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Hou D, Yin B, Wang S, Li H, Weng S, Jiang X, Li H, Li C, He J, Huang Z. Intestine bacterial community affects the growth of the Pacific white shrimp (Litopenaeus vannamei). Appl Microbiol Biotechnol 2024; 108:59. [PMID: 38180551 DOI: 10.1007/s00253-023-12897-3] [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: 07/03/2023] [Revised: 10/07/2023] [Accepted: 10/18/2023] [Indexed: 01/06/2024]
Abstract
Increasing evidence suggests that intestine microorganisms are closely related to shrimp growth, but there is no existing experiment to prove this hypothesis. Here, we compared the intestine bacterial community of fast- and slow-growing shrimp at the same developmental stage with a marked difference in body size. Our results showed that the intestine bacterial communities of slow-growing shrimp exhibited less diversity but were more heterogeneous than those of fast-growing shrimp. Uncultured_bacterium_g_Candidatus Bacilloplasma, Tamlana agarivorans, Donghicola tyrosinivorans, and uncultured_bacterium_f_Flavobacteriaceae were overrepresented in the intestines of fast-growing shrimp, while Shimia marina, Vibrio sp., and Vibrio campbellii showed the opposite trends. We further found that the bacterial community composition was significantly correlated with shrimp length, and some bacterial species abundances were found to be significantly correlated with shrimp weight and length, including T. agarivorans and V. campbellii, which were chosen as indicators for a reverse gavage experiment. Finally, T. agarivorans was found to significantly promote shrimp growth after the experiment. Collectively, these results suggest that intestine bacterial community could be important factors in determining the growth of shrimp, indicating that specific bacteria could be tested in further studies against shrimp growth retardation. KEY POINTS: • A close relationship between intestine bacterial community and shrimp growth was proven by controllable experiments. • The bacterial signatures of the intestine were markedly different between slow- and fast-growing shrimp, and the relative abundances of some intestine bacterial species were correlated significantly with shrimp body size. • Reverse gavage by Tamlana agarivorans significantly promoted shrimp growth.
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Affiliation(s)
- Dongwei Hou
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Bin Yin
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sheng Wang
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Haoyang Li
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Xiewu Jiang
- Guangdong Hisenor Group Co., Ltd, Guangzhou, People's Republic of China
| | - Hui Li
- Guangdong Hisenor Group Co., Ltd, Guangzhou, People's Republic of China
| | - Chaozheng Li
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, People's Republic of China
| | - Jianguo He
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, People's Republic of China.
| | - Zhijian Huang
- State Key Laboratory of Biocontrol/School of Marine Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
- China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology/Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, People's Republic of China.
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Jin H, Li L, Lu W, Zhang Z, Xing Y, Wu D. Identification of the regulatory roles of water qualities on the spatio-temporal dynamics of microbiota communities in the water and fish guts in the Heilongjiang River. Front Microbiol 2024; 15:1435360. [PMID: 39234540 PMCID: PMC11372393 DOI: 10.3389/fmicb.2024.1435360] [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: 05/21/2024] [Accepted: 07/23/2024] [Indexed: 09/06/2024] Open
Abstract
The Heilongjiang River is one of the largest rivers in the cool temperate zone and has an abundant fish source. To date, the microbiota community in water samples and fish guts from the Heilongjiang River is still unclear. In the present study, water samples and fish guts were collected from four locations of the Heilongjiang River during both the dry season and the wet season to analyze the spatio-temporal dynamics of microbiota communities in the water environment and fish guts through 16s ribosome RNA sequencing. The water qualities showed seasonal changes in which the pH value, dissolved oxygen, and total dissolved solids were generally higher during the dry season, and the water temperature was higher during the wet season. RDA indicated that higher pH values, dissolved oxygen, and total dissolved solids promoted the formation of microbiota communities in the water samples of the dry season, while higher water temperature positively regulated the formation of microbiota communities in the water samples of the wet season. LEFSe identified five biomarkers with the most abundant difference at the genus level, of which TM7a was upregulated in the water samples of the dry season, and SM1A02, Rheinheimera, Gemmatimonas, and Vogesella were upregulated in the water samples of the wet season. Pearson analysis revealed that higher pH values and dissolved oxygen positively regulated the formation of TM7a and negatively regulated the formation of SM1A02, Rheinheimera, Gemmatimonas, and Vogesella (p < 0.05), while higher water temperature had the opposite regulatory roles in the formation of these biomarkers. The relative abundance of microbiota diversity in fish guts varies greatly between different fish species, even if the fishes were collected from the same water source, indicating that dietary habits and fish species may be key factors, affecting the formation and construction of microbiome community in fish gut. P. glenii, P. lagowskii, G. cynocephalus, and L. waleckii were the main fish resources, which were collected and identified from at least six sample points. RDA indicated that the microbiota in the water environment regulated the formation of microbiota community in the guts of G. cynocephalus and L. waleckii and had limited regulated effects on P. glenii and P. lagowskii. The present study identified the regulatory effects of water qualities on the formation of microbiota communities in the water samples and fish guts, providing valuable evidence for the protection of fish resources in the Heilongjiang River.
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Affiliation(s)
- Hongyu Jin
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Heilongjiang River Basin, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National Agricultural Experimental Station for Fishery Resources and Environment in Fuyuan, Harbin, China
| | - Lei Li
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Heilongjiang River Basin, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National Agricultural Experimental Station for Fishery Resources and Environment in Fuyuan, Harbin, China
| | - Wanqiao Lu
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Heilongjiang River Basin, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National Agricultural Experimental Station for Fishery Resources and Environment in Fuyuan, Harbin, China
| | - Zepeng Zhang
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Heilongjiang River Basin, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National Agricultural Experimental Station for Fishery Resources and Environment in Fuyuan, Harbin, China
| | - Yue Xing
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Heilongjiang River Basin, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National Agricultural Experimental Station for Fishery Resources and Environment in Fuyuan, Harbin, China
| | - Di Wu
- Scientific Observing and Experimental Station of Fishery Resources and Environment in Heilongjiang River Basin, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fishery Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
- National Agricultural Experimental Station for Fishery Resources and Environment in Fuyuan, Harbin, China
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Jung Y, Ku JY, Kim B, Kim Y, Park KM, Baek J, Yu D, Park J. Determining lactate concentrations in Korean indigenous calves and evaluating its role as a predictor for acidemia in calf diarrhea. BMC Vet Res 2024; 20:373. [PMID: 39164760 PMCID: PMC11334453 DOI: 10.1186/s12917-024-04235-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 08/14/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND Calf diarrhea leads to high mortality rates and decreases in growth and productivity, causing negative effects on the livestock industry. Lactate is closely associated with metabolic acidosis in diarrheic calves. However, there have been no reports on lactate concentrations in Korean indigenous (Hanwoo) calves, especially those with diarrhea. This study aimed to determine the reference range of L-lactate and D-lactate concentrations in Hanwoo calves and to better understand the utility of lactate as predictive factors for acidemia in diarrheic calves. RESULTS L-lactate and D-lactate concentrations were measured in healthy (n = 44) and diarrheic (n = 93) calves, and blood gas analysis was performed on diarrheic calves. The reference range in healthy calves was 0.2-2.25 mmol/L for L-lactate and 0.42-1.38 mmol/L for D-lactate. Diarrheic calves had higher concentrations of L-lactate and D-lactate than healthy calves. In diarrheic calves, L-lactate and D-lactate each had weak negative correlation with pH (r = - 0.31 and r = - 0.35). In diarrheic calves with hyper-L-lactatemia, the combined concentrations of L-lactate and D-lactate had moderate correlation with pH (r = - 0.51) and anion gap (r = 0.55). Receiver operating characteristic analysis showed D-lactate had fair predictive performance (AUC = 0.74) for severe acidemia, with an optimal cut-off value of > 1.43 mmol/L. The combined concentrations of L-lactate and D-lactate showed fair predictive performance for predicting acidemia (AUC = 0.74) and severe acidemia (AUC = 0.72), with cut-off values of > 6.05 mmol/L and > 5.95 mmol/L. CONCLUSIONS The determined reference ranges for L-lactate and D-lactate in Hanwoo calves enable the identification of hyper-L-lactatemia and hyper-D-lactatemia. Diarrheic calves exhibited increased lactate concentrations correlated with acid-base parameters. While the concentrations of L-lactate and D-lactate have limitations as single diagnostic biomarkers for predicting acidemia or severe acidemia, their measurement remains important, and L-lactate has the advantage of being measurable at the point-of-care. Assessing lactate concentrations should be considered by clinicians, especially when used alongside other clinical indicators and diagnostic tests. This approach can improve calf diarrhea management, contributing positively to animal welfare and providing economic benefits to farms.
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Affiliation(s)
- Youngwoo Jung
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan, 54596, Republic of Korea
| | - Ji-Yeong Ku
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan, 54596, Republic of Korea
| | - Byoungsoo Kim
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan, 54596, Republic of Korea
| | - Youngjun Kim
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan, 54596, Republic of Korea
- Hanwoo (Korean Indigenous Cattle) Genetic Improvement Center, National Agricultural Cooperative Federation, Seosan, Republic of Korea
| | - Kwang-Man Park
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan, 54596, Republic of Korea
| | - Jonghun Baek
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan, 54596, Republic of Korea
| | - DoHyeon Yu
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Jinho Park
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan, 54596, Republic of Korea.
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Kobel CM, Merkesvik J, Burgos IMT, Lai W, Øyås O, Pope PB, Hvidsten TR, Aho VTE. Integrating host and microbiome biology using holo-omics. Mol Omics 2024; 20:438-452. [PMID: 38963125 DOI: 10.1039/d4mo00017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Holo-omics is the use of omics data to study a host and its inherent microbiomes - a biological system known as a "holobiont". A microbiome that exists in such a space often encounters habitat stability and in return provides metabolic capacities that can benefit their host. Here we present an overview of beneficial host-microbiome systems and propose and discuss several methodological frameworks that can be used to investigate the intricacies of the many as yet undefined host-microbiome interactions that influence holobiont homeostasis. While this is an emerging field, we anticipate that ongoing methodological advancements will enhance the biological resolution that is necessary to improve our understanding of host-microbiome interplay to make meaningful interpretations and biotechnological applications.
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Affiliation(s)
- Carl M Kobel
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Jenny Merkesvik
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Wanxin Lai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Ove Øyås
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Velma T E Aho
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
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5
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Sadeghi J, Zaib F, Heath DD. Genetic architecture and correlations between the gut microbiome and gut gene transcription in Chinook salmon (Oncorhynchus tshawytscha). Heredity (Edinb) 2024; 133:54-66. [PMID: 38822131 PMCID: PMC11222526 DOI: 10.1038/s41437-024-00692-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 06/02/2024] Open
Abstract
Population divergence through selection can drive local adaptation in natural populations which has implications for the effective restoration of declining and extirpated populations. However, adaptation to local environmental conditions is complicated when both the host and its associated microbiomes must respond via co-evolutionary change. Nevertheless, for adaptation to occur through selection, variation in both host and microbiome traits should include additive genetic effects. Here we focus on host immune function and quantify factors affecting variation in gut immune gene transcription and gut bacterial community composition in early life-stage Chinook salmon (Oncorhynchus tshawytscha). Specifically, we utilized a replicated factorial breeding design to determine the genetic architecture (sire, dam and sire-by-dam interaction) of gut immune gene transcription and microbiome composition. Furthermore, we explored correlations between host gut gene transcription and microbiota composition. Gene transcription was quantified using nanofluidic qPCR arrays (22 target genes) and microbiota composition using 16 S rRNA gene (V5-V6) amplicon sequencing. We discovered limited but significant genetic architecture in gut microbiota composition and transcriptional profiles. We also identified significant correlations between gut gene transcription and microbiota composition, highlighting potential mechanisms for functional interactions between the two. Overall, this study provides support for the co-evolution of host immune function and their gut microbiota in Chinook salmon, a species recognized as locally adapted. Thus, the inclusion of immune gene transcription profile and gut microbiome composition as factors in the development of conservation and commercial rearing practices may provide new and more effective approaches to captive rearing.
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Affiliation(s)
- Javad Sadeghi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Department of Physical & Environmental Sciences, University of Toronto-Scarborough, Toronto, ON, Canada
| | - Farwa Zaib
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada.
- Department of Integrative Biology, University of Windsor, Ontario, ON, Canada.
