to target the V3-V4 region of the 16S rRNA gene. Proteobacteria was the main phylum detected in broiler carcasses and on contact surfaces, whereas Bacteroidetes and Firmicutes had high abundances of the prechilling water in both seasons. At the genus level, Psychrobacter and Acinetobacter were much more abundant on broiler carcasses in the warm season, while Flavobacterium and Psychrobacter dominated in the cold season. LEfSe analysis showed that the chilling tank was a key location where carcass contamination occurred. Therefore, the risk of carcass contamination can be reduced by improving sanitary conditions during processing, installing longer chilling tanks, or increasing the water exchange rate in chilling tanks. The results of this study may be useful for better slaughterhouse environmental hygiene management in different seasons. PRACTICAL APPLICATION: This study will help poultry processing managers better understand the impact of different seasons on the environmental microbiota in the environment and their abundance in poultry processing plants, thus allowing them to adopt proper disinfection strategies for different seasons and environments, further improving the safety and shelf life of products.
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Affiliation(s)
- Xiangyu Song
- Key Laboratory of Animal Products Processing, Ministry of Agriculture, Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Jiangsu Synergetic Innovation Center of Meat Production and Processing, and College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China
| | - Huhu Wang
- Key Laboratory of Animal Products Processing, Ministry of Agriculture, Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Jiangsu Synergetic Innovation Center of Meat Production and Processing, and College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China
| | - Xinglian Xu
- Key Laboratory of Animal Products Processing, Ministry of Agriculture, Key Laboratory of Meat Processing and Quality Control, Ministry of Education, Jiangsu Synergetic Innovation Center of Meat Production and Processing, and College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, P. R. China
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19
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Aricha H, Simujide H, Wang C, Zhang J, Lv W, Jimisi X, Liu B, Chen H, Zhang C, He L, Cui Y, Gao R, Aorigele C. Comparative Analysis of Fecal Microbiota of Grazing Mongolian Cattle from Different Regions in Inner Mongolia, China. Animals (Basel) 2021; 11:ani11071938. [PMID: 34209653 PMCID: PMC8300212 DOI: 10.3390/ani11071938] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Recently, there has been increasing attention focused on the intestinal microflorae of animals due to their critical role in maintaining health and preventing disease. With the improvement of the Chinese national economy and the people’s material standard of living, the beef cattle industry is growing rapidly to meet the growing market demand for beef. Mongolian cattle is a precious genetic resource in China and an excellent cattle breed in Inner Mongolia. However, updated research on topics concerning the gut microbiota of Mongolian cattle are absent. Therefore, this study focused on the differences in the gut microbiota composition of Mongolian cattle in different geographical environments. The gut microbiota composition of the Mongolian cattle from the grasslands was relatively similar, while that from the desert areas was different. The results of this study contribute to our understanding of the influence of geographical factors on the composition of gut microbiota in Mongolian cattle. Abstract Mongolian cattle from China have strong adaptability and disease resistance. We aimed to compare the gut microbiota community structure and diversity in grazing Mongolian cattle from different regions in Inner Mongolia and to elucidate the influence of geographical factors on the intestinal microbial community structure. We used high throughput 16S rRNA sequencing to analyze the fecal microbial community and diversity in samples from 60 grazing Mongolian cattle from Hulunbuir Grassland, Xilingol Grassland, and Alxa Desert. A total of 2,720,545 high-quality reads and sequences that were 1,117,505,301 bp long were obtained. Alpha diversity among the three groups showed that the gut microbial diversity in Mongolian cattle in the grasslands was significantly higher than that in the desert. The dominant phyla were Firmicutes and Bacteroidetes, whereas Verrucomicrobia presented the highest abundance in the gut of cattle in the Alxa Desert. The gut bacterial communities in cattle from the grasslands versus the Alxa Desert were distinctive, and those from the grasslands were closely clustered. Community composition analysis revealed significant differences in species diversity and richness. Overall, the composition of the gut microbiota in Mongolian cattle is affected by geographical factors. Gut microbiota may play important roles in the geographical adaptations of Mongolian cattle.
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Affiliation(s)
- Han Aricha
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.A.); (H.S.); (J.Z.); (X.J.); (B.L.); (H.C.); (C.Z.); (L.H.); (Y.C.)
| | - Huasai Simujide
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.A.); (H.S.); (J.Z.); (X.J.); (B.L.); (H.C.); (C.Z.); (L.H.); (Y.C.)
| | - Chunjie Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.W.); (W.L.); (R.G.)
| | - Jian Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.A.); (H.S.); (J.Z.); (X.J.); (B.L.); (H.C.); (C.Z.); (L.H.); (Y.C.)
| | - Wenting Lv
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.W.); (W.L.); (R.G.)
| | - Xirnud Jimisi
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.A.); (H.S.); (J.Z.); (X.J.); (B.L.); (H.C.); (C.Z.); (L.H.); (Y.C.)
| | - Bo Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.A.); (H.S.); (J.Z.); (X.J.); (B.L.); (H.C.); (C.Z.); (L.H.); (Y.C.)
| | - Hao Chen
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.A.); (H.S.); (J.Z.); (X.J.); (B.L.); (H.C.); (C.Z.); (L.H.); (Y.C.)
| | - Chen Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.A.); (H.S.); (J.Z.); (X.J.); (B.L.); (H.C.); (C.Z.); (L.H.); (Y.C.)
| | - Lina He
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.A.); (H.S.); (J.Z.); (X.J.); (B.L.); (H.C.); (C.Z.); (L.H.); (Y.C.)
| | - Yinxue Cui
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.A.); (H.S.); (J.Z.); (X.J.); (B.L.); (H.C.); (C.Z.); (L.H.); (Y.C.)
| | - Ruijuan Gao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China; (C.W.); (W.L.); (R.G.)
| | - Chen Aorigele
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.A.); (H.S.); (J.Z.); (X.J.); (B.L.); (H.C.); (C.Z.); (L.H.); (Y.C.)
- Correspondence:
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20
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Chen Y, Chen H, Zhong Q, Yun YH, Chen W, Chen W. Determination of Microbial Diversity and Community Composition in Unfermented and Fermented Washing Rice Water by High-Throughput Sequencing. Curr Microbiol 2021; 78:1730-1740. [PMID: 33704531 DOI: 10.1007/s00284-021-02400-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/10/2021] [Indexed: 11/28/2022]
Abstract
Washing rice water (WRW) refers to the sewage produced by rice washing in China and other parts of Asia people's daily life. As in the WRW is rich a variety of nutrients, microorganisms are prone to multiply and pollute the environment. In this article, high-throughput sequencing is used to describe the microbial diversity in different fermentation time WRW. The results showed that the sequencing depth effectively covered the microbial species in the samples, and the bacterial community structure in the samples of WRW at different fermentation periods was rich in diversity. Preominant taxa included Proteobacteria (62%), Firmicutes (28%), approximately Cyanobacteria (10%) and Bacteroidetes (0.5%). The core WRW microbiome comprises Trabulsiella, Pseudomonas, Serratia, Lactobacillus, Erwinia, Enterobacter, Clostridium and Acinetobacter, some of which are potential beneficial microbes. The change of microbial community composition with the change of habitat was assessed. It was found that environmental factors had significant influence on the assembly structure of microbial community.
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Affiliation(s)
- Youlin Chen
- College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou, 570228, China
| | - Haiming Chen
- College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou, 570228, China
| | - Qiuping Zhong
- College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou, 570228, China
| | - Yong-Huan Yun
- College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou, 570228, China
| | - Weijun Chen
- College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou, 570228, China. .,Chunguang Agro-Product Processing Institute, Wenchang, 571333, China.
| | - Wenxue Chen
- College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou, 570228, China.
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21
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Ji S, Pan Y, Zhu L, Tan J, Tang S, Yang Q, Zhang Z, Lou D, Wang B. A novel 7α-hydroxysteroid dehydrogenase: Magnesium ion significantly enhances its activity and thermostability. Int J Biol Macromol 2021; 177:111-118. [PMID: 33592267 DOI: 10.1016/j.ijbiomac.2021.02.082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 10/22/2022]
Abstract
7α-Hydroxysteroid dehydrogenase (7α-HSDH) plays an important role in the efficient biotransformation of taurochenodeoxycholic acid (TCDCA) to tauroursodeoxycholic acid (TUDCA). In this paper, a novel NADP(H)-dependent 7α-HSDH (named J-1-1) was discovered, heterologously expressed in Escherichia coli and biochemically characterized. J-1-1 exhibited high enzymatic activities. The specific activities of J-1-1 toward TCDCA, glycochenodeoxycholic acid (GCDCA) and ethyl benzoylacetate (EBA) were 188.3 ± 0.2, 217.6 ± 0.4, and 20.0 ± 0.2 U·mg-1, respectively, in 50 mM Glycine-NaOH, pH 10.5. Simultaneously, J-1-1 showed high thermostability; 73% of its activity maintained after heat treatment at 40 °C for 100 h. Particularly noteworthy is that magnesium ion could stabilize the structure of J-1-1, resulting in the enhancement of its enzymatic activity and thermostability. The enzymatic activity of J-1-1 increased 40-fold in the presence of 50 mM Mg2+, and T0.5 increased by approximately 6 °C. Furthermore, after heat treatment at 40 °C for 20 min, the control group only retained 52% of the residual enzyme activity, while the residual enzyme activity of the experimental group was still 77% of the J-1-1 enzyme activity with Mg2+ and without heat treatment. These properties of 7α-HSDH would be expected to contribute to more extensive applications in the biotransformation of related substrates.
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Affiliation(s)
- Shunlin Ji
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, PR China
| | - Yinping Pan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, PR China
| | - Liancai Zhu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, PR China; Modern Life Science Experiment Teaching Center, College of Bioengineering, Chongqing University, Chongqing 400030, PR China.
| | - Jun Tan
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological & Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Shijin Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, PR China
| | - Qiong Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, PR China; Chongqing Key Laboratory of Inorganic Special Functional Materials, Collaborative Innovation Center for Green Development in Wuling Mountain Areas, Yangtze Normal University, Chongqing 408100, PR China
| | - Zhi Zhang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, PR China
| | - Deshuai Lou
- Chongqing Key Laboratory of Medicinal Resources in the Three Gorges Reservoir Region, School of Biological & Chemical Engineering, Chongqing University of Education, Chongqing 400067, PR China
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, PR China.
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22
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Sun Y, Song Z, Zhang H, Liu P, Hu X. Seagrass vegetation affect the vertical organization of microbial communities in sediment. MARINE ENVIRONMENTAL RESEARCH 2020; 162:105174. [PMID: 33099080 DOI: 10.1016/j.marenvres.2020.105174] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/11/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Seagrasses represent high primary productivity and provide important ecosystem services to the marine environment. Seagrass-associated microbial communities are playing essential ecological functional roles in biogeochemical cycles. However, little is known about the effect of seagrass vegetation on microbial communities in sediment. In the present study, the sediment cores of seagrass bed (dominated by Zostera japonica and Zostera marine) and degradation area in Swan Lake (China) were sampled; then, biogeochemical parameters were analyzed, and microbial community composition was investigated by using high-throughput sequencing of the 16S rRNA gene. The results showed that the presence of seagrass could lead to a decrease in the richness and diversity of the microbial community. In the vertical direction, a pronounced shift from Proteobacteria-dominated upper layers to Chloroflexi and Crenarchaeota-dominated deep layers in all sediment cores were observed. Besides, Bathyarchaeia is more abundant at degradation area, while Vibrionaceae, Sulfurovum and Lokiarchaeial overrepresent at the seagrass bed area. Vibrionaceae was abundant in the rhizosphere of Z. marina and Z. japonica, and the proportions reached 84.45% and 63.89%, respectively. This enrichment of Vibrio spp. may be caused by the macrobenthic species near the seagrass rhizosphere, and these Vibrio spp. reduced the diversity and stability of microbial community, which may lead to the degradation of seagrass. This study would provide clues for the distribution patterns and niche preferences of seagrass microbiome. The conservation strategy of seagrass would be further elucidated from the perspective of the microbiome.
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Affiliation(s)
- Yanyu Sun
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zenglei Song
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haikun Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China
| | - Pengyuan Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China.
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23
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Wild black bears harbor simple gut microbial communities with little difference between the jejunum and colon. Sci Rep 2020; 10:20779. [PMID: 33247155 PMCID: PMC7695734 DOI: 10.1038/s41598-020-77282-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 11/05/2020] [Indexed: 12/24/2022] Open
Abstract
The gut microbiome (GMB), comprising the commensal microbial communities located in the gastrointestinal tract, has co-evolved in mammals to perform countless micro-ecosystem services to facilitate physiological functions. Because of the complex inter-relationship between mammals and their gut microbes, the number of studies addressing the role of the GMB on mammalian health is almost exclusively limited to human studies and model organisms. Furthermore, much of our knowledge of wildlife-GMB relationships is based on studies of colonic GMB communities derived from the feces of captive specimens, leaving our understanding of the GMB in wildlife limited. To better understand wildlife-GMB relationships, we engaged hunters as citizen scientists to collect biological samples from legally harvested black bears (Ursus americanus) and used 16S rRNA gene amplicon sequencing to characterize wild black bear GMB communities in the colon and jejunum, two functionally distinct regions of the gastrointestinal tract. We determined that the jejunum and colon of black bears do not harbor significantly different GMB communities: both gastrointestinal sites were dominated by Firmicutes and Proteobacteria. However, a number of bacteria were differentially enriched in each site, with the colon harboring twice as many enriched taxa, primarily from closely related lineages.
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24
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Guo X, Lei H, Zhang K, Ke F, Song C. Diversification of animal gut microbes and NRPS gene clusters in some carnivores, herbivores and omnivores. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1835536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Xiurong Guo
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, PR China
| | - Hui Lei
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, PR China
| | - Kailian Zhang
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, PR China
| | - Famin Ke
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, PR China
| | - Can Song
- Department of Microbial and Biochemical Pharmacy, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, PR China
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25
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Cao J, Wang M, Gong C, Amakye WK, Sun X, Ren J. Identification of Microbiota within Aβ Plaque in APP/PS1 Transgenic Mouse. J Mol Neurosci 2020; 71:953-962. [PMID: 33098544 DOI: 10.1007/s12031-020-01715-4] [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: 05/19/2020] [Accepted: 09/17/2020] [Indexed: 10/23/2022]
Abstract
Microbes like viruses, bacteria, and fungi have all been reported in the brain of Alzheimer's postmortem patients and/or AD mouse model; however, the relationship between brain microbes and Aβ plaque deposition remains to be elucidated. In the present study, we first analyzed bacteria populations in the brain of 4-, 5-, and 6-month-old APP/PS1 mice and then examined the Aβ-positive loads of APP/PS1 mouse at 9 months old to identify bacteria in the brain by 16S rDNA sequencing. Finally, blood-brain barrier permeability was measured by injecting dextrans through the tail vein. Surprisingly, the diversity of microbial community gradually decreased in APP/PS1 mouse while wild-type mouse showed no obvious regularity. Moreover, Aβ-positive deposits in the brain showed a significantly higher relative abundance of microbiota than Aβ-negative tissues and age-matched wild-type mouse brain tissues. In addition, an increase in blood-brain barrier permeability was also observed in APP/PS1 mouse. The present study revealed the exact location of microbes within the Aβ plaques in the brain and suggested the potential antimicrobial effect of the Aβ peptide. We strongly recommend that future research on microbiota-related AD pathology should focus on the migration route of microbiota into the brain and how the microbiota enhance AD progression.