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Bessegatto JA, Lisbôa JAN, Santos BP, Curti JM, Montemor C, Alfieri AA, Mach N, Costa MC. Fecal Microbial Communities of Nellore and Crossbred Beef Calves Raised at Pasture. Animals (Basel) 2024; 14:1447. [PMID: 38791664 PMCID: PMC11117347 DOI: 10.3390/ani14101447] [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: 04/06/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
This study aimed to investigate the effect of age and genetics on the fecal microbiota of beef calves. Ten purebred Nellore (Bos taurus indicus) and ten crossbreed 50% Nellore-50% European breed (Bos taurus taurus) calves co-habiting on the same pasture paddock had fecal samples collected on days five (5 d), 14 d, 28 d, 60 d, 90 d, 180 d, 245 d (weaning) and 260 d after birth. All calves were kept with their mothers, and six Nellore dams were also sampled at weaning. Microbiota analysis was carried out by amplification of the V4 region of the 16S rRNA gene following high-throughput sequencing with a MiSeq Illumina platform. Results revealed that bacterial richness increased with age and became more similar to adults near weaning. Differences in microbiota membership between breeds were found at 60 d and 90 d and for structure at 60 d, 90 d, 245 d, and 260 d (p < 0.05). In addition, crossbreed calves presented less variability in their microbiota. In conclusion, the genetic composition significantly impacted the distal gut microbiota of calves co-habiting in the same environment, and further studies investigating food intake can reveal possible associations between microbiota composition and performance.
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Affiliation(s)
- José Antônio Bessegatto
- Department of Cinical Sciences, Faculdade de Medicina Veterinária, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid (PR 445) Km 380, Londrina 86057-970, Brazil; (J.A.B.)
| | - Júlio Augusto Naylor Lisbôa
- Department of Cinical Sciences, Faculdade de Medicina Veterinária, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid (PR 445) Km 380, Londrina 86057-970, Brazil; (J.A.B.)
| | - Bruna Parapinski Santos
- Department of Cinical Sciences, Faculdade de Medicina Veterinária, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid (PR 445) Km 380, Londrina 86057-970, Brazil; (J.A.B.)
| | - Juliana Massitel Curti
- Department of Cinical Sciences, Faculdade de Medicina Veterinária, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid (PR 445) Km 380, Londrina 86057-970, Brazil; (J.A.B.)
| | - Carlos Montemor
- Department of Cinical Sciences, Faculdade de Medicina Veterinária, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid (PR 445) Km 380, Londrina 86057-970, Brazil; (J.A.B.)
| | - Amauri Alcindo Alfieri
- Department of Cinical Sciences, Faculdade de Medicina Veterinária, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid (PR 445) Km 380, Londrina 86057-970, Brazil; (J.A.B.)
| | - Núria Mach
- Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), École Nationale Vétérinaire de Toulouse, 31076 Toulouse, France
| | - Marcio Carvalho Costa
- Department of Biomedical Sciences, Faculté de Médecine Vétérinaire, Université de Montréal, 3200 Sicotte, St-Hyacinthe, QC J2S 2M2, Canada
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Wei L, Zeng B, Li B, Guo W, Mu Z, Gan Y, Li Y. Hybridization alters red deer gut microbiome and metabolites. Front Microbiol 2024; 15:1387957. [PMID: 38784815 PMCID: PMC11112572 DOI: 10.3389/fmicb.2024.1387957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
The host genes play a crucial role in shaping the composition and structure of the gut microbiome. Red deer is listed as an endangered species by the International Union for the Conservation of Nature, and its pilose antlers have good medicinal value. Hybridization can lead to heterosis, resulting in increased pilose antler production and growth performance in hybrid deer. However, the role of the gut microbiome in hybrid deer remains largely unknown. In this study, alpha and beta diversity analysis showed that hybridization altered the composition and structure of the gut microbiome of the offspring, with the composition and structure of the hybrid offspring being more similar to those of the paternal parents. Interestingly, the LefSe differential analysis showed that there were some significantly enriched gut microbiome in the paternal parents (such as g_Prevotellaceae UCG-003, f_Bacteroidales RF16 group; Ambiguous_taxa, etc.) and the maternal parents (including g_Alistipes, g_Anaerosporobacter, etc.), which remained significantly enriched in the hybrid offspring. Additionally, the hybrid offspring exhibited a significant advantage over the parental strains, particularly in taxa that can produce short-chain fatty acids, such as g_Prevotellaceae UCG-003, g_Roseburia, g_Succinivibrio, and g_Lachnospiraceae UCG-006. Similar to bacterial transmission, metagenomic analysis showed that some signaling pathways related to pilose antler growth ("Wnt signaling pathway," "PI3K Akt signaling pathway," "MAPK signaling pathway") were also enriched in hybrid red deer after hybridization. Furthermore, metabolomic analysis revealed that compared with the paternal and maternal parents, the hybrid offspring exhibited significant enrichment in metabolites related to "Steroid hormone biosynthesis," "Tryptophan metabolism," "Valine, leucine and isoleucine metabolism," and "Vitamin B metabolism." Notably, the metagenomic analysis also showed that these metabolic pathways were significantly enriched in hybrid deer. Finally, a correlation analysis between the gut microbiome and metabolites revealed a significant positive correlation between the enriched taxa in hybrid deer, including the Bacteroidales RF16 group, Prevotellaceae, and Succinivibrio, and metabolites, such as 7α-hydroxytestosterone, L-kynurenine, indole, L-isoleucine, and riboflavin. The study contributes valuable data toward understanding the role of the gut microbiome from red deer in hybridization and provides reference data for further screening potential probiotics and performing microbial-assisted breeding that promotes the growth of red deer pilose antlers and bodies, development, and immunity.
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Affiliation(s)
- Limin Wei
- Chongqing Key Laboratory of High Active Traditional Chinese Drug Delivery System, Chongqing Medical and Pharmaceutical College, Chongqing, China
- College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Bo Li
- College of Resources and Environment, Aba Teachers University, Aba, China
| | - Wei Guo
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Zhenqiang Mu
- Chongqing Key Laboratory of High Active Traditional Chinese Drug Delivery System, Chongqing Medical and Pharmaceutical College, Chongqing, China
| | - Yunong Gan
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Yanhong Li
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, & Collaborative Innovation Center for Prevention and Control of Endemic and Ethnic Regional Diseases Co-constructed by the Province and Ministry, Guizhou Medical University, Guiyang, Guizhou, China
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8
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Scully S, Earley B, Smith PE, McAloon C, Waters SM. Health-associated changes of the fecal microbiota in dairy heifer calves during the pre-weaning period. Front Microbiol 2024; 15:1359611. [PMID: 38737409 PMCID: PMC11082272 DOI: 10.3389/fmicb.2024.1359611] [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: 12/21/2023] [Accepted: 04/01/2024] [Indexed: 05/14/2024] Open
Abstract
Introduction Neonatal calf diarrhea is a multifactorial condition that occurs in early life when calves are particularly susceptible to enteric infection and dysbiosis of the gut microbiome. Good calf health is dependent on successful passive transfer of immunity from the dam through colostrum. There are limited studies on the developing gut microbiota from birth to weaning in calves. Methodology Therefore, the objective of this study was to examine the effect of immune status and diarrheal incidence on the development of the fecal microbiota in Jersey (n = 22) and Holstein (n = 29) heifer calves throughout the pre-weaning period. Calves were hand-fed a colostrum volume equivalent to 8.5% of their birthweight, from either the calf's dam (n = 28) or re-heated mixed colostrum (≤2 cows, ≤1d; n = 23) within 2 h of birth. All calves were clinically assessed using a modified Wisconsin-Madison calf health scoring system and rectal temperature at day (d) 0, d7, d21, or disease manifestation (DM) and weaning (d83). Weights were recorded at d0, d21, and d83. Calf blood samples were collected at d7 for the determination of calf serum IgG (sIgG). Fecal samples were obtained at d7, d21/DM [mean d22 (SE 0.70)], and at weaning for 16S rRNA amplicon sequencing of the fecal microbiota. Data were processed in R using DADA2; taxonomy was assigned using the SILVA database and further analyzed using Phyloseq and MaAsLin 2. Results and discussion Significant amplicon sequence variants (ASVs) and calf performance data underwent a Spearman rank-order correlation test. There was no effect (p > 0.05) of colostrum source or calf breed on serum total protein. An effect of calf breed (p < 0.05) was observed on sIgG concentrations such that Holstein calves had 6.49 (SE 2.99) mg/ml higher sIgG than Jersey calves. Colostrum source and calf breed had no effect (p > 0.05) on health status or the alpha diversity of the fecal microbiota. There was a relationship between health status and time interaction (p < 0.001), whereby alpha diversity increased with time; however, diarrheic calves had reduced microbial diversity at DM. No difference (p > 0.05) in beta diversity of the microbiota was detected at d7 or d83. At the genus level, 33 ASVs were associated (adj.p < 0.05) with health status over the pre-weaning period.
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Affiliation(s)
- Sabine Scully
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc Grange, Meath, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Bernadette Earley
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc Grange, Meath, Ireland
| | - Paul E. Smith
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc Grange, Meath, Ireland
| | - Catherine McAloon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Sinéad M. Waters
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
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Yao Z, Zhao W, Tang B, Li Q, Wang Z. Effects of host identity on the gut microbiota: A comparative study on three microtinae species. Animal Model Exp Med 2024; 7:98-105. [PMID: 38567747 PMCID: PMC11079152 DOI: 10.1002/ame2.12404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/29/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Gut microbiota exert an immense effect on host health and host environmental adaptation. Furthermore, the composition and structure of gut microbiota are determined by the environment and host genetic factors. However, the relative contribution of the environment and host genetic factors toward shaping the structure of gut microbiota has been poorly understood. METHODS In this study, we characterized the fecal microbial communities of the closely related voles Neodon fuscus, Lasiopodomys brandtii, and L. mandarinus after caged feeding in the laboratory for 6 months, through high-throughput sequencing and bioinformatics analysis. RESULTS The results of pairwise comparisons of N. fuscus vs. L. brandtii and L. mandarinus vs. L. brandtii revealed significant differences in bacterial diversity and composition after domestication. While 991 same operational taxonomic units (OTUs) were shared in three voles, there were 362, 291, and 303 species-specific OTUs in N. fuscus, L. brandtii, and L. mandarinus, respectively. The relative abundances of Proteobacteria and Prevotella, which are reported to be enriched in high-altitude populations, were significantly higher in high-altitude N. fuscus than in low-altitude L. brandtii after domestication. Firmicutes, which produce various digestive enzymes for energy metabolism, and Spirochaetes, which can degrade cellulose, were found in higher abundance in subterranean L. mandarinus than that in L. brandtii which dwells on the earth surface. CONCLUSION Our findings showed that some components of gut microbiota still maintained dominance even when different host species are reared under the same environmental conditions, suggesting that these bacteria are substantially influenced by host factors.
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Affiliation(s)
- Zhen Yao
- School of Life SciencesZhengzhou UniversityZhengzhouHenan ProvinceP.R. China
| | - Wenli Zhao
- School of Life SciencesZhengzhou UniversityZhengzhouHenan ProvinceP.R. China
| | - Baohong Tang
- School of Life SciencesZhengzhou UniversityZhengzhouHenan ProvinceP.R. China
| | - Qinghua Li
- School of Life SciencesZhengzhou UniversityZhengzhouHenan ProvinceP.R. China
| | - Zhenlong Wang
- School of Life SciencesZhengzhou UniversityZhengzhouHenan ProvinceP.R. China
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10
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Tang W, Xiang X, Wang H, Zhou W, He L, Yin Y, Li T. Zinc lactate alleviates oxidative stress by modulating crosstalk between constitutive androstane receptor signaling pathway and gut microbiota profile in weaned piglets. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2024; 16:23-33. [PMID: 38131030 PMCID: PMC10730354 DOI: 10.1016/j.aninu.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 12/23/2023]
Abstract
This study aimed to determine the regulatory mechanism of dietary zinc lactate (ZL) supplementation on intestinal oxidative stress damage in a paraquat (PQ)-induced piglet model. Twenty-eight piglets (mean body weight 9.51 ± 0.23 kg) weaned at 28 d of age were randomly divided into control, ZL, PQ, and ZL + PQ groups (n = 7 in each group). The ZL-supplemented diet had little effect on growth performance under normal physiological conditions. However, under PQ challenge, ZL supplementation significantly improved average daily gain (P < 0.05) and reduced the frequency of diarrhea. ZL improved intestinal morphology and ultrastructure by significantly increasing the expression level of the jejunal tight junction protein, zonula occludens-1 (ZO-1) (P < 0.05), and intestinal zinc transport and absorption in PQ-induced piglets, which reduced intestinal permeability. ZL supplementation also enhanced the expression of antioxidant and anti-inflammatory factor-related genes and decreased inflammatory cytokine expression and secretion in PQ-induced piglets. Furthermore, ZL treatment significantly inhibited the activation of constitutive androstane receptor (CAR) signaling (P < 0.01) in PQ-induced piglets and altered the structure of the gut microbiota, especially by significantly increasing the abundance of beneficial gut microbes, including UCG_002, Ruminococcus, Rikenellaceae_RC9_gut_group, Christensenellaceae_R_7_group, Treponema, unclassified_Christensenellaceae, and unclassified_Erysipelotrichaceae (P < 0.05). These data reveal that pre-administration of ZL to piglets can suppress intestinal oxidative stress by improving antioxidant and anti-inflammatory capacity and regulating the crosstalk between CAR signaling and gut microbiota.
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Affiliation(s)
- Wenjie Tang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Sichuan Academy of Animal Sciences, Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, China
- Livestock and Poultry Biological Products Key Laboratory of Sichuan Province, Sichuan Animtech Feed Co., Ltd, Chengdu 610000, China
| | - Xuan Xiang
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- College of Advanced Agricultural Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Houfu Wang
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Wentao Zhou
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Liuqin He
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Yulong Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- College of Advanced Agricultural Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tiejun Li
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process, CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- College of Advanced Agricultural Science, University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Alawneh JI, Ramay H, Olchowy T, Allavena R, Soust M, Jassim RA. Effect of a Lactobacilli-Based Direct-Fed Microbial Product on Gut Microbiota and Gastrointestinal Morphological Changes. Animals (Basel) 2024; 14:693. [PMID: 38473078 DOI: 10.3390/ani14050693] [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: 01/31/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
The calf's gastrointestinal tract (GIT) microbiome undergoes rapid shifts during early post-natal life, which can directly affect calf performance. The objectives of this study were to characterise and compare differences in the establishment and succession of GIT microbiota, GIT morphological changes, and the growth of dairy calves from birth until weaned. Forty-four newborn Holstein-Friesian calves were randomly selected and assigned to Treatment (TRT) and Control (CON) groups. The TRT group calves received a once-daily dose of a direct-fed microbial (DFM) liquid product containing Lacticaseibacillus paracasei, Lentilactobacillus buchneri, and Lacticaseibacillus casei, all formerly known as Lactobacillus. Fresh faecal samples were manually taken from the rectum of all calves, and gross necropsy was performed on the forestomachs and gastrointestinal tracts. Bacterial DNA was extracted from frozen faecal samples for 16S rRNA gene amplicon sequencing. Calves in the TRT group had greater live weights (p = 0.02) at weaning compared with calves in the CON group (mean = 69.18 kg, SD = 13.37 kg). The average daily live weight gain (ADG) and total feed intake were similar between the two groups. Calves in the TRT group had greater duodenum, abomasum, and reticulum weights (p = 0.05). Rumen and intestinal development (p < 0.05) and faecal microbial diversity (p < 0.05) were more pronounced in the TRT group. The relative abundances of eight genera differed (p < 0.001) between the groups. Supplementing calves with the LAB-based DFM increased live weight at weaning and had a more pronounced effect on the development of rumen and the gastrointestinal tract and on microbiota diversity and evenness. Future work is needed to better understand the potential association of LAB-DFM products on gut mucosa-associated microbiota.
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Affiliation(s)
- John I Alawneh
- School of Veterinary Science, University of Queensland, Gatton, QLD 4343, Australia
| | - Hena Ramay
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T3R 1J3, Canada
| | - Timothy Olchowy
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T3R 1J3, Canada
| | - Rachel Allavena
- School of Veterinary Science, University of Queensland, Gatton, QLD 4343, Australia
| | - Martin Soust
- Terragen Biotech Pty Ltd., Coolum Beach, QLD 4573, Australia
| | - Rafat Al Jassim
- Queensland Alliance for Agriculture and Food Innovation, St Lucia, QLD 4072, Australia
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12
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Mizoguchi Y, Guan LL. - Invited Review - Translational gut microbiome research for strategies to improve beef cattle production sustainability and meat quality. Anim Biosci 2024; 37:346-359. [PMID: 38186252 PMCID: PMC10838664 DOI: 10.5713/ab.23.0387] [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: 09/26/2023] [Revised: 11/06/2023] [Accepted: 12/12/2023] [Indexed: 01/09/2024] Open
Abstract
Advanced and innovative breeding and management of meat-producing animals are needed to address the global food security and sustainability challenges. Beef production is an important industry for securing animal protein resources in the world and meat quality significantly contributes to the economic values and human needs. Improvement of cattle feed efficiency has become an urgent task as it can lower the environmental burden of methane gas emissions and the reduce the consumption of human edible cereal grains. Cattle depend on their symbiotic microbiome and its activity in the rumen and gut to maintain growth and health. Recent developments in high-throughput omics analysis (metagenome, metatranscriptome, metabolome, metaproteome and so on) have made it possible to comprehensively analyze microbiome, hosts and their interactions and to define their roles in affecting cattle biology. In this review, we focus on the relationships among gut microbiome and beef meat quality, feed efficiency, methane emission as well as host genetics in beef cattle, aiming to determine the current knowledge gaps for the development of the strategies to improve the sustainability of beef production.
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Affiliation(s)
- Yasushi Mizoguchi
- School of Agriculture, Meiji University, Tama-ku, Kawasaki, Kanagawa 214-8571,
Japan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5,
Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5,
Canada
- Faculty of Land and Food Systems, the University of British Columbia, Vancouver, British Columbia, V6T 1Z4,
Canada
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13
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Yan P, Luo S, Guo L, Wang X, Ren X, Lv J, Chen Y, Lin X, Chen J, Wang R. Unraveling Intestinal Microbial Shifts in ESRD and Kidney Transplantation: Implications for Disease-Related Dysbiosis. Microorganisms 2023; 11:2747. [PMID: 38004758 PMCID: PMC10673061 DOI: 10.3390/microorganisms11112747] [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: 08/24/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The composition of the gut microbiome is profoundly influenced by the accumulation of toxins in end-stage renal disease (ESRD) and specific medical treatments during kidney transplantation (KT). However, variations in results may arise due to factors such as genetics, dietary habits, and the strategy of anti-rejection therapy. Therefore, we conducted a 16S rRNA sequencing study to characterize intestinal microbiomes by using 75 fecal specimens obtained from 25 paired Chinese living donors (LDs) of kidneys and recipients before and after KT. Surprisingly, similar enterotypes were observed between healthy LDs and ESRD recipients. Nonetheless, following KT, the fecal communities of recipients exhibited distinct clustering, which was primarily characterized by Escherichia-Shigella and Streptococcus at the genus level, along with a reduction in the diversity of microbiota. To further explore the characteristics of gut microorganisms in early rejection episodes, two recipients with biopsy-proven borderline changes during follow-up were enrolled in a preliminary sub-cohort study. Our findings reveal a comparable construction of gut microbiota between ESRD patients and their healthy relatives while also highlighting the significant impact of KT on gut microbial composition.
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Affiliation(s)
- Pengpeng Yan
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China; (P.Y.); (S.L.); (L.G.); (X.W.); (X.R.); (J.L.); (Y.C.); (X.L.); (J.C.)
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou 310003, China
- National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China
- Institute of Nephrology, Zhejiang University, Hangzhou 310003, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou 310003, China
| | - Sulin Luo
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China; (P.Y.); (S.L.); (L.G.); (X.W.); (X.R.); (J.L.); (Y.C.); (X.L.); (J.C.)
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou 310003, China
- National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China
- Institute of Nephrology, Zhejiang University, Hangzhou 310003, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou 310003, China
| | - Luying Guo
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China; (P.Y.); (S.L.); (L.G.); (X.W.); (X.R.); (J.L.); (Y.C.); (X.L.); (J.C.)
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou 310003, China
- National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China
- Institute of Nephrology, Zhejiang University, Hangzhou 310003, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou 310003, China
| | - Xingxia Wang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China; (P.Y.); (S.L.); (L.G.); (X.W.); (X.R.); (J.L.); (Y.C.); (X.L.); (J.C.)
- Department of Nephrology, 903rd Hospital of PLA, Hangzhou 310013, China
| | - Xue Ren
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China; (P.Y.); (S.L.); (L.G.); (X.W.); (X.R.); (J.L.); (Y.C.); (X.L.); (J.C.)
- Department of Nephrology, Huzhou Central Hospital, Huzhou 313000, China
| | - Junhao Lv
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China; (P.Y.); (S.L.); (L.G.); (X.W.); (X.R.); (J.L.); (Y.C.); (X.L.); (J.C.)
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou 310003, China
- National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China
- Institute of Nephrology, Zhejiang University, Hangzhou 310003, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou 310003, China
| | - Ying Chen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China; (P.Y.); (S.L.); (L.G.); (X.W.); (X.R.); (J.L.); (Y.C.); (X.L.); (J.C.)
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou 310003, China
- National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China
- Institute of Nephrology, Zhejiang University, Hangzhou 310003, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou 310003, China
| | - Xinyu Lin
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China; (P.Y.); (S.L.); (L.G.); (X.W.); (X.R.); (J.L.); (Y.C.); (X.L.); (J.C.)
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou 310003, China
- National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China
- Institute of Nephrology, Zhejiang University, Hangzhou 310003, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou 310003, China
| | - Jianghua Chen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China; (P.Y.); (S.L.); (L.G.); (X.W.); (X.R.); (J.L.); (Y.C.); (X.L.); (J.C.)
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou 310003, China
- National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China
- Institute of Nephrology, Zhejiang University, Hangzhou 310003, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou 310003, China
| | - Rending Wang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China; (P.Y.); (S.L.); (L.G.); (X.W.); (X.R.); (J.L.); (Y.C.); (X.L.); (J.C.)
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou 310003, China
- National Key Clinical Department of Kidney Diseases, Hangzhou 310003, China
- Institute of Nephrology, Zhejiang University, Hangzhou 310003, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou 310003, China
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14
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Du J, Gan M, Xie Z, Du G, Luo Y, Liu B, Zhu K, Chen L, Zhao Y, Niu L, Wang Y, Wang J, Zhu L, Shen L. A Comparative Study on the Growth Performance and Gut Microbial Composition of Duroc and Yorkshire Boars. Genes (Basel) 2023; 14:1726. [PMID: 37761866 PMCID: PMC10531244 DOI: 10.3390/genes14091726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
The intestinal microbiota is required for maintaining the development and health of the host. However, the gut microbiota contributing to the regulation of the growth performance and health of Duroc and Yorkshire boars remains largely unknown. In this study, we first evaluated the difference in the growth performance between Duroc and Yorkshire boars when their body weight reached 100 kg. Relative to Duroc boars, Yorkshire boars weighed 100 kg at a younger age and exhibited a significantly lower backfat thickness and eye muscle area. Microbial analysis of the fecal samples revealed a marked difference in gut microbiota composition between the two pig models and remarkably increased α-diversity in Yorkshire boars compared to Duroc boars. Further analysis indicated that Bacteroidota, Prevotellaceae, and Ruminococcaceae might be associated with the growth performance and lean meat rate of Yorkshire boars. Taken together, these results highlight that Yorkshire boars exhibit a faster growth rate and higher lean meat rate compared to Duroc boars, and these differences may be attributed to the influence of the gut microbiota, thereby providing valuable insight into optimizing pig breeding systems and selecting terminal paternal sires to enhance overall productivity and quality.