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Affiliation(s)
- Jianing Cao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, People's Republic of China
| | - Min Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, People's Republic of China
| | - Congcong Gong
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, People's Republic of China
| | - William Kwame Amakye
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, People's Republic of China
| | - Xiaoyu Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, People's Republic of China
| | - Jiaoyan Ren
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, People's Republic of China. .,, Wushan Road 381, Guangzhou, 510641, China.
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26
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Zhan M, Wang L, Xie C, Fu X, Zhang S, Wang A, Zhou Y, Xu C, Zhang H. Succession of Gut Microbial Structure in Twin Giant Pandas During the Dietary Change Stage and Its Role in Polysaccharide Metabolism. Front Microbiol 2020; 11:551038. [PMID: 33072012 PMCID: PMC7537565 DOI: 10.3389/fmicb.2020.551038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/27/2020] [Indexed: 12/23/2022] Open
Abstract
Adaptation to a bamboo diet is an essential process for giant panda growth, and gut microbes play an important role in the digestion of the polysaccharides in bamboo. The dietary transition in giant panda cubs is particularly complex, but it is an ideal period in which to study the effects of gut microbes on polysaccharide use because their main food changes from milk to bamboo (together with some bamboo shoot and coarse pastry). Here, we used 16S rDNA and internal transcribed spacer 1 (ITS1) DNA sequencing and metagenomic sequencing analysis to investigate the succession of the gut microbial structure in feces sampled from twin giant panda cubs during the completely dietary transition and determine the abundances of polysaccharide-metabolizing genes and their corresponding microbes to better understand the degradation of bamboo polysaccharides. Successive changes in the gut microbial diversity and structure were apparent in the growth of pandas during dietary shift process. Microbial diversity increased after the introduction of supplementary foods and then varied in a complex way for 1.5–2 years as bamboo and complex food components were introduced. They then stabilized after 2 years, when the cubs consumed a specialized bamboo diet. The microbes had more potential to metabolize the cellulose in bamboo than the hemicellulose, providing genes encoding cellulase systems corresponding to glycoside hydrolases (GHs; such as GH1, GH3, GH5, GH8, GH9, GH74, and GH94). The cellulose-metabolizing species (or genes) of gut bacteria was more abundant than that of gut fungi. Although cellulose-metabolizing species did not predominate in the gut bacterial community, microbial interactions allowed the giant pandas to achieve the necessary dietary shift and ultimately adapt to a bamboo diet.
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Affiliation(s)
- Mingye Zhan
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | - Lei Wang
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | - Chunyu Xie
- Shanghai Wild Animal Park Development Co., Ltd., Shanghai, China
| | - Xiaohua Fu
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | | | | | - Yingmin Zhou
- China Conservation and Research Centre for the Giant Panda, Dujiangyan, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park Development Co., Ltd., Shanghai, China
| | - Hemin Zhang
- China Conservation and Research Centre for the Giant Panda, Dujiangyan, China
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27
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Zhang Y, Chen L, Hu M, Kim JJ, Lin R, Xu J, Fan L, Qi Y, Wang L, Liu W, Deng Y, Si J, Chen S. Dietary type 2 resistant starch improves systemic inflammation and intestinal permeability by modulating microbiota and metabolites in aged mice on high-fat diet. Aging (Albany NY) 2020; 12:9173-9187. [PMID: 32452830 PMCID: PMC7288951 DOI: 10.18632/aging.103187] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/17/2020] [Indexed: 12/13/2022]
Abstract
Type 2 resistant starch (RS2) is a fermentable dietary fiber conferring health benefits. We investigated the effects of RS2 on host, gut microbiota, and metabolites in aged mice on high-fat diet. In eighteen-month old mice randomly assigned to control, high-fat (HF), or high-fat+20% RS2 (HFRS) diet for 16 weeks, RS2 reversed the weight gain and hepatic steatosis induced by high-fat diet. Serum and fecal LPS, colonic IL-2 and hepatic IL-4 mRNA expressions decreased while colonic mucin 2 mRNA and protein expressions increased in the HFRS compared to the HF and the control group. 16s rRNA sequencing of fecal microbial DNA demonstrated that RS2 decreased the abundance of pathogen taxa associated with obesity, inflammation, and aging including Desulfovibrio (Proteobacteria phylum), Ruminiclostridium 9, Lachnoclostridium, Helicobacteria, Oscillibacter, Alistipes, Peptococcus, and Rikenella. Additionally, RS2 increased the colonic butyric acid by 2.6-fold while decreasing the isobutyric and isovaleric acid levels by half compared to the HF group. Functional analyses based on Clusters of Orthologous Groups showed that RS2 increased carbohydrate while decreasing amino acid metabolism. These findings demonstrate that RS2 can reverse weight gain, hepatic steatosis, inflammation, and increased intestinal permeability in aged mice on high-fat diet mediated by changes in gut microbiome and metabolites.
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Affiliation(s)
- Yawen Zhang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Luyi Chen
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Mengjia Hu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - John J Kim
- Division of Gastroenterology, Loma Linda University Health, Loma Linda, CA 92354, USA
| | - Renbin Lin
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Jilei Xu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Lina Fan
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Yadong Qi
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Lan Wang
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Weili Liu
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Yanyong Deng
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Jianmin Si
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
| | - Shujie Chen
- Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang Province, China.,Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, Zhejiang Province, China
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28
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Zhang Y, Liang Z, Tang C, Liao W, Yu Y, Li G, Yang Y, An T. Malodorous gases production from food wastes decomposition by indigenous microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137175. [PMID: 32062272 DOI: 10.1016/j.scitotenv.2020.137175] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 06/10/2023]
Abstract
Volatile organic compounds (VOCs) produced during the degradation of food wastes may harm to the health of people and create annoyance in adjacent communities. In this work, the VOCs emitted from the decomposition food wastes including fruit, meat and vegetable, and their microbial communities were measured in three individual 57-L reactors for 61 days. Total of 232.8, 373.5, and 191.1 μg·kg-1·h-1 VOCs with oxygenated VOCs (57.6%), volatile organic sulfur compounds (VOSCs, 58.6%) and VOSCs (54.9%) as the main group were detected during fruit, meat and vegetable fermentation, respectively. 2-Butanone (55.1%) and ethyl acetate (13.8%) were the two most abundant VOCs from fruit wastes, while dimethyl sulfide (68.0 and 26.6%) and dimethyl disulfide (89.2 and 10.1%) were in vegetable and meat wastes. The predominant Firmicutes represented 93.0-99.9% of the bacterial communities of meat decomposition, while Firmicutes and Proteobacteria were the dominant phyla throughout the fruit digestion process. Proteobacteria (16.9%-83.6%) was the dominant phylum in vegetable wastes, followed by Bacteroidetes, Firmicutes, and Actinobacteria. Malodorous VOCs emissions were highly affected by microbial activity, the abundant Weissella, Leuconostoc and Enterobacteriaceae in vegetable wastes showed correlation with carbon disulfide and dimethyl sulfide, while dominant Peptococcus, Bacteroides, Lactobacillales and Peptoniphilus in meat wastes was related to dimethyl disulfide. Overall, significant differences and correlation between VOCs emission profiles and bacterial communities among different food wastes decomposition were observed. These data contribute to a more comprehensive understanding the relationship between microbial community dynamics and malodorous VOCs emission.
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Affiliation(s)
- Yuna Zhang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhishu Liang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Changcheng Tang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Wen Liao
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Yun Yu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Guiying Li
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Synergy Innovation Institute of GDUT, Shantou 515100, China.
| | - Yan Yang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Synergy Innovation Institute of GDUT, Shantou 515100, China
| | - Taicheng An
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
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29
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Growth Kinetics and Spoilage Potential of Co-culturing Acinetobacter johnsonii and Pseudomonas fluorescens from Bigeye Tuna (Thunnus obesus) During Refrigerated Storage. Curr Microbiol 2020; 77:1637-1646. [DOI: 10.1007/s00284-020-01978-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/30/2020] [Indexed: 12/18/2022]
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30
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Guo B, Li D, Zhou B, Jiang Y, Bai H, Zhang Y, Xu Q, Yongzhang, Chen G. Research Note: Effect of diet with different proportions of ryegrass on breast meat quality of broiler geese. Poult Sci 2020; 99:2500-2507. [PMID: 32359586 PMCID: PMC7597400 DOI: 10.1016/j.psj.2019.10.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/13/2019] [Accepted: 10/15/2019] [Indexed: 11/24/2022] Open
Abstract
This study was conducted to determine the effects of diet with different proportions of ryegrass on breast meat quality of geese. In total, 240 healthy male Yangzhou geese (28-day-old) with similar body weight were divided randomly into 4 diet groups (control group: fed commercial diets; treatment groups I, II, and III: fed ryegrass and commercial diet in the ratios of 1.5:1, 2:1, and 3:1, respectively), the birds being fed from the age of 29 to 70 D. The results shows that the body weights of 70-day-old geese of treatment groups II and III were lower than those in the control group, whereas those of geese of treatment group I were similar to those of the control group. The contents of flavor amino acid and total (essential) amino acids in treatment groups I and II were higher than those in treatment group III (P < 0.05). In addition, grass supplementation reduced saturated fatty acid content and increased that of omega-3 (n-3) polyunsaturated fatty acids, relative to the control group (P < 0.05). Finally, among the 6 minerals analyzed in breast muscle, differences existed in Zn, Se, and Cu contents among the geese fed with different proportions of ryegrass. Zn content of geese from treatment groups II and III was significantly higher than that of those of the control group; Cu content was lower with grass intake and was significantly higher in the control group than in treatment group III; Se content was significantly higher in the control group than in both groups II and III (all at P < 0.05). The results from this study indicated that geese fed with low proportions of ryegrass (1.5:1 or 2:1) showed good growth performance and increased total (essential) amino acid, flavor amino acid, n-3 polyunsaturated fatty acid, and Zn content in meat, which had a certain guiding value for the production of high-quality goose meat under intensive feeding conditions.
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Affiliation(s)
- Baodi Guo
- Laboratory of Animal Geneti cs and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, P.R. China
| | - Dianhui Li
- Laboratory of Animal Geneti cs and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, P.R. China
| | - Beibei Zhou
- Laboratory of Animal Geneti cs and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, P.R. China
| | - Yong Jiang
- Laboratory of Animal Geneti cs and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, P.R. China
| | - Hao Bai
- Laboratory of Animal Geneti cs and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, P.R. China
| | - Yang Zhang
- Laboratory of Animal Geneti cs and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, P.R. China
| | - Qi Xu
- Laboratory of Animal Geneti cs and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, P.R. China
| | - Yongzhang
- Waterfowl Institute of Yangzhou, Songqiao 225651, P.R. China
| | - Guohong Chen
- Laboratory of Animal Geneti cs and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, P.R. China.
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Guo W, Chen Y, Wang C, Ning R, Zeng B, Tang J, Li C, Zhang M, Li Y, Ni Q, Ni X, Zhang H, li D, Zhao J, Li Y. The carnivorous digestive system and bamboo diet of giant pandas may shape their low gut bacterial diversity. CONSERVATION PHYSIOLOGY 2020; 8:coz104. [PMID: 32190328 PMCID: PMC7066643 DOI: 10.1093/conphys/coz104] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/16/2019] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
The gut microbiota diversity of eight panda cubs was assessed during a dietary switch.Gut microbiota diversity of panda cubs significantly decreased after bamboo consumption.Carnivorous species living on a plant-based diet possess low microbial diversity.Mice were fed a bamboo diet but did not display low gut microbiota diversity. Giant pandas have an exclusive diet of bamboo; however, their gut microbiotas are more similar to carnivores than herbivores in terms of bacterial composition and their functional potential. This is inconsistent with observations that typical herbivores possess highly diverse gut microbiotas. It is unclear why the gut bacterial diversity of giant pandas is so low. Herein, the dynamic variations in the gut microbiota of eight giant panda cubs were measured using 16S rRNA gene paired-end sequencing during a dietary switch. Similar data from red panda (an herbivorous carnivore) and carnivorous species were compared with that of giant pandas. In addition, mice were fed a high-bamboo diet (80% bamboo and 20% rat feed) to determine whether a bamboo diet could lower the gut bacterial diversity in a non-carnivorous digestive tract. The diversity of giant panda gut microbiotas decreased significantly after switching from milk and complementary food to bamboo diet. Carnivorous species living on a plant-based diet, including giant and red pandas, possess a lower microbial diversity than other carnivore species. Mouse gut microbiota diversity significantly increased after adding high-fibre bamboo to their diet. Findings suggest that a very restricted diet (bamboo) within a carnivorous digestive system might be critical for shaping a low gut bacterial diversity in giant pandas.
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Affiliation(s)
- Wei Guo
- Department of Laboratory Medicine, School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, 783 Xindu Road, Xindu, Chengdu, Sichuan, 610500, China
| | - Yinfeng Chen
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Chengdong Wang
- Department of Feeding, China Conservation and Research Center for the Giant Panda, 155 Xianfeng Road, Ya’an, Sichuan, 611830, China
| | - Ruihong Ning
- Department of Laboratory Medicine, School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, 783 Xindu Road, Xindu, Chengdu, Sichuan, 610500, China
| | - Bo Zeng
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Jingsi Tang
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Caiwu Li
- Department of Feeding, China Conservation and Research Center for the Giant Panda, 155 Xianfeng Road, Ya’an, Sichuan, 611830, China
| | - Mingwang Zhang
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Yan Li
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Qingyong Ni
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Xueqin Ni
- Department of animal medicine, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Hemin Zhang
- Department of Feeding, China Conservation and Research Center for the Giant Panda, 155 Xianfeng Road, Ya’an, Sichuan, 611830, China
| | - Desheng li
- Department of Feeding, China Conservation and Research Center for the Giant Panda, 155 Xianfeng Road, Ya’an, Sichuan, 611830, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, 2404 North University Avenue Little Rock, Fayetteville, Arkansas, 72207, USA
| | - Ying Li
- Department of Animal Science, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, Sichuan, 611130, China
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Rath S, Rud T, Pieper DH, Vital M. Potential TMA-Producing Bacteria Are Ubiquitously Found in Mammalia. Front Microbiol 2020; 10:2966. [PMID: 31998260 PMCID: PMC6964529 DOI: 10.3389/fmicb.2019.02966] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/09/2019] [Indexed: 01/10/2023] Open
Abstract
Human gut bacteria metabolize dietary components such as choline and carnitine to trimethylamine (TMA) that is subsequently oxidized to trimethylamine-N-oxide (TMAO) by hepatic enzymes. Increased plasma levels of TMAO are associated with the development of cardiovascular and renal disease. In this study, we applied gene-targeted assays in order to quantify (qPCR) and characterize (MiSeq) bacterial genes encoding enzymes responsible for TMA production, namely choline-TMA lyase (CutC), carnitine oxygenase (CntA) and betaine reductase (GrdH) in 89 fecal samples derived from various mammals spanning three dietary groups (carnivores, omnivores and herbivores) and four host orders (Carnivora, Primates, Artiodactyla and Perissodactyla). All samples contained potential TMA-producing bacteria, however, at low abundances (<1.2% of total community). The cutC gene was more abundant in omnivores and carnivores compared with herbivores. CntA was almost absent from herbivores and grdH showed lowest average abundance of all three genes. Bacteria harboring cutC and grdH displayed high diversities where sequence types affiliated with various taxa within Firmicutes dominated, whereas cntA comprised sequences primarily linked to Escherichia. Composition of TMA-forming communities was strongly influenced by diet and host taxonomy and despite their high correlation, both factors contributed uniquely to community structure. Furthermore, Random Forest (RF) models could differentiate between groups at high accuracies. This study gives a comprehensive overview of potential TMA-producing bacteria in the mammalian gut demonstrating that both diet and host taxonomy govern their abundance and composition. It highlights the role of functional redundancy sustaining potential TMA formation in distinct gut environments.