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Affiliation(s)
- Junhua Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mailin Gan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongwei Xie
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Gao Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yi Luo
- Sichuan Dekon Livestock Foodstuff Group, Chengdu 610200, China; (Y.L.); (B.L.); (K.Z.)
| | - Bin Liu
- Sichuan Dekon Livestock Foodstuff Group, Chengdu 610200, China; (Y.L.); (B.L.); (K.Z.)
| | - Kangping Zhu
- Sichuan Dekon Livestock Foodstuff Group, Chengdu 610200, China; (Y.L.); (B.L.); (K.Z.)
| | - Lei Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ye Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingyong Wang
- Chongqing Academy of Animal Science, Chongqing 402460, China;
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linyuan Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (J.D.); (M.G.); (Z.X.); (G.D.); (L.C.); (Y.Z.); (L.N.); (Y.W.); (L.Z.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
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15
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Zhu J, Liu X, Lu Y, Yue D, He X, Deng W, Zhao S, Xi D. Exploring the Impact of Ampelopsis Grossedentata Flavonoids on Growth Performance, Ruminal Microbiota, and Plasma Physiology and Biochemistry of Kids. Animals (Basel) 2023; 13:2454. [PMID: 37570263 PMCID: PMC10417322 DOI: 10.3390/ani13152454] [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: 06/02/2023] [Revised: 07/08/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
This study was conducted to evaluate the influences of supplementing Ampelopsis grossedentata flavonoids (AGF) on the rumen bacterial microbiome, plasma physiology and biochemistry, and growth performance of goats. Twenty-four Nubian kids were randomly allocated to three dietary treatments: the control (CON, basal diet), the 1.0 g/kg AGF treatment (AGF), and the 12.5 mg/kg monensin treatment (MN). This trial consisted of 10 days for adaptation and 90 days for data and sample collection. The results reveal that Bacteroidetes, Firmicutes, and Proteobacteria are the dominant phyla in kids' rumen. Compared with the CON group, the alpha diversity in the MN and AGF groups significantly increased (p < 0.01). Beta-diversity shows that rumen microbial composition is more similar in the MN and AGF groups. LEfSe analysis shows that Prevotella_1 in the AGF group were significantly higher than those in the MN and CON group. The high-density lipoprotein cholesterol and glucose levels in the AGF group were significantly higher than those in the CON group (p < 0.05), whereas the low-density lipoprotein cholesterol, glutamic-pyruvic transaminase, and alkaline phosphatase levels exhibited the opposite trend. The average daily gains in the AGF and MN groups significantly increased, while the feed-to-gain ratios were significantly decreased (p < 0.05). The results suggest that adding AGF to the diet improves microbial composition and has important implications for studying juvenile livestock growth and improving economic benefits.
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Affiliation(s)
- Junhong Zhu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (X.L.); (Y.L.); (D.Y.); (X.H.); (W.D.)
| | - Xingneng Liu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (X.L.); (Y.L.); (D.Y.); (X.H.); (W.D.)
- Institute of Animal Husbandry, Yunnan Vocational College of Agriculture, Kunming 650201, China
| | - Ying Lu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (X.L.); (Y.L.); (D.Y.); (X.H.); (W.D.)
| | - Dan Yue
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (X.L.); (Y.L.); (D.Y.); (X.H.); (W.D.)
| | - Xiaoming He
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (X.L.); (Y.L.); (D.Y.); (X.H.); (W.D.)
| | - Weidong Deng
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (X.L.); (Y.L.); (D.Y.); (X.H.); (W.D.)
| | - Sumei Zhao
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (X.L.); (Y.L.); (D.Y.); (X.H.); (W.D.)
| | - Dongmei Xi
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (X.L.); (Y.L.); (D.Y.); (X.H.); (W.D.)
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Mariadassou M, Nouvel LX, Constant F, Morgavi DP, Rault L, Barbey S, Helloin E, Rué O, Schbath S, Launay F, Sandra O, Lefebvre R, Le Loir Y, Germon P, Citti C, Even S. Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd. Anim Microbiome 2023; 5:32. [PMID: 37308970 DOI: 10.1186/s42523-023-00252-w] [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: 09/22/2022] [Accepted: 06/06/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Host-associated microbes are major determinants of the host phenotypes. In the present study, we used dairy cows with different scores of susceptibility to mastitis with the aim to explore the relationships between microbiota composition and different factors in various body sites throughout lactation as well as the intra- and inter-animal microbial sharing. RESULTS Microbiotas from the mouth, nose, vagina and milk of 45 lactating dairy cows were characterized by metataxonomics at four time points during the first lactation, from 1-week pre-partum to 7 months post-partum. Each site harbored a specific community that changed with time, likely reflecting physiological changes in the transition period and changes in diet and housing. Importantly, we found a significant number of microbes shared among different anatomical sites within each animal. This was between nearby anatomic sites, with up to 32% of the total number of Amplicon Sequence Variants (ASVs) of the oral microbiota shared with the nasal microbiota but also between distant ones (e.g. milk with nasal and vaginal microbiotas). In contrast, the share of microbes between animals was limited (< 7% of ASVs shared by more than 50% of the herd for a given site and time point). The latter widely shared ASVs were mainly found in the oral and nasal microbiotas. These results thus indicate that despite a common environment and diet, each animal hosted a specific set of bacteria, supporting a tight interplay between each animal and its microbiota. The score of susceptibility to mastitis was slightly but significantly related to the microbiota associated to milk suggesting a link between host genetics and microbiota. CONCLUSIONS This work highlights an important sharing of microbes between relevant microbiotas involved in health and production at the animal level, whereas the presence of common microbes was limited between animals of the herd. This suggests a host regulation of body-associated microbiotas that seems to be differently expressed depending on the body site, as suggested by changes in the milk microbiota that were associated to genotypes of susceptibility to mastitis.
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Affiliation(s)
| | | | - Fabienne Constant
- Ecole Nationale Vétérinaire d'Alfort, Université Paris-Saclay, UVSQ, INRAE, BREED, Maisons-Alfort, France
| | - Diego P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, Saint-Genes-Champanelle, France
| | - Lucie Rault
- INRAE, Institut Agro, UMR1253 STLO, Rennes, France
| | - Sarah Barbey
- INRAE, UE326 Unité Expérimentale du Pin, Gouffern en Auge, France
| | | | - Olivier Rué
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Jouy-en-Josas, France
| | - Sophie Schbath
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Frederic Launay
- INRAE, UE326 Unité Expérimentale du Pin, Gouffern en Auge, France
| | - Olivier Sandra
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
| | - Rachel Lefebvre
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Yves Le Loir
- INRAE, Institut Agro, UMR1253 STLO, Rennes, France
| | - Pierre Germon
- INRAE, Université de Tours, UMR ISP, 37380, Nouzilly, France
| | | | - Sergine Even
- INRAE, Institut Agro, UMR1253 STLO, Rennes, France.
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17
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Wang D, Tang G, Zhao L, Wang M, Chen L, Zhao C, Liang Z, Chen J, Cao Y, Yao J. Potential roles of the rectum keystone microbiota in modulating the microbial community and growth performance in goat model. J Anim Sci Biotechnol 2023; 14:55. [PMID: 37029437 PMCID: PMC10080759 DOI: 10.1186/s40104-023-00850-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/05/2023] [Indexed: 04/09/2023] Open
Abstract
BACKGROUND Ruminal microbiota in early life plays critical roles in the life-time health and productivity of ruminant animals. However, understanding of the relationship between gut microbiota and ruminant phenotypes is very limited. Here, the relationship between the rectum microbiota, their primary metabolites, and growth rate of a total of 76 young dairy goats (6-month-old) were analyzed, and then 10 goats with the highest or lowest growth rates respectively were further compared for the differences in the rectum microbiota, metabolites, and animal's immune parameters, to investigate the potential mechanisms by which the rectum microbiota contributes to the health and growth rate. RESULTS The analysis of Spearman correlation and microbial co-occurrence network indicated that some keystone rectum microbiota, including unclassified Prevotellaceae, Faecalibacterium and Succinivibrio, were the key modulators to shape the rectum microbiota and closely correlated with the rectum SCFA production and serum IgG, which contribute to the health and growth rate of young goats. In addition, random forest machine learning analysis suggested that six bacterial taxa in feces could be used as potential biomarkers for differentiating high or low growth rate goats, with 98.3% accuracy of prediction. Moreover, the rectum microbiota played more important roles in gut fermentation in early life (6-month-old) than in adulthood stage (19-month-old) of goats. CONCLUSION We concluded that the rectum microbiota was associated with the health and growth rate of young goats, and can be a focus on the design of the early-life gut microbial intervention.
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Affiliation(s)
- Dangdang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Guangfu Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lichao Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mengya Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Luyu Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Congcong Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ziqi Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jie Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yangchun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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18
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Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem. Sci Rep 2023; 13:4056. [PMID: 36906688 PMCID: PMC10008532 DOI: 10.1038/s41598-023-30916-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/03/2023] [Indexed: 03/13/2023] Open
Abstract
Metataxonomy has become the standard for characterizing the diversity and composition of microbial communities associated with multicellular organisms and their environment. Currently available protocols for metataxonomy assume a uniform DNA extraction, amplification and sequencing efficiency for all sample types and taxa. It has been suggested that the addition of a mock community (MC) to biological samples before the DNA extraction step could aid identification of technical biases during processing and support direct comparisons of microbiota composition, but the impact of MC on diversity estimates of samples is unknown. Here, large and small aliquots of pulverized bovine fecal samples were extracted with no, low or high doses of MC, characterized using standard Illumina technology for metataxonomics, and analysed with custom bioinformatic pipelines. We demonstrated that sample diversity estimates were distorted only if MC dose was high compared to sample mass (i.e. when MC > 10% of sample reads). We also showed that MC was an informative in situ positive control, permitting an estimation of the sample 16S copy number, and detecting sample outliers. We tested this approach on a range of sample types from a terrestrial ecosystem, including rhizosphere soil, whole invertebrates, and wild vertebrate fecal samples, and discuss possible clinical applications.
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19
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Effects of Sodium Nitrate and Coated Methionine on Lactation Performance, Rumen Fermentation Characteristics, Amino Acid Metabolism, and Microbial Communities in Lactating Buffaloes. Microorganisms 2023; 11:microorganisms11030675. [PMID: 36985248 PMCID: PMC10057408 DOI: 10.3390/microorganisms11030675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/11/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Sodium nitrate is used as a non-protein nitrogen supplement while methionine is considered as a common methionine additive for ruminants. This study investigated the effects of sodium nitrate and coated methionine supplementation on milk yield, milk composition, rumen fermentation parameters, amino acid composition, and rumen microbial communities in lactating buffaloes. Forty mid-lactation multiparous Murrah buffaloes within the initial days in milk (DIM) = 180.83 ± 56.78 d, milk yield = 7.63 ± 0.19 kg, body weight = 645 ± 25 kg were selected and randomly allocated into four groups (N = 10). All of animals received the same total mixed ratio (TMR) diet. Furthermore, the groups were divided into the control group (CON), 70 g/d sodium nitrate group (SN), 15 g/d palmitate coated L-methionine group (MET), and 70 g/d sodium nitrate +15 g/d palmitate coated L-methionine group (SN+MET). The experiment lasted for six weeks, including two weeks of adaption. The results showed that most rumen-free amino acids, total essential amino acids, and total amino acids in Group SN increased (p < 0.05), while the dry matter intake (DMI) and rumen acetate, propionate, valerate, and total volatile fatty acids (TVFA) in Group MET decreased (p < 0.05). However, there was no significant difference in milk yield, milk protein, milk fat, lactose, total solid content, and sodium nitrate residue in milk among groups (p > 0.05). Group SN+MET had a decreased rumen propionate and valerate (p < 0.05), while increasing the Ace, Chao, and Simpson indices of alpha diversity of rumen bacteria. Proteobacteria and Actinobacteriota were significantly increased (p < 0.05) in Group SN+MET, but Bacteroidota, and Spirochaetota were decreased (p < 0.05). In addition, Group SN+MET also increased the relative abundance of Acinetobacter, Lactococcus, Microbacterium, Chryseobacterium, and Klebsiella, which were positively correlated with cysteine and negatively correlated with rumen acetate, propionate, valerate, and TVFA. Rikenellaceae_RC9_gut_group was identified as a biomarker in Group SN. Norank_f__UCG-011 was identified as a biomarker in Group MET. Acinetobacter, Kurthia, Bacillus, and Corynebacterium were identified as biomarkers in Group SN+MET. In conclusion, sodium nitrate increased rumen free amino acids, while methionine decreased dry matter intake (DMI) and rumen volatile fatty acids. The combined use of sodium nitrate and methionine enriched the species abundance of microorganisms in the rumen and affected the composition of microorganisms in the rumen. However, sodium nitrate, methionine, and their combination had no significant effect on the milk yield and milk composition. It was suggested that the combined use of sodium nitrate and methionine in buffalo production was more beneficial.