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Affiliation(s)
- Silke Rath
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tatjana Rud
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marius Vital
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
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Guo B, Li D, Zhou B, Jiang Y, Bai H, Zhang Y, Xu Q, Zhao W, Chen G. Comparative characterization of bacterial communities in geese consuming of different proportions of ryegrass. PLoS One 2019; 14:e0223445. [PMID: 31652267 PMCID: PMC6814310 DOI: 10.1371/journal.pone.0223445] [Citation(s) in RCA: 18] [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: 04/22/2019] [Accepted: 09/20/2019] [Indexed: 12/16/2022] Open
Abstract
Geese are extremely well-adapted to utilizing plant-derived roughage in their diet, so the grass must be added to commercial diets under intensive rearing systems. However, it is unclear whether the gut microbiota will change significantly when adding different proportions of ryegrass. In this study, 240 healthy male Yangzhou geese (28 days old) with similar body weights were randomly divided into four groups and fed different proportions grass (CK, whole commercial diets; EG1, ryegrass: commercial diets = 1.5:1; EG2, ryegrass: commercial diets = 2:1; EG3, ryegrass: commercial diets = 3:1) respectively. When the geese grew to 70 days old, their intestines were collected and high-throughput sequencing technology was performed to investigate the microbial diversity in the caecum of geese with different dietary supplements. There was no obvious change in the alpha diversity of gut microbiota of geese with ryegrass intake (P > 0.05) and the composition of dominant bacterium (including Bacteroidetes and Firmicutes) was also similar. However, the ratio between Firmicutes and Bacteroidetes was remarkably reduced with ryegrass intake (P < 0.05), and the relative abundance of 30 operational taxonomic units (OTUs) significantly differed. Additionally, the content of cellulose-degrading microbiota such as Ruminiclostridium and Ruminococcaceae UCG-010 were significantly increased in geese fed with increasing amounts of grass. Finally, the functional profiles of the goose gut microbiota were explored using the PICRUSt tool. Carbohydrate metabolism and amino acid metabolism were dominant metabolic pathways. Lipid metabolism was significantly increased in EG3 compared that in the CK group (P < 0.05). Interestingly, Turicibacter and Parasutterella may have affected abdominal fat deposition as grass intake increased. Taken together, although the diversity of bacterial communities was similar in geese fed with different proportions of ryegrass, cellulose-degrading microbiota (Ruminiclostridium and Ruminococcaceae UCG-010) were abundant and the lipid metabolic pathway was enriched, which may reduce abdominal fat accumulation in high-ryegrass fed geese.
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Affiliation(s)
- Baodi Guo
- Laboratory of Animal Genetics and Rearing and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, PR, China
| | - Dianhui Li
- Laboratory of Animal Genetics and Rearing and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, PR, China
| | - Beibei Zhou
- Laboratory of Animal Genetics and Rearing and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, PR, China
| | - Yong Jiang
- Laboratory of Animal Genetics and Rearing and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, PR, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Jiangsu Yangzhou, China
| | - Yang Zhang
- Laboratory of Animal Genetics and Rearing and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, PR, China
| | - Qi Xu
- Laboratory of Animal Genetics and Rearing and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, PR, China
| | - Wenming Zhao
- Laboratory of Animal Genetics and Rearing and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, PR, China
| | - Guohong Chen
- Laboratory of Animal Genetics and Rearing and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, PR, China
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Wang H, Qin X, Mi S, Li X, Wang X, Yan W, Zhang C. Contamination of yellow-feathered broiler carcasses: Microbial diversity and succession during processing. Food Microbiol 2019; 83:18-26. [DOI: 10.1016/j.fm.2019.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 12/22/2022]
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Comparative analysis of the gut microbiota of the blue fox (Alopex lagopus) and raccoon dog (Nyctereutes procyonoides). Arch Microbiol 2019; 202:135-142. [PMID: 31535158 DOI: 10.1007/s00203-019-01721-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 07/27/2019] [Accepted: 08/27/2019] [Indexed: 12/28/2022]
Abstract
The goal of this study is to compare the gut microbiota of domestic blue fox (Alopex lagopus) and raccoon dog (Nyctereutes procyonoides) to provide better understanding of their intestinal gut microbiota. We analyzed the structure of fecal microbes in 40 blue foxes and 40 raccoon dogs that were raised under same conditions, using high-throughput Illumina sequencing targeting the V3-V4 region of the 16S rRNA gene. In total, 295,146 sequence reads were obtained. The average number of operational taxonomical units in the two group samples was 194 to 286. Firmicutes (blue fox 73.40%, raccoon dog 46.90%) and Bacteroidetes (blue fox 21.92%, raccoon dog 44.25%) were the most abundant phyla in the gut of blue fox and raccoon dog. At the genus level, Prevotella (blue fox 16.89%, raccoon dog 36.22%), Blautia (blue fox 9.02%, raccoon dog 13.72%), and Peptostreptococcaeae_incertae_sedi (blue fox 22.41%, raccoon dog 2.84%) were commonly presented in the gut of two kinds of animal. Principal coordinates analysis showed that the microbial communities were different between blue fox and raccoon dog. The Firmicutes-to-Bacteroidetes ratio was higher in blue foxes (3:1) than in raccoon dogs (1:1). Moreover, Peptostreptococcaeae_incertae_sedi and Prevotella, were more abundant in the gut of blue fox, whereas the abundance of Prevotella and Blautia were higher in the gut of raccoon dog. In conclusion, the present study revealed the difference of the gut microbial composition between blue fox and raccoon dog under the same diet conditions.
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Yao R, Yang Z, Zhang Z, Hu T, Chen H, Huang F, Gu X, Yang X, Lu G, Zhu L. Are the gut microbial systems of giant pandas unstable? Heliyon 2019; 5:e02480. [PMID: 31687574 PMCID: PMC6819816 DOI: 10.1016/j.heliyon.2019.e02480] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/11/2019] [Accepted: 09/12/2019] [Indexed: 12/29/2022] Open
Abstract
Animals have stable dominant gut microbiomes under similar diets. Similar diets can also lead to similar gut microbial communities within host species levels. Giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens) have had long-term and stable bamboo diets, and seem well adapted to this highly fibrous diet. When compared to the gut microbiomes of Père David's deer (Elaphurus davidianus), humans, cheetah (Acinonyx jubatus), black-backed jackal (Canis-mesomelas), and black bear (Ursus thibetanus), giant panda gut microbiomes have high variation in the abundance of Pseudomonadaceae and Clostridiaceae, and are somewhat unstable. This high instability and dissimilarity may reflect an unstable gut environment, perturbation or selective pressure because of their carnivorous gastrointestinal system. A short digestive tract, brief digestion time and fast intestinal peristalsis may result in higher oxygen concentrations that select for the growth of aerobes and facultative anaerobes in giant pandas. Potential selection of high proportion of Pseudomonadaceae in giant panda (GP-HP) and red panda gut microbiomes may arise because of their postulated ability to degrade secondary compounds (e.g., cyanide compounds and aromatic compounds). However, high proportion of Clostridiaceae (GP-HF) may focus on cellulose and hemicellulose digestion. Thus, GP-HP and GP-HF groups have high dissimilarity on the functional level. These findings show that long-term similarities in diet do not always lead to similar or stable gut microbial system within the same host species and that other factors can drive the selection of gut taxa.
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Affiliation(s)
- Ran Yao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zhisong Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637002, China
| | - Zheng Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ting Hu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Hua Chen
- Shanghai Biozeron Bioinfmatics Center, Shanghai, 201800, China
| | - Feng Huang
- Sichuan Lizhiping Giant Panda National Nature Reserve, Shimian, China
| | - Xiaodong Gu
- Sichuan Station of Wild Life Survey and Management, Chengdu, 610082, China
| | - Xuyu Yang
- Sichuan Station of Wild Life Survey and Management, Chengdu, 610082, China
| | - Guoqing Lu
- University of Nebraska at Omaha, Omaha, USA
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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Watson SE, Hauffe HC, Bull MJ, Atwood TC, McKinney MA, Pindo M, Perkins SE. Global change-driven use of onshore habitat impacts polar bear faecal microbiota. ISME JOURNAL 2019; 13:2916-2926. [PMID: 31378786 DOI: 10.1038/s41396-019-0480-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 07/04/2019] [Accepted: 07/11/2019] [Indexed: 12/16/2022]
Abstract
The gut microbiota plays a critical role in host health, yet remains poorly studied in wild species. Polar bears (Ursus maritimus), key indicators of Arctic ecosystem health and environmental change, are currently affected by rapid shifts in habitat that may alter gut homeostasis. Declining sea ice has led to a divide in the southern Beaufort Sea polar bear subpopulation such that an increasing proportion of individuals now inhabit onshore coastal regions during the open-water period ('onshore bears') while others continue to exhibit their typical behaviour of remaining on the ice ('offshore bears'). We propose that bears that have altered their habitat selection in response to climate change will exhibit a distinct gut microbiota diversity and composition, which may ultimately have important consequences for their health. Here, we perform the first assessment of abundance and diversity in the faecal microbiota of wild polar bears using 16S rRNA Illumina technology. We find that bacterial diversity is significantly higher in onshore bears compared to offshore bears. The most enriched OTU abundance in onshore bears belonged to the phylum Proteobacteria, while the most depleted OTU abundance within onshore bears was seen in the phylum Firmicutes. We conclude that climate-driven changes in polar bear land use are associated with distinct microbial communities. In doing so, we present the first case of global change mediated alterations in the gut microbiota of a free-roaming wild animal.
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Affiliation(s)
- Sophie E Watson
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, UK. .,Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, TN, Italy.
| | - Heidi C Hauffe
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, TN, Italy
| | - Matthew J Bull
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, UK.,Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, TN, Italy
| | - Todd C Atwood
- United States Geological Survey (USGS), University Drive, Anchorage, AK, USA
| | - Melissa A McKinney
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Massimo Pindo
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all' Adige, TN, Italy
| | - Sarah E Perkins
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, UK.,Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, TN, Italy
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Zhou D, Jing T, Chen Y, Wang F, Qi D, Feng R, Xie J, Li H. Deciphering microbial diversity associated with Fusarium wilt-diseased and disease-free banana rhizosphere soil. BMC Microbiol 2019; 19:161. [PMID: 31299891 PMCID: PMC6626388 DOI: 10.1186/s12866-019-1531-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 06/26/2019] [Indexed: 11/18/2022] Open
Abstract
Background Fusarium wilt of banana (Musa spp.) caused by the fungal pathogen Fusarium oxysporum f. sp. cubense (Foc) is a typical soilborne disease, that severely devastates the banana industry worldwide, and soil microbial diversity is closely related to the spread of Fusarium wilt. To understand the relationship between microbial species and Fusarium wilt, it is important to understand the microbial diversity of the Fusarium wilt-diseased and disease-free soils from banana fields. Results Based on sequencing analysis of the bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) sequences, Foc abundance, fungal or bacterial richness and diversity were higher in the diseased soils than in the disease-free soils. Although Ascomycota and Zygomycota were the most abundant fungi phyla in all soil samples, Ascomycota abundance was significantly reduced in the disease-free soils. Mortierella (36.64%) was predominant in the disease-free soils. Regarding bacterial phyla, Proteobacteria, Acidobacteria, Chloroflexi, Firmicutes, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Nitrospirae, Verrucomicrobia and Planctomycetes were dominant phyla in all soil samples. In particular, Firmicutes contributed 16.20% of the total abundance of disease-free soils. At the bacterial genus level, Bacillus, Lactococcus and Pseudomonas were abundant in disease-free soils with abundances of 8.20, 5.81 and 2.71%, respectively; lower abundances, of 4.12, 2.35 and 1.36%, respectively, were found in diseased soils. The distribution characteristics of fungal and bacterial genera may contribute to the abundance decrease of Foc in the disease-free soils. Conclusion Unique distributions of bacteria and fungi were observed in the diseased and disease-free soil samples from banana fields. These specific genera are useful for constructing a healthy microbial community structure of soil.
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Affiliation(s)
- Dengbo Zhou
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Tao Jing
- Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Yufeng Chen
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Fei Wang
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Dengfeng Qi
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Renjun Feng
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Jianghui Xie
- Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.
| | - Huaping Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
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Xia Y, Kong J, Zhang G, Zhang X, Seviour R, Kong Y. Effects of dietary supplementation with lysozyme on the structure and function of the cecal microbiota in broiler chickens. PLoS One 2019; 14:e0216748. [PMID: 31216277 PMCID: PMC6583987 DOI: 10.1371/journal.pone.0216748] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/27/2019] [Indexed: 02/07/2023] Open
Abstract
Lysozyme is known to eliminate intestinal pathogens in poultry and improve their growth performance. However, whether it can replace antibiotic growth promoters without the associated risk of the emergence of antibiotic-resistant bacterial strains is not known, and the effects of lysozyme supplementation on the composition, biodiversity, and function of the chicken gut microbiota remain unclear. Here, we used the 16S rRNA gene and ITS fragment Illumina sequencing combined with transcriptomic analysis to address this issue. A total of 400 1-d-old Di Gao chicks were allocated randomly to five groups, each consisting of four replicates (20 birds/group). The chicks were fed a starter (1–21 d) and a grower (22–42 d) diet supplemented with 0 (control), 40 (LYS40), 100 (LYS100), or 200 ppm (LYS200) lysozyme, or 400 ppm flavomycin as an antibiotic control for 6 weeks. Lysozyme administration did not contribute significantly (P > 0.05) to the growth of the broiler chickens. No significant (P > 0.05) differences in the diversity and composition of the bacterial and fungal communities in the cecal microbiota of chickens in the different diet groups were found. However, lysozyme supplementation led to a significant (P < 0.05) enrichment of genes involved in the synthesis/degradation of bacterial outer membranes and cell walls, cross-cell substrate transport, and carbohydrate metabolic processes, thus possibly promoting the cecal microbiota carbon and energy metabolism. Bacteroides contributed 31.9% of glycoside hydrolase genes (17,681–24,590), 26.1% of polysaccharide lyase genes (479–675), 20.7% of carbohydrate esterase genes (3,509–4,101), 8.8% of auxiliary activity genes (705–1,000), 16.2% of glycosyltransferase genes (5,301–6,844), and 13.9% of carbohydrate-binding module genes (8838–15,172) identified in the cecal samples. Thus, they were the main players in the breakdown of non-starch polysaccharides in the cecum, although Parabacteroides, Alistipes, Prevotella, Clostridium, Blastocystis, Barnesiella, Blautia, Faecalibacterium, Subdoligranulum, Megamonas, Eubacterium, Ruminococcus, Paenibacillus, Bifidobacterium, Akkermansia, and other bacteria also participated.