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20
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Guo W, Bi SS, Wang WW, Zhou M, Neves ALA, Degen AA, Guan LL, Long RJ. Maternal rumen and milk microbiota shape the establishment of early-life rumen microbiota in grazing yak calves. J Dairy Sci 2023; 106:2054-2070. [PMID: 36710176 DOI: 10.3168/jds.2022-22655] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/05/2022] [Indexed: 01/30/2023]
Abstract
Early-life gut microbial colonization and development exert a profound impact on the health and metabolism of the host throughout the life span. The transmission of microbes from the mother to the offspring affects the succession and establishment of the early-life rumen microbiome in newborns, but the contributions of different maternal sites to the rumen microbial establishment remain unclear. In the present study, samples from different dam sites (namely, oral, rumen fluid, milk, and teat skin) and rumen fluid of yak calves were collected at 6 time points between d 7 and 180 postpartum to determine the contributions of the different maternal sites to the establishment of the bacterial and archaeal communities in the rumen during early life. Our analysis demonstrated that the dam's microbial communities clustered according to the sites, and the calves' rumen microbiota resembled that of the dam consistently regardless of fluctuations at d 7 and 14. The dam's rumen microbiota was the major source of the calves' rumen bacteria (7.9%) and archaea (49.7%) compared with the other sites, whereas the potential sources of the calf rumen microbiota from other sites varied according to the age. The contribution of dam's rumen bacteria increased with age from 0.36% at d 7 to 14.8% at d 180, whereas the contribution of the milk microbiota showed the opposite trend, with its contribution reduced from 2.7% at d 7 to 0.2% at d 180. Maternal oral archaea were the main sources of the calves' rumen archaea at d 14 (50.4%), but maternal rumen archaea became the main source gradually and reached 66.2% at d 180. These findings demonstrated the potential microbial transfer from the dam to the offspring that could influence the rumen microbiota colonization and establishment in yak calves raised under grazing regimens, providing the basis for future microbiota manipulation strategies during their early life.
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Affiliation(s)
- W Guo
- State Key Laboratory of Grassland Agro-ecosystems, International Centre of Tibetan Plateau Ecosystem Management, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China; Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - S S Bi
- State Key Laboratory of Grassland Agro-ecosystems, International Centre of Tibetan Plateau Ecosystem Management, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - W W Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - M Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - A L A Neves
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870, Frederiksberg C, Denmark
| | - A A Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 8410500, Israel
| | - L L Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada.
| | - R J Long
- State Key Laboratory of Grassland Agro-ecosystems, International Centre of Tibetan Plateau Ecosystem Management, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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21
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Fu L, Wang L, Liu L, Zhang L, Zhou Z, Zhou Y, Wang G, Loor JJ, Zhou P, Dong X. Effects of inoculation with active microorganisms derived from adult goats on growth performance, gut microbiota and serum metabolome in newborn lambs. Front Microbiol 2023; 14:1128271. [PMID: 36860489 PMCID: PMC9969556 DOI: 10.3389/fmicb.2023.1128271] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023] Open
Abstract
This study evaluated the effects of inoculation with adult goat ruminal fluid on growth, health, gut microbiota and serum metabolism in lambs during the first 15 days of life. Twenty four Youzhou dark newborn lambs were selected and randomly distributed across 3 treatments (n = 8/group): autoclaved goat milk inoculated with 20 mL sterilized normal saline (CON), autoclaved goat milk inoculated with 20 mL fresh ruminal fluid (RF) and autoclaved goat milk inoculated with 20 mL autoclaved ruminal fluid (ARF). Results showed that RF inoculation was more effective at promoting recovery of body weight. Compared with CON, greater serum concentrations of ALP, CHOL, HDL and LAC in the RF group suggested a better health status in lambs. The relative abundance of Akkermansia and Escherichia-Shigella in gut was lower in the RF group, whereas the relative abundance of Rikenellaceae_RC9_gut_group tended to increase. Metabolomics analysis shown that RF stimulated the metabolism of bile acids, small peptides, fatty acids and Trimethylamine-N-Oxide, which were found the correlation relationship with gut microorganisms. Overall, our study demonstrated that ruminal fluid inoculation with active microorganisms had a beneficial impact on growth, health and overall metabolism partly through modulating the gut microbial community.
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Affiliation(s)
- Lin Fu
- Chongqing Academy of Animal Sciences, Chongqing, China
| | - Liaochuan Wang
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Li Liu
- Chongqing Chemical Industry Vocational College, Chongqing, China
| | - Li Zhang
- Chongqing Academy of Animal Sciences, Chongqing, China
| | - Ziyao Zhou
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yan Zhou
- Chongqing Academy of Animal Sciences, Chongqing, China
| | - Gaofu Wang
- Chongqing Academy of Animal Sciences, Chongqing, China
| | - Juan J. Loor
- Mammalian NutriPhysioGenomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
| | - Peng Zhou
- Chongqing Academy of Animal Sciences, Chongqing, China,*Correspondence: Peng Zhou, ; Xianwen Dong,
| | - Xianwen Dong
- Chongqing Academy of Animal Sciences, Chongqing, China,*Correspondence: Peng Zhou, ; Xianwen Dong,
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22
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Kibegwa FM, Bett RC, Gachuiri CK, Machuka E, Stomeo F, Mujibi FD. Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle. PLoS One 2023; 18:e0274371. [PMID: 36638091 PMCID: PMC9838872 DOI: 10.1371/journal.pone.0274371] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/29/2022] [Indexed: 01/14/2023] Open
Abstract
The objective of this study was to investigate the effect of varying roughage and concentrate proportions, in diet of crossbreed dairy cattle, on the composition and associated functional genes of rumen and fecal microbiota. We also explored fecal samples as a proxy for rumen liquor samples. Six crossbred dairy cattle were reared on three diets with an increasing concentrate and reducing roughage amount in three consecutive 10-day periods. After each period, individual rumen liquor and fecal samples were collected and analyzed through shotgun metagenomic sequencing. Average relative abundance of identified Operational Taxonomic Units (OTU) and microbial functional roles from all animals were compared between diets and sample types (fecal and rumen liquor). Results indicated that dietary modifications significantly affected several rumen and fecal microbial OTUs. In the rumen, an increase in dietary concentrate resulted in an upsurge in the abundance of Proteobacteria, while reducing the proportions of Bacteroidetes and Firmicutes. Conversely, changes in microbial composition in fecal samples were not consistent with dietary modification patterns. Microbial functional pathway classification identified that carbohydrate metabolism and protein metabolism pathways dominated microbial roles. Assessment of dietary effects on the predicted functional roles of these microbiota revealed that a high amount of dietary concentrate resulted in an increase in central carbohydrate metabolism and a corresponding reduction in protein synthesis. Moreover, we identified several microbial stress-related responses linked to dietary changes. Bacteroides and Clostridium genera were the principal hosts of these microbial functions. Therefore, the roughage to concentrate proportion has more influence on the microbial composition and microbial functional genes in rumen samples than fecal samples. As such, we did not establish a significant relationship between the rumen and fecal metagenome profiles, and the rumen and fecal microbiota from one animal did not correlate more than those from different animals.
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Affiliation(s)
- Felix M. Kibegwa
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
- * E-mail:
| | - Rawlynce C. Bett
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - Charles K. Gachuiri
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - Eunice Machuka
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Francesca Stomeo
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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23
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Huang L, Chen C. Employing pigs to decipher the host genetic effect on gut microbiome: advantages, challenges, and perspectives. Gut Microbes 2023; 15:2205410. [PMID: 37122143 PMCID: PMC10153013 DOI: 10.1080/19490976.2023.2205410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
The gut microbiota is a complex and diverse ecosystem comprised of trillions of microbes and plays an essential role in host's immunity, metabolism, and even behaviors. Environmental and host factors drive the huge variations in the gut microbiome among individuals. Here, we summarize accumulated evidences about host genetic effect on the gut microbial compositions with emphases on the correlation between host genetic kinship and the similarity of microbial compositions, heritability estimates of microbial taxa, and identification of genomic variants associated with the gut microbiome in pigs as well as in humans. A proportion of bacterial taxa have been reported to be heritable, and numerous variants associated with the diversity of the gut microbiota or specific taxa have been identified in both humans and pigs. LCT and ABO gene have been replicated in multiple studies, and its mechanism have been elucidated clearly. We also discuss the main advantages and challenges using pigs as experimental animals in exploring host genetic effect on the gut microbial composition and provided our insights on the perspectives in this area.
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Affiliation(s)
- Lusheng Huang
- National Key Laboratory of Pig Genetic Improvement, Jiangxi Agricultural University, Nanchang, China
| | - Congying Chen
- National Key Laboratory of Pig Genetic Improvement, Jiangxi Agricultural University, Nanchang, China
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24
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Exploring variation in the fecal microbial communities of Kasaragod Dwarf and Holstein crossbred cattle. Antonie Van Leeuwenhoek 2023; 116:53-65. [PMID: 36450879 DOI: 10.1007/s10482-022-01791-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 10/30/2022] [Indexed: 12/02/2022]
Abstract
The gut microbiota and its impact on health and nutrition in animals, including cattle has been of intense interest in recent times. Cattle, in particular indigenous varieties like Kasaragod Dwarf cow, have not received the due consideration given to other non-native cattle breeds, and the composition of their fecal microbiome is yet to be established. This study applied 16S rRNA high-throughput sequencing of fecal samples and compared the Kasaragod Dwarf with the highly prevalent Holstein crossbred cattle. Variation in their microbial composition was confirmed by marker gene-based taxonomic analysis. Principle Coordinate Analysis (PCoA) showed the distinct microbial architecture of the two cattle types. While the two cattle types possess unique signature taxa, in Kasaragod Dwarf cattle, many of the identified genera, including Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Paludibacter, Sutterella, Coprobacillus, and Ruminobacter, have previously been shown to be present in higher abundance in animals with higher feed efficiency. This is the first report of Kasaragod Dwarf cattle fecal microbiome profiling. Our findings highlight the predominance of specific taxa potentially associated with different fermentation products and feed efficiency phenotypes in Kasaragod Dwarf cattle compared to Holstein crossbred cattle.
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25
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Jones HE, Wilson PB. Progress and opportunities through use of genomics in animal production. Trends Genet 2022; 38:1228-1252. [PMID: 35945076 DOI: 10.1016/j.tig.2022.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/08/2022] [Accepted: 06/17/2022] [Indexed: 01/24/2023]
Abstract
The rearing of farmed animals is a vital component of global food production systems, but its impact on the environment, human health, animal welfare, and biodiversity is being increasingly challenged. Developments in genetic and genomic technologies have had a key role in improving the productivity of farmed animals for decades. Advances in genome sequencing, annotation, and editing offer a means not only to continue that trend, but also, when combined with advanced data collection, analytics, cloud computing, appropriate infrastructure, and regulation, to take precision livestock farming (PLF) and conservation to an advanced level. Such an approach could generate substantial additional benefits in terms of reducing use of resources, health treatments, and environmental impact, while also improving animal health and welfare.
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Affiliation(s)
- Huw E Jones
- UK Genetics for Livestock and Equines (UKGLE) Committee, Department for Environment, Food and Rural Affairs, Nobel House, 17 Smith Square, London, SW1P 3JR, UK; Nottingham Trent University, Brackenhurst Campus, Brackenhurst Lane, Southwell, NG25 0QF, UK.
| | - Philippe B Wilson
- UK Genetics for Livestock and Equines (UKGLE) Committee, Department for Environment, Food and Rural Affairs, Nobel House, 17 Smith Square, London, SW1P 3JR, UK; Nottingham Trent University, Brackenhurst Campus, Brackenhurst Lane, Southwell, NG25 0QF, UK
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26
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Zeng S, Wang S, Ross RP, Stanton C. The road not taken: host genetics in shaping intergenerational microbiomes. Trends Genet 2022; 38:1180-1192. [PMID: 35773025 DOI: 10.1016/j.tig.2022.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 02/09/2023]
Abstract
The early-life gut microbiome is linked to human phenotypes as an imbalanced microbiome of this period is implicated in diseases throughout life. Several determinants of early-life gut microbiome are explored, however, mechanisms of acquisition, colonization, and stability of early-life gut microbiome and their interindividual variability remain elusive. Host genetics play a vital role to shape the gut microbiome and interact with it to modulate individual phenotypes in human studies and animal models. Given the microbial linkage between host generations, we discuss the current state of roles of host genetics in forming intergenerational microbiomes associated with mothers, offspring, and those vertically transmitted, providing a basis for taking into account host genetics in future early-life microbiome research. We further expand our discussion to the bidirectional interactions between host gene expression and microbiome in human health.
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Affiliation(s)
- Shuqin Zeng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China; APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland
| | - Shaopu Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China; APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland
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Effects of a farm-specific fecal microbial transplant (FMT) product on clinical outcomes and fecal microbiome composition in preweaned dairy calves. PLoS One 2022; 17:e0276638. [PMID: 36269743 PMCID: PMC9586405 DOI: 10.1371/journal.pone.0276638] [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: 01/20/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Gastrointestinal disease (GI) is the most common illness in pre-weaned dairy calves. Therefore, effective strategies to manipulate the microbiome of dairy calves under commercial dairy operations are of great importance to improve animal health and reduce antimicrobial usage. The objective of this study was to develop a farm-specific FMT product and to investigate its effects on clinical outcomes and fecal microbial composition of dairy calves. The FMT product was derived from feces from healthy donors (5–24 days of age) raised in the same calf ranch facility as the FMT recipients. Healthy and diarrheic calves were randomly enrolled to a control (n = 115) or FMT (n = 112) treatment group (~36 g of processed fecal matter once daily for 3 days). Fecal samples were collected at enrollment and again 9 days later after the first FMT dose. Although the FMT product was rich in organisms typically known for their beneficial probiotic properties, the FMT therapy did not prevent or ameliorate GI disease in dairy calves. In fact, calves that received FMT were less likely to recover from GI disease, and more likely to die due to GI disease complications. Fecal microbial community analysis revealed an increase in the alpha-diversity in FMT calves; however, no major differences across treatment groups were observed in the beta-diversity analysis. Calves that received FMT had higher relative abundance of an uncultured organism of the genus Lactobacillus and Lactobacillus reuteri on day 10. Moreover, FMT calves had lower relative abundance of Clostridium nexile and Bacteroides vulgatus on day 10. Our results indicate the need to have an established protocol when developing FMT products, based on rigorous inclusion and exclusion criteria for the selection of FMT donors free of potential pathogens, no history of disease or antibiotic treatment.
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Yang H, Heirbaut S, Jing X, De Neve N, Vandaele L, Jeyanathan J, Fievez V. Susceptibility of dairy cows to subacute ruminal acidosis is reflected in both prepartum and postpartum bacteria as well as odd- and branched-chain fatty acids in feces. J Anim Sci Biotechnol 2022; 13:87. [PMID: 36195941 PMCID: PMC9533591 DOI: 10.1186/s40104-022-00738-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background The transition period is a challenging period for high-producing dairy cattle. Cows in early lactation are considered as a group at risk of subacute ruminal acidosis (SARA). Variability in SARA susceptibility in early lactation is hypothesized to be reflected in fecal characteristics such as fecal pH, dry matter content, volatile and odd- and branched-chain fatty acids (VFA and OBCFA, respectively), as well as fecal microbiota. This was investigated with 38 periparturient dairy cows, which were classified into four groups differing in median and mean time of reticular pH below 6 as well as area under the curve of pH below 6. Furthermore, we investigated whether fecal differences were already obvious during a period prior to the SARA risk (prepartum). Results Variation in reticular pH during a 3-week postpartum period was not associated with differences in fecal pH and VFA concentration. In the postpartum period, the copy number of fecal bacteria and methanogens of unsusceptible (UN) cows was higher than moderately susceptible (MS) or susceptible (SU) cows, while the genera Ruminococcus and Prevotellacea_UCG-001 were proportionally less abundant in UN compared with SU cows. Nevertheless, only a minor reduction was observed in iso-BCFA proportions in fecal fatty acids of SU cows, particularly iso-C15:0 and iso-C16:0, compared with UN cows. Consistent with the bacterial changes postpartum, the lower abundance of Ruminococcus was already observed in the prepartum fecal bacterial communities of UN cows, whereas Lachnospiraceae_UCG-001 was increased. Nevertheless, no differences were observed in the prepartum fecal VFA or OBCFA profiles among the groups. Prepartum fecal bacterial communities of cows were clustered into two distinct clusters with 70% of the SU cows belonging to cluster 1, in which they represented 60% of the animals. Conclusions Inter-animal variation in postpartum SARA susceptibility was reflected in post- and prepartum fecal bacterial communities. Differences in prepartum fecal bacterial communities could alert for susceptibility to develop SARA postpartum. Our results generated knowledge on the association between fecal bacteria and SARA development which could be further explored in a prevention strategy. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00738-8.
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Affiliation(s)
- Hong Yang
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, building F, 1st floor, Coupure Links 653, 9000, Ghent, Belgium
| | - Stijn Heirbaut
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, building F, 1st floor, Coupure Links 653, 9000, Ghent, Belgium
| | - Xiaoping Jing
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, building F, 1st floor, Coupure Links 653, 9000, Ghent, Belgium.,State Key Laboratory of Grassland and Agro-Ecosystems, International Centre for Tibetan Plateau Ecosystem Management, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Nympha De Neve
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, building F, 1st floor, Coupure Links 653, 9000, Ghent, Belgium
| | - Leen Vandaele
- Animal Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Scheldeweg 68, 9090, Melle, Belgium
| | - Jeyamalar Jeyanathan
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, building F, 1st floor, Coupure Links 653, 9000, Ghent, Belgium
| | - Veerle Fievez
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Campus Coupure, building F, 1st floor, Coupure Links 653, 9000, Ghent, Belgium.
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Huang G, Qu Q, Wang M, Huang M, Zhou W, Wei F. Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156178. [PMID: 35618126 DOI: 10.1016/j.scitotenv.2022.156178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/07/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Multiple factors influence gut microbiome diversity in vertebrate hosts. Most previous studies have only investigated specific factors and certain host species or taxa. However, a comprehensive assessment of the relative contributions of individual factors towards gut microbial diversity within a broader evolutionary context remains lacking. Here, 2202 16S rRNA gene sequencing samples of gut bacterial communities collected from 452 host species across seven classes were analyzed together to understand the factors broadly affecting vertebrate gut microbiomes across hosts with different diets, threatened status, captivity status, and habitat environmental factors. Among wild vertebrates, diet was most significantly associated with gut microbiome alpha diversity, while host phylogeny and diet were significantly associated with beta diversity, consistent with a previous study. Host threatened status and habitat environmental factors (e.g., geography and climate) were also associated with gut bacterial community beta diversity. Subsequent ecological modeling revealed a strong association between stochastic assembly processes and patterns of gut bacterial diversity among free-ranging vertebrates. In addition, metagenomic analysis of gut microbiomes from 62 captive vertebrates and sympatric humans revealed similar diversity and resistome profiles despite differences in host phylogeny, diet, and threatened status. These results thus suggest that captivity diminishes the effects of host phylogeny, diet, and threatened status on the diversity of vertebrate gut bacterial communities. The most overrepresented antibiotic resistant genes (ARGs) observed in these samples are involved in resistance to β-lactams, aminoglycosides, and tetracycline. These results also revealed potential horizontal transfers of ARGs between captive animals and humans, thereby jointly threatening public health and vertebrate conservation. Together, this study provides a comprehensive overview of the diversity and resistomes of vertebrate gut microbiomes. These combined analyses will help guide future vertebrate conservation via the rational manipulation of microbial diversity and reducing antibiotic usage.
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Affiliation(s)
- Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingyue Qu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingpan Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
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Zhao C, Wang L, Ke S, Chen X, Kenéz Á, Xu W, Wang D, Zhang F, Li Y, Cui Z, Qiao Y, Wang J, Sun W, Zhao J, Yao J, Yu Z, Cao Y. Yak rumen microbiome elevates fiber degradation ability and alters rumen fermentation pattern to increase feed efficiency. ANIMAL NUTRITION 2022; 11:201-214. [PMID: 36263411 PMCID: PMC9556794 DOI: 10.1016/j.aninu.2022.07.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/21/2022] [Accepted: 07/28/2022] [Indexed: 11/28/2022]
Abstract
Rumen microbes play an important role in ruminant energy supply and animal performance. Previous studies showed that yak (Bos grunniens) rumen microbiome and fermentation differ from other ruminants. However, little is understood about the features of the rumen microbiome that make yak adapted to their unique environmental and dietary conditions. This study was to investigate the rumen microbiome and metabolome to understand how yak adapt to the coarse forage and harsh environment in the Qinghai-Tibetan plateau. Nine female Qaidam yellow cattle (Bos taurus), 9 dzomo (hybrids of cattle and yak) and 9 female plateau yak (B. grunniens), about 5 to 6 years old, were used in this study. Rumen fermentation parameters, fibrolytic enzyme activities, and rumen metataxonomic were determined. Then 18 (6 samples per group) were selected for rumen metagenomic and metabolome analysis. Metataxonomic analysis revealed that the rumen microbiota was significantly different among plateau yak, Qaidam yellow cattle, and dzomo (P < 0.05). Metagenomic analysis displayed a larger gene pool encoding a richer repertoire of carbohydrate-active enzymes in the rumen microbiome of plateau yak and dzomo than Qaidam yellow cattle (P < 0.05). Some of the genes encoding glycoside hydrolases that mediate the digestion of cellulose and hemicellulose were significantly enriched in the rumen of plateau yak than Qaidam yellow cattle, but glycoside hydrolase 57 that primarily includes amylases was abundant in Qaidam yellow cattle (P < 0.05). The rumen fermentation profile differed also, Qaidam yellow cattle having a higher molar proportion of acetate but a lower molar proportion of propionate than dzomo and plateau yak (P < 0.05). Based on metabolomic analysis, rumen microbial metabolic pathways and metabolites were different. Differential metabolites are mainly amino acids, carboxylic acids, sugars, and bile acids. Changes in rumen microbial composition could explain the above results. The present study showed that the rumen microbiome of plateau yak helps its host to adapt to the Qinghai-Tibetan plateau. In particular, the plateau yak rumen microbiome has more enzymes genes involved in cellulase and hemicellulase than that of cattle, resulting higher fibrolytic enzyme activities in yak, further providing stronger fiber degradation function.
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Wen X, Luo S, Lv D, Jia C, Zhou X, Zhai Q, Xi L, Yang C. Variations in the fecal microbiota and their functions of Thoroughbred, Mongolian, and Hybrid horses. Front Vet Sci 2022; 9:920080. [PMID: 35968025 PMCID: PMC9366519 DOI: 10.3389/fvets.2022.920080] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022] Open
Abstract
The horse gut is colonized by a rich and complex microbial community that has important roles in horse physiology, metabolism, nutrition, and immune functions. Fewer across-breed variations in horse gut microbial diversity have been illustrated. In this article, the gut microbiota of Thoroughbred, Mongolian, and Hybrid horses [first filial generation (F1) of Mongolian (maternal) and Thoroughbred (paternal)] were studied by second-generation high-throughput sequencing technology. Differences in gut microbiota composition and function between breeds were determined using diversity and functional prediction analysis. The alpha diversity analysis showed that Thoroughbred horses had a more abundant and diverse gut microbiota, while the diversity of gut microbiota in Hybrid horses was intermediate between Thoroughbred and Mongolian horses. Subsequent cluster analysis showed that Hybrid horses have a microbiota composition more similar to Mongolian horses. LEfSe analysis revealed that the bacterial biomarkers for Thoroughbred horses at the family level were Prevotellaceae, Rikenellaceae, Fibrobacteraceae, p_251_o5, Lactobacillaceae, and uncultured_bacterium_o_WCHB1_41; the bacterial biomarker for Mongolian horses was Planococcaceae; and the bacterial biomarkers for Hybrid horses were Moraxellaceae, Enterobacteriaceae, and Ruminococcaceae. The functional prediction results indicated that the metabolic pathways differ significantly between the breeds. Regarding metabolism, the Hybrid horses had the lowest proportion of the carbohydrate metabolic pathways, while the energy metabolic pathway had the highest proportion. The abundance ratios of the remaining eight metabolic pathways in Hybrid horses were between Thoroughbred and Mongolian horses. In conclusion, the results of this study showed an association between horse breeds and gut microbiota.
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Affiliation(s)
- Xiaohui Wen
- Institute of Animal Health, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shengjun Luo
- Institute of Animal Health, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dianhong Lv
- Institute of Animal Health, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chunling Jia
- Institute of Animal Health, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiurong Zhou
- Institute of Animal Health, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qi Zhai
- Institute of Animal Health, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Li Xi
- Department of Animal Science, College of Biology and Food, Shangqiu Normal University, Shangqiu, China
- *Correspondence: Li Xi
| | - Caijuan Yang
- National S&T Innovation Center for Modern Agricultural Industry, Guangzhou, China
- Caijuan Yang
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Mansilla FI, Ficoseco CA, Miranda MH, Puglisi E, Nader-Macías MEF, Vignolo GM, Fontana CA. Administration of probiotic lactic acid bacteria to modulate fecal microbiome in feedlot cattle. Sci Rep 2022; 12:12957. [PMID: 35902668 PMCID: PMC9334624 DOI: 10.1038/s41598-022-16786-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 07/15/2022] [Indexed: 11/20/2022] Open
Abstract
Modulation of animal gut microbiota is a prominent function of probiotics to improve the health and performance of livestock. In this study, a large-scale survey to evaluate the effect of lactic acid bacteria probiotics on shaping the fecal bacterial community structure of feedlot cattle during three experimental periods of the fattening cycle (163 days) was performed. A commercial feedlot located in northwestern Argentina was enrolled with cattle fed mixed rations (forage and increasing grain diet) and a convenience-experimental design was conducted. A pen (n = 21 animals) was assigned to each experimental group that received probiotics during three different periods. Groups of n = 7 animals were sampled at 40, 104 and 163 days and these samples were then pooled to one, thus giving a total of 34 samples that were subjected to high-throughput sequencing. The microbial diversity of fecal samples was significantly affected (p < 0.05) by the administration period compared with probiotic group supplementation. Even though, the three experimental periods of probiotic administration induced changes in the relative abundance of the most representative bacterial communities, the fecal microbiome of samples was dominated by the Firmicutes (72-98%) and Actinobacteria (0.8-27%) phyla, while a lower abundance of Bacteroidetes (0.08-4.2%) was present. Probiotics were able to modulate the fecal microbiota with a convergence of Clostridiaceae, Lachnospiraceae, Ruminococcaceae and Bifidobacteriaceae associated with health and growth benefits as core microbiome members. Metabolic functional prediction comparing three experimental administration periods (40, 104 and 163 days) showed an enrichment of metabolic pathways related to complex plant-derived polysaccharide digestion as well as amino acids and derivatives during the first 40 days of probiotic supplementation. Genomic-based knowledge on the benefits of autochthonous probiotics on cattle gastrointestinal tract (GIT) microbiota composition and functions will contribute to their selection as antibiotic alternatives for commercial feedlot.
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Affiliation(s)
| | | | | | - Edoardo Puglisi
- Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Cremona-Piacenza, Italy
| | | | | | - Cecilia Alejandra Fontana
- Instituto Nacional de Tecnología Agropecuaria INTA EEA-Famaillá, Tucumán, Argentina.
- Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Cremona-Piacenza, Italy.
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Dorbek-Kolin E, Husso A, Niku M, Loch M, Pessa-Morikawa T, Niine T, Kaart T, Iivanainen A, Orro T. Faecal microbiota in two-week-old female dairy calves during acute cryptosporidiosis outbreak - Association with systemic inflammatory response. Res Vet Sci 2022; 151:116-127. [PMID: 35901524 DOI: 10.1016/j.rvsc.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/15/2022] [Accepted: 07/17/2022] [Indexed: 11/25/2022]
Abstract
In the present study, relationships between the intestinal microbiota and innate immunity response, acute cryptosporidiosis, and weight gain in female dairy calves were investigated. A total of 112 calves born during a natural outbreak of cryptosporidiosis on one dairy farm was included in the study. Microbiota composition was analysed by means of 16S ribosomal RNA gene amplicon sequencing from faecal samples collected during the second week of life, while the status of Cryptosporidium spp. infection was determined using immunofluorescence. Serum samples from the second week of life were colourimetrically analysed for the following markers of acute inflammation: acute-phase proteins (serum amyloid A and haptoglobin) and pro-inflammatory cytokines (interleukin-1 beta, interleukin-6, and tumour necrosis factor-alpha). Statistical analyses were performed using random forest analysis, variance-partitioning, and negative binomial regression. The faecal microbiota of the two-week old calves was composed of the phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, and Actinobacteria (in order of decreasing abundance). Microbial diversity, measured in terms of the Shannon index, increased with the age of the calves and decreased if a high count of Cryptosporidium spp. oocysts was found in the faeces. Fusobacterium was positively associated with Cryptosporidium spp. oocyst count and serum amyloid A concentration. Peptostreptococcus was positively associated with haptoglobin and serum amyloid A concentrations, and negatively associated with average daily weight gain at 9 months of age. The markers of innate immunity, in combination with age, explained 6% of the microbial variation. These results suggest that some components of the intestinal microbiota may have a long-lasting negative effect on animal growth through the stimulation of the systemic innate immune response.
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Affiliation(s)
- Elisabeth Dorbek-Kolin
- Veterinary Biomedicine and Food Hygiene, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia.
| | - Aleksi Husso
- Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, P.O. Box 66, Helsinki, Finland
| | - Mikael Niku
- Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, P.O. Box 66, Helsinki, Finland
| | - Marina Loch
- Clinical Veterinary Medicine, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia
| | - Tiina Pessa-Morikawa
- Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, P.O. Box 66, Helsinki, Finland
| | - Tarmo Niine
- Veterinary Biomedicine and Food Hygiene, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia
| | - Tanel Kaart
- Animal Breeding and Biotechnology, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia
| | - Antti Iivanainen
- Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, P.O. Box 66, Helsinki, Finland
| | - Toomas Orro
- Clinical Veterinary Medicine, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia
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Feng Y, Liu D, Liu Y, Yang X, Zhang M, Wei F, Li D, Hu Y, Guo Y. Host-genotype-dependent cecal microbes are linked to breast muscle metabolites in Chinese chickens. iScience 2022; 25:104469. [PMID: 35707722 PMCID: PMC9189123 DOI: 10.1016/j.isci.2022.104469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/08/2022] [Accepted: 05/20/2022] [Indexed: 11/18/2022] Open
Abstract
In chickens, the effect of host genetics on the gut microbiota is not fully understood, and the extent to which the heritable gut microbes affect chicken metabolism and physiology is still an open question. Here, we explored the interactions among chicken genetics, the cecal microbiota and metabolites in breast muscle from ten chicken breeds in China. We found that different chicken breeds displayed distinct cecal microbial community structures and functions, and 15 amplicon sequence variants (ASVs) were significantly associated with host genetics through different genetic loci, such as those related to the intestinal barrier function. We identified five heritable ASVs significantly associated with 53 chicken muscle metabolites, among which the Megamonas probably affected lipid metabolism through the production of propionate. Our study revealed that the chicken genetically associated cecal microbes may have the potential to affect the bird’s physiology and metabolism. The cecal microbiota are different among ten chicken breeds The chicken genetics influences the cecal microbiota structures and functions The chicken heritable cecal microbes are associated with muscle metabolites Megamonas may affect lipid metabolism by the production of propionate
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Affiliation(s)
- Yuqing Feng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Dan Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Yan Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Xinyue Yang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Meihong Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Fuxiao Wei
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Depeng Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
- Corresponding author
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
- Corresponding author
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Zhang J, Liang Z, Ding Kao R, Han J, Du M, Ahmad AA, Wang S, Salekdeh GH, Long R, Yan P, Ding X. Maternal Fecal Microbes Contribute to Shaping the Early Life Assembly of the Intestinal Microbiota of Co-inhabiting Yak and Cattle Calves. Front Microbiol 2022; 13:916735. [PMID: 35733965 PMCID: PMC9208665 DOI: 10.3389/fmicb.2022.916735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The Qinghai-Tibetan Plateau offers one of the most extreme environments for yaks (Bos grunniens). Although the genetic adaptability of yak and rumen metagenomes is increasingly understood, the relative contribution of host genetics and maternal symbiotic microbes throughout early intestinal microbial successions in yaks remains elusive. In this study, we assessed the intestinal microbiota succession of co-inhabiting yak and cattle (Bos taurus) calves at different weeks after birth as well as the modes of transmission of maternal symbiotic microbes (i.e., rumen fluid, feces, oral cavity, and breast skin) to their calves' intestinal microbiota colonization. We found that the fecal microbiota of yak and cattle calves after birth was dominated by members of the families Ruminococcaceae, Bacteroidaceae, and Lachnospiraceae. The Source Tracker model revealed that maternal fecal microbes played an important role (the average contribution was about 80%) in the intestinal microbial colonization of yak and cattle calves at different weeks after birth. Unlike cattle calves, there was no significant difference in the fecal microbiota composition of yak calves between 5 and 9 weeks after birth (Wilcoxon test, P > 0.05), indicating that yak may adapt to its natural extreme environment to stabilize its intestinal microbiota composition. Additionally, our results also find that the intestinal microbial composition of yak and cattle calves, with age, gradually tend to become similar, and the differences between species gradually decrease. The findings of this study are vital for developing strategies to manipulate the intestinal microbiota in grazing yaks and cattle for better growth and performance on the Qinghai-Tibetan Plateau.
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Affiliation(s)
- Jianbo Zhang
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zeyi Liang
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | | | - Jianlin Han
- Livestock Genetics Program, International Livestock Research Institute, Nairobi, Kenya
- Chinese Academy of Agricultural Sciences (CAAS) and International Livestock Research Institute (ILRI) Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, CAAS, Beijing, China
| | - Mei Du
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Anum Ali Ahmad
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shengyi Wang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Ruijun Long
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuezhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
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36
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Harutyunyan N, Kushugulova A, Hovhannisyan N, Pepoyan A. One Health Probiotics as Biocontrol Agents: One Health Tomato Probiotics. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11101334. [PMID: 35631758 PMCID: PMC9145216 DOI: 10.3390/plants11101334] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/08/2022] [Accepted: 05/08/2022] [Indexed: 05/06/2023]
Abstract
Tomato (Lycopersicon esculentum) is one of the most popular and valuable vegetables in the world. The most common products of its industrial processing in the food industry are juice, tomato paste, various sauces, canned or sun-dried fruits and powdered products. Tomato fruits are susceptible to bacterial diseases, and bacterial contamination can be a risk factor for the safety of processed tomato products. Developments in bioinformatics allow researchers to discuss target probiotic strains from an existing large number of probiotic strains for any link in the soil-plant-animal-human chain. Based on the literature and knowledge on the "One Health" concept, this study relates to the suggestion of a new term for probiotics: "One Health probiotics", beneficial for the unity of people, animals, and the environment. Strains of Lactiplantibacillus plantarum, having an ability to ferment a broad spectrum of plant carbohydrates, probiotic effects in human, and animal health, as well as being found in dairy products, vegetables, sauerkraut, pickles, some cheeses, fermented sausages, fish products, and rhizospheric soil, might be suggested as one of the probable candidates for "One Health" probiotics (also, for "One Health-tomato" probiotics) for the utilization in agriculture, food processing, and healthcare.
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Affiliation(s)
- Natalya Harutyunyan
- Food Safety and Biotechnology Department, Armenian National Agrarian University, 74 Teryan St., Yerevan 0009, Armenia;
| | - Almagul Kushugulova
- Laboratory of Human Microbiome and Longevity, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Ave., Nur-Sultan 010000, Kazakhstan;
| | - Narine Hovhannisyan
- Plant Origin Raw Material Processing Technology Department, Armenian National Agrarian University, 74 Teryan St., Yerevan 0009, Armenia;
| | - Astghik Pepoyan
- Food Safety and Biotechnology Department, Armenian National Agrarian University, 74 Teryan St., Yerevan 0009, Armenia;
- Correspondence: ; Tel.: +374-91-432-493
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37
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Gastrointestinal Microbiota of Spiny Lobster: A Review. FISHES 2022. [DOI: 10.3390/fishes7030108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The gastrointestinal (GI) microbiota is a group of complex and dynamic microorganisms present in the GI tract of an organism that live in symbiosis with the host and benefit the host with various biological functions. The communities of GI microbiota are formed by various aerobic, anaerobic, and facultatively anaerobic bacteria in aquatic species. In spiny lobsters, common GI microorganisms found in the GI tract are Vibrio, Pseudomonas, Bacillus, Micrococcus, and Flavobacterium, where the structure and abundance of these microbes are varied depending on the environment. GI microbiotas hold an important role and significantly affect the overall condition of spiny lobsters, such as secreting digestive enzymes (lipase, protease, and cellulase), helping in digesting food intake, providing nutrition and synthesising vitamins needed by the host system, and protecting the host against infection from pathogens and diseases by activating an immune mechanism in the GI tract. The microorganisms in the water column, sediment, and diet are primarily responsible for altering, manipulating, and shaping GI microbial structures and communities. This review also highlights the possibilities of isolating the indigenous GI microbiota as a potential probiotic strain and introducing it to spiny lobster juveniles and larvae for better health management.