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Affiliation(s)
- Yun Xia
- Department of Life Science and Technology, Kunming University, Kunming, China
- * E-mail: (YK); (YX)
| | - James Kong
- Computer Science, York University, York, Canada
| | - Guobing Zhang
- Department of Life Science and Technology, Kunming University, Kunming, China
| | - Xuxiang Zhang
- First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Robert Seviour
- Microbiology Department, La Trobe University, Bundoora, Victoria, Australia
| | - Yunhong Kong
- Department of Life Science and Technology, Kunming University, Kunming, China
- * E-mail: (YK); (YX)
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40
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Do different livestock dwellings on single grassland share similar faecal microbial communities? Appl Microbiol Biotechnol 2019; 103:5023-5037. [PMID: 31055653 DOI: 10.1007/s00253-019-09849-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/25/2019] [Accepted: 04/11/2019] [Indexed: 12/27/2022]
Abstract
Huge numbers of microorganisms reside in livestock faeces and constitute one of the most complex microbial ecosystems. Here, faecal microbial communities of three typical livestock in Xilingol steppe grassland, i.e. sheep, cattle, and horse, were investigated by Illumina MiSeq sequencing and quantitative real-time polymerase chain reaction (qPCR). Firmicutes and Bacteroidetes comprised the majority of bacterial communities in three livestock faeces. Sordariomycetes, Leotiomycetes, and Dothideomycetes were dominant in fungal communities, as well as Methanobacteria and Methanomicrobia were dominant in archaeal communities in three livestock faeces. Similar fungal community dominated in these samples, with 95.51% of the sequences falling into the overlap of three livestock faeces. In contrast, bacterial communities were quite variable among three different livestock faeces, but a similar community was observed in sheep and cattle faeces. Nearly all the archaea were identified as methanogens, whilst the most diverse and abundant methanogens were detected in cattle faeces. Potential pathogens including Bacteroides spp., Desulfovibrio spp., and Fusarium spp. were also detected in livestock faeces. Overall, this study provides the first detailed microbial comparison of typical livestock faeces dwelling on single grassland, and may be help guide management strategies for livestock grazing and grassland restoration.
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41
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Zhang B, Ren J, Yang D, Liu S, Gong X. Comparative analysis and characterization of the gut microbiota of four farmed snakes from southern China. PeerJ 2019; 7:e6658. [PMID: 30956901 PMCID: PMC6442672 DOI: 10.7717/peerj.6658] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/22/2019] [Indexed: 12/26/2022] Open
Abstract
Background The gut microbiota plays an important role in host immunity and metabolic homeostasis. Although analyses of gut microbiotas have been used to assess host health and foster disease prevention and treatment, no comparative comprehensive study, assessing gut microbiotas among several species of farmed snake, is yet available. In this study, we characterized and compared the gut microbiotas of four species of farmed snakes (Naja atra, Ptyas mucosa, Elaphe carinata, and Deinagkistrodon acutus) using high-throughput sequencing of the 16S rDNA gene in southern China and tested whether there was a relationship between gut microbiotal composition and host species. Results A total of 629 operational taxonomic units across 22 samples were detected. The five most abundant phyla were Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Actinobacteria, while the five most abundant genera were Bacteroides, Cetobacterium, Clostridium, Plesiomonas, and Paeniclostridium. This was the first report of the dominance of Fusobacteria and Cetobacterium in the snake gut. Our phylogenetic analysis recovered a relatively close relationship between Fusobacteria and Bacteroidetes. Alpha diversity analysis indicated that species richness and diversity were highest in the gut microbiota of D. acutus and lowest in that of E. carinata. Significant differences in alpha diversity were detected among the four farmed snake species. The gut microbiotas of conspecifics were more similar to each other than to those of heterospecifics. Conclusion This study provides the first comparative study of gut microbiotas among several species of farmed snakes, and provides valuable data for the management of farmed snakes. In farmed snakes, host species affected the species composition and diversity of the gut microbiota.
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Affiliation(s)
- Bing Zhang
- Institute of Wildlife Conservation, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Jing Ren
- Institute of Wildlife Conservation, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Daode Yang
- Institute of Wildlife Conservation, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Shuoran Liu
- Institute of Wildlife Conservation, Central South University of Forestry and Technology, Changsha, Hunan, China.,Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
| | - Xinguo Gong
- Qiyang Gong Xinguo Breeding Co., Ltd, Yongzhou, Hunan, China
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42
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Yang S, Gao X, Meng J, Zhang A, Zhou Y, Long M, Li B, Deng W, Jin L, Zhao S, Wu D, He Y, Li C, Liu S, Huang Y, Zhang H, Zou L. Metagenomic Analysis of Bacteria, Fungi, Bacteriophages, and Helminths in the Gut of Giant Pandas. Front Microbiol 2018; 9:1717. [PMID: 30108570 PMCID: PMC6080571 DOI: 10.3389/fmicb.2018.01717] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/10/2018] [Indexed: 11/13/2022] Open
Abstract
To obtain full details of gut microbiota, including bacteria, fungi, bacteriophages, and helminths, in giant pandas (GPs), we created a comprehensive microbial genome database and used metagenomic sequences to align against the database. We delineated a detailed and different gut microbiota structures of GPs. A total of 680 species of bacteria, 198 fungi, 185 bacteriophages, and 45 helminths were found. Compared with 16S rRNA sequencing, the dominant bacterium phyla not only included Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria but also Cyanobacteria and other eight phyla. Aside from Ascomycota, Basidiomycota, and Glomeromycota, Mucoromycota, and Microsporidia were the dominant fungi phyla. The bacteriophages were predominantly dsDNA Myoviridae, Siphoviridae, Podoviridae, ssDNA Inoviridae, and Microviridae. For helminths, phylum Nematoda was the dominant. In addition to previously described parasites, another 44 species of helminths were found in GPs. Also, differences in abundance of microbiota were found between the captive, semiwild, and wild GPs. A total of 1,739 genes encoding cellulase, β-glucosidase, and cellulose β-1,4-cellobiosidase were responsible for the metabolism of cellulose, and 128,707 putative glycoside hydrolase genes were found in bacteria/fungi. Taken together, the results indicated not only bacteria but also fungi, bacteriophages, and helminths were diverse in gut of giant pandas, which provided basis for the further identification of role of gut microbiota. Besides, metagenomics revealed that the bacteria/fungi in gut of GPs harbor the ability of cellulose and hemicellulose degradation.
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Affiliation(s)
- Shengzhi Yang
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xin Gao
- Department of Nutrition and Food Science, University of Maryland, College Park, College Park, MD, United States
| | - Jianghong Meng
- Department of Nutrition and Food Science, University of Maryland, College Park, College Park, MD, United States
| | - Anyun Zhang
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Yingmin Zhou
- The China Conservation and Research Center for the Giant Panda, Wolong, China
| | - Mei Long
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Bei Li
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Wenwen Deng
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Lei Jin
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Siyue Zhao
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Daifu Wu
- The China Conservation and Research Center for the Giant Panda, Wolong, China
| | - Yongguo He
- The China Conservation and Research Center for the Giant Panda, Wolong, China
| | - Caiwu Li
- The China Conservation and Research Center for the Giant Panda, Wolong, China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya’an, China
| | - Yan Huang
- The China Conservation and Research Center for the Giant Panda, Wolong, China
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), Wolong, China
| | - Hemin Zhang
- The China Conservation and Research Center for the Giant Panda, Wolong, China
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park (China Conservation and Research Center of Giant Panda), Wolong, China
| | - Likou Zou
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
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43
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Wang W, Liu Y, Yang Y, Wang A, Sharshov K, Li Y, Cao M, Mao P, Li L. Comparative analyses of the gut microbiota among three different wild geese species in the genus Anser. J Basic Microbiol 2018; 58:543-553. [PMID: 29668076 DOI: 10.1002/jobm.201800060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 03/27/2018] [Accepted: 04/02/2018] [Indexed: 12/31/2022]
Abstract
In this study, we characterized for the first time the gut microbiota of Greylag geese (Anser anser) using high-throughput 16S rRNA gene sequencing technology. The results showed that the phyla Firmicutes (78.55%), Fusobacteria (9.38%), Proteobacteria (7.55%), Bacteroidetes (1.82%), Cyanobacteria (1.44%), and Actinobacteria (0.61%) dominated the gut microbial communities in the Greylag geese. Then, the variations of gut microbial community structures and functions among the three geese species, Greylag geese, Bar-headed geese (Anser indicus), and Swan geese (Anser cygnoides), were explored. The greatest gut microbial diversity was found in Bar-headed geese group, while other two groups had the least. The dominant bacterial phyla across all samples were Firmicutes and Proteobacteria, but several characteristic bacterial phyla and genera associated with each group were also detected. At all taxonomic levels, the microbial community structure of Swan geese was different from those of Greylag geese and Bar-headed geese, whereas the latter two groups were less different. Functional KEGG categories and pathways associated with carbohydrate metabolism, energy metabolism, and amino acid metabolism were differentially expressed among different geese species. Taken together, this study could provide valuable information to the vast, and yet little explored, research field of wild birds gut microbiome.