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38
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Rumen sampling methods bias bacterial communities observed. PLoS One 2022; 17:e0258176. [PMID: 35511785 PMCID: PMC9070869 DOI: 10.1371/journal.pone.0258176] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/10/2022] [Indexed: 01/04/2023] Open
Abstract
The rumen is a complex ecosystem that plays a critical role in our efforts to improve feed efficiency of cattle and reduce their environmental impacts. Sequencing of the 16S rRNA gene provides a powerful tool to survey the bacterial and some archaeal. Oral stomach tubing a cow to collect a rumen sample is a rapid, cost-effective alternative to rumen cannulation for acquiring rumen samples. In this study, we determined how sampling method (oral stomach tubing vs cannulated grab sample), as well as rumen fraction type (liquid vs solid), bias the bacterial and archaeal communities observed. Liquid samples were further divided into liquid strained through cheesecloth and unstrained. Fecal samples were also collected to determine how these differed from the rumen sample types. The abundance of major archaeal communities was not different at the family level in samples acquired via rumen cannula or stomach tube. In contrast to the stable archaeal communities across sample type, the bacterial order WCHB1-41 (phylum Kiritimatiellaeota) was enriched in both liquid strained and unstrained samples as well as the family Prevotellaceae as compared to grab samples. However, these liquid samples had significantly lower abundance of Lachnospiraceae compared with grab samples. Solid samples strained of rumen liquid most closely resembled the grab samples containing both rumen liquid and solid particles obtained directly from the rumen cannula; therefore, inclusion of particulate matter is important for an accurate representation of the rumen bacteria. Stomach tube samples were the most variable and were most representative of the liquid phase. In comparison with a grab sample, stomach tube samples had significantly lower abundance of Lachnospiraceae, Fibrobacter and Treponema. Fecal samples did not reflect the community composition of the rumen, as fecal samples had significantly higher relative abundance of Ruminococcaceae and significantly lower relative abundance of Lachnospiraceae compared with grab samples.
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39
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Ryu EP, Davenport ER. Host Genetic Determinants of the Microbiome Across Animals: From Caenorhabditis elegans to Cattle. Annu Rev Anim Biosci 2022; 10:203-226. [PMID: 35167316 PMCID: PMC11000414 DOI: 10.1146/annurev-animal-020420-032054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Animals harbor diverse communities of microbes within their gastrointestinal tracts. Phylogenetic relationship, diet, gut morphology, host physiology, and ecology all influence microbiome composition within and between animal clades. Emerging evidence points to host genetics as also playing a role in determining gut microbial composition within species. Here, we discuss recent advances in the study of microbiome heritability across a variety of animal species. Candidate gene and discovery-based studies in humans, mice, Drosophila, Caenorhabditis elegans, cattle, swine, poultry, and baboons reveal trends in the types of microbes that are heritable and the host genes and pathways involved in shaping the microbiome. Heritable gut microbes within a host species tend to be phylogenetically restricted. Host genetic variation in immune- and growth-related genes drives the abundances of these heritable bacteria within the gut. With only a small slice of the metazoan branch of the tree of life explored to date, this is an area rife with opportunities to shed light into the mechanisms governing host-microbe relationships.
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Affiliation(s)
- Erica P Ryu
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA; ,
| | - Emily R Davenport
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA; ,
- Huck Institutes of the Life Sciences and Institute for Computational and Data Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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40
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Sun G, Yang X, Wei Q, Xia T, Zhang L, Wang X, Zhang H. Characterization of gut microbiota in captive Himalayan tahr (Hemitragus jemlahicus) and the limited effect of sex on intestinal microorganisms of tahrs. THE EUROPEAN ZOOLOGICAL JOURNAL 2021. [DOI: 10.1080/24750263.2021.1994045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- G. Sun
- College of Life Science, Qufu Normal University, Qufu, China
| | - X. Yang
- College of Life Science, Qufu Normal University, Qufu, China
| | - Q. Wei
- College of Life Science, Qufu Normal University, Qufu, China
| | - T. Xia
- College of Life Science, Qufu Normal University, Qufu, China
| | - L. Zhang
- College of Life Science, Qufu Normal University, Qufu, China
| | - X. Wang
- College of Life Science, Qufu Normal University, Qufu, China
| | - H. Zhang
- College of Life Science, Qufu Normal University, Qufu, China
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41
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Fan P, Kim M, Liu G, Zhai Y, Liu T, Driver JD, Jeong KC. The Gut Microbiota of Newborn Calves and Influence of Potential Probiotics on Reducing Diarrheic Disease by Inhibition of Pathogen Colonization. Front Microbiol 2021; 12:772863. [PMID: 34745079 PMCID: PMC8567051 DOI: 10.3389/fmicb.2021.772863] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 09/30/2021] [Indexed: 01/17/2023] Open
Abstract
Calf diarrhea is one of the most concerning challenges facing both the dairy and beef cattle industry. Maintaining healthy gut microbiota is essential for preventing gastrointestinal disorders. Here, we observed significantly less bacterial richness in the abnormal feces with watery or hemorrhagic morphology compared to the normal solid feces. The normal solid feces showed high relative abundances of Osllospiraceae, Christensenellaceae, Barnesiella, and Lactobacillus, while the abnormal feces contained more bacterial taxa of Negativicutes, Tyzzerella, Parasutterella, Veillonella, Fusobacterium, and Campylobacter. Healthy calves had extensive bacterial-bacterial correlations, with negative correlation between Lactobacillus and potential diarrheagenic Escherichia coli-Shigella, but not in the abnormal feces. We isolated Lactobacillus species (L. reuteri, L. johnsonii, L. amylovorus, and L. animalis), with L. reuteri being the most abundant, from the healthy gut microbiota. Isolated Lactobacillus strains inhibited pathogenic strains including E. coli K88 and Salmonella Typhimurium. These findings indicate the importance of a diverse gut microbiota in newborn calf’s health and provide multiple potential probiotics that suppress pathogen colonization in the gastrointestinal tract to prevent calf diarrhea.
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Affiliation(s)
- Peixin Fan
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.,Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Miju Kim
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.,Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Grace Liu
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.,Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Yuting Zhai
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.,Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Ting Liu
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.,Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Joseph Danny Driver
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Kwangcheol C Jeong
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.,Department of Animal Sciences, University of Florida, Gainesville, FL, United States
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42
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Fontaine SS, Mineo PM, Kohl KD. Changes in the gut microbial community of the eastern newt (Notophthalmus viridescens) across its three distinct life stages. FEMS Microbiol Ecol 2021; 97:6129798. [PMID: 33547890 DOI: 10.1093/femsec/fiab021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/04/2021] [Indexed: 12/30/2022] Open
Abstract
Understanding the forces that shape vertebrate gut microbial community assembly and composition throughout development is a major focus of the microbiome field. Here, we utilize the complex life cycle of the eastern newt (Notophthalmus viridescens) as a natural wild model to compare the effects of host and environmental factors on gut microbiome development. We compared bacterial inventories of each of the newt's three physiologically distinct developmental stages to determine if each hosted a unique community, or if the two stages which share an aquatic habitat (larvae and adults) harbored more similar communities than those of the third stage, the terrestrial juvenile eft. Additionally, we assessed how the contribution of selective processes to gut microbial assembly changed through development. We found that structurally, each life stage harbored a distinct community, which may be attributable to host factors. Further, across development, we found that community assembly processes shifted from a predominance of neutral to selective forces. However, habitat may also be important in determining community membership and diversity due the uniqueness of eft communities based on these metrics. Our results are similar to those in other vertebrate taxa, suggesting that gut microbiota assembly processes may be conserved across diverse lineages.
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Affiliation(s)
- Samantha S Fontaine
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Patrick M Mineo
- Department of Biology, Elmhurst University, Elmhurst, IL 60126, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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43
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De La Guardia-Hidrogo VM, Paz HA. Influence of industry standard feeding frequencies on behavioral patterns and rumen and fecal bacterial communities in Holstein and Jersey cows. PLoS One 2021; 16:e0248147. [PMID: 33667259 PMCID: PMC7935240 DOI: 10.1371/journal.pone.0248147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/22/2021] [Indexed: 01/02/2023] Open
Abstract
This study aimed to evaluate the effects of feeding frequency on behavioral patterns and on diurnal fermentation and bacteriome profiles of the rumen and feces in Holstein and Jersey cows. Ten Holstein and 10 Jersey cows were offered a TMR (53:47 forage-to-concentrate ratio dry matter basis) for ad libitum consumption and were randomly allocated within breed to one of the following feeding frequencies: (1) TMR delivered 1×/d (at 0600 h) or (2) TMR delivered 2×/d (at 0600 and 1800 h). The experiment lasted for 28 d with the first 14 d for cow adaptation to the Calan gates and the next 14 d for data collection. On d 23 and 24, an observer manually recorded the time budget (time spent lying, eating, drinking, standing, and milking), rumination activity, and number of visits to the feeding gate from each animal. On d 28, 5 concomitant collections of rumen and fecal samples were performed at intervals of 6 h via esophageal tubing and fecal grab, respectively. The bacteriome composition from these samples was determined through sequencing of the V4 region of the 16S rRNA gene. Feeding frequency did not affect behavioral patterns; however, Holstein cows spend more time lying (15.4 vs. 13.5 ± 0.8 h) and ruminating (401 vs. 331 ± 17.5 min) than Jersey cows. Fermentation profiles were similar by feeding frequency in both breeds. While no major diurnal fluctuations were observed in the fecal bacterial community from both breeds, diurnal fluctuations were identified in the rumen bacterial community from Holstein cows which appeared to follow pH responses. Overall, the bacterial community composition was not differentiated by industry standard feeding frequencies but was differentiated by breed and sample type.
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Affiliation(s)
| | - Henry A. Paz
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
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44
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Guo H, Zhou G, Tian G, Liu Y, Dong N, Li L, Zhang S, Chai H, Chen Y, Yang Y. Changes in Rumen Microbiota Affect Metabolites, Immune Responses and Antioxidant Enzyme Activities of Sheep under Cold Stimulation. Animals (Basel) 2021; 11:ani11030712. [PMID: 33807979 PMCID: PMC7999998 DOI: 10.3390/ani11030712] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/26/2021] [Accepted: 02/28/2021] [Indexed: 01/10/2023] Open
Abstract
Simple Summary Under a cold environment, the animal’s weight is reduced and even health is affected. As we all know, microbiota is beneficial to animal health. It can produce metabolites to improve animal immunity and avoid damage. Therefore, we aimed to understand the self-protection mechanisms of sheep under cold stress. To investigate this mechanism, we designed two experiments to explore the effects of low temperature and wind speed on sheep phenotypes, rumen microbes, immune cytokines and oxidative stress. Our results identified that the sheep remained healthy in a cold environment. This may be due to the enrichment of Lachnospiraceae in the rumen. A large amount of propionate may enter into the gluconeogenesis reaction, resulting in a decrease in the content of propionate in the rumen, thereby reducing animal’s immunity. In summary, the increase of Lachnospiraceae and propionate in the rumen may help sheep live in a cold environment. Our experiments provide some direction for the healthy feeding of animals in cold environments. Abstract Low-temperature environments can strongly affect the normal growth and health of livestock. In winter, cold weather can be accompanied by strong winds that aggravate the effects of cold on livestock. In this study, two experiments were conducted to investigate the effect of low temperature and/or wind speed on physiological indices, rumen microbiota, immune responses and oxidative stress in sheep. When sheep were exposed to cold temperature and/or stronger wind speeds, the average daily gain (ADG) decreased (p < 0.05), and the abundance of Lachnospiraceae was significantly higher (p < 0.05). The acetate and propionate contents and the proportion of propionate in the rumen also significantly reduced (p < 0.05). The immunoglobulin G (IgG) and TH1-related cytokines in the blood were significantly lower (p < 0.05). However, antioxidant enzyme contents were significantly increased and the concentration of malondialdehyde (MDA) was reduced (p < 0.05). In a cold environment, the