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Affiliation(s)
- Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, Qinghai Province, China
| | - Yingbao Liu
- College of Life Science, Yangtze University, Jingzhou, Hubei Province, China
| | - Yongsheng Yang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, Qinghai Province, China
| | - Aizhen Wang
- College of Eco-Environmental Engineering, Qinghai University, Xi'ning, Qinghai Province, China
| | - Kirill Sharshov
- Research Institute of Experimental and Clinical Medicine, Novosibirsk, Russia
| | - Yao Li
- College of Eco-Environmental Engineering, Qinghai University, Xi'ning, Qinghai Province, China
| | - Mengyao Cao
- KunLun College of Qinghai University, Xi'ning, Qinghai Province, China
| | - Puzhen Mao
- KunLun College of Qinghai University, Xi'ning, Qinghai Province, China
| | - Laixing Li
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, Qinghai Province, China
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Guo W, Mishra S, Zhao J, Tang J, Zeng B, Kong F, Ning R, Li M, Zhang H, Zeng Y, Tian Y, Zhong Y, Luo H, Liu Y, Yang J, Yang M, Zhang M, Li Y, Ni Q, Li C, Wang C, Li D, Zhang H, Zuo Z, Li Y. Metagenomic Study Suggests That the Gut Microbiota of the Giant Panda ( Ailuropoda melanoleuca) May Not Be Specialized for Fiber Fermentation. Front Microbiol 2018; 9:229. [PMID: 29503636 PMCID: PMC5820910 DOI: 10.3389/fmicb.2018.00229] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/30/2018] [Indexed: 11/13/2022] Open
Abstract
Bamboo-eating giant panda (Ailuropoda melanoleuca) is an enigmatic species, which possesses a carnivore-like short and simple gastrointestinal tract (GIT). Despite the remarkable studies on giant panda, its diet adaptability status continues to be a matter of debate. To resolve this puzzle, we investigated the functional potential of the giant panda gut microbiome using shotgun metagenomic sequencing of fecal samples. We also compared our data with similar data from other animal species representing herbivores, carnivores, and omnivores from current and earlier studies. We found that the giant panda hosts a bear-like gut microbiota distinct from those of herbivores indicated by the metabolic potential of the microbiome in the gut of giant pandas and other mammals. Furthermore, the relative abundance of genes involved in cellulose- and hemicellulose-digestion, and enrichment of enzymes associated with pathways of amino acid degradation and biosynthetic reactions in giant pandas echoed a carnivore-like microbiome. Most significantly, the enzyme assay of the giant panda's feces indicated the lowest cellulase and xylanase activity among major herbivores, shown by an in-vitro experimental assay of enzyme activity for cellulose and hemicellulose-degradation. All of our results consistently indicate that the giant panda is not specialized to digest cellulose and hemicellulose from its bamboo diet, making the giant panda a good mammalian model to study the unusual link between the gut microbiome and diet. The increased food intake of the giant pandas might be a strategy to compensate for the gut microbiome functions, highlighting a strong need of conservation of the native bamboo forest both in high- and low-altitude ranges to meet the great demand of bamboo diet of giant pandas.
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Affiliation(s)
- Wei Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Sudhanshu Mishra
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jiangchao Zhao
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Jingsi Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Fanli Kong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ruihong Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Miao Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hengzhi Zhang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Yutian Zeng
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Yuanliangzi Tian
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Yihang Zhong
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Hongdi Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Yunhan Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Jiandong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Caiwu Li
- China Conservation and Research Center for the Giant Panda, Ya'an, China
| | - Chengdong Wang
- China Conservation and Research Center for the Giant Panda, Ya'an, China
| | - Desheng Li
- China Conservation and Research Center for the Giant Panda, Ya'an, China
| | - Hemin Zhang
- China Conservation and Research Center for the Giant Panda, Ya'an, China
| | - Zhili Zuo
- Chengdu Zoo, Chengdu Institute of Wildlife, Chengdu, China
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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Borbón-García A, Reyes A, Vives-Flórez M, Caballero S. Captivity Shapes the Gut Microbiota of Andean Bears: Insights into Health Surveillance. Front Microbiol 2017; 8:1316. [PMID: 28751883 PMCID: PMC5507997 DOI: 10.3389/fmicb.2017.01316] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/29/2017] [Indexed: 12/31/2022] Open
Abstract
The Andean bear is an endemic species of the tropical Andes who has an almost exclusively plant-based diet. Since herbivorous mammals do not carry enzymes for fiber degradation, the establishment of symbiosis with cellulolytic microorganisms in their gastrointestinal (GI) tract is necessary to help them fulfill their nutritional needs. Furthermore, as described for other mammals, a stable, diverse, and balanced gut microbial composition is an indicator of a healthy status of the host; under disturbances this balance can be lost, leading to potential diseases of the host. The goal of this study was to describe the gut microbiota of wild and captive Andean bears and determine how habitat status influences the composition and diversity of the gut symbiotic community. Fecal samples from wild (n = 28) and captive (n = 8) Andean bears were collected in "Reserva Pantano de Martos" and "Fundación Bioandina", Colombia. Composition and diversity analyses were performed using amplicons from the V4 region of the 16S rDNA gene sequenced using the Ion PGM platform. PICRUSt algorithm was applied to predict the gene content of the gut microbiome of wild and captive Andean bears. A total of 5,411 and 838 OTUs were identified for wild and captive bears, respectively. Captive bears contained a lower number of bacterial phyla (n = 7) compared to wild individuals (n = 9). Proteobacteria (59.03%) and Firmicutes (14.03%) were the phyla that contributed the most to differences between wild and captive bears (overall dissimilarity = 87.72%). At family level, Enterobacteriaceae drove the main differences between the two groups (13.7%). PICRUSt metagenomics predictions suggested a similar pattern of relative abundance of gene families associated with the metabolism of carbohydrates across samples in wild individuals, despite the taxonomic differences of their gut microbiota. Captivity alters the availability and diversity of food resources, which likely reduces microbiota richness and diversity compared to wild individuals. Further considerations should be taken into account for nutritional schemes improving ex-situ conservation and its potential as a surveillance tool of endangered populations of wild Andean bears.
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Affiliation(s)
- Andrea Borbón-García
- Research Group on Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia.,Max Planck Tandem Group in Computational Biology, Universidad de los AndesBogotá, Colombia.,Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia
| | - Alejandro Reyes
- Research Group on Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia.,Max Planck Tandem Group in Computational Biology, Universidad de los AndesBogotá, Colombia.,Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint LouisMO, United States
| | - Martha Vives-Flórez
- Centro de Investigaciones Microbiológicas, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia
| | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Department of Biological Sciences, Universidad de los AndesBogotá, Colombia
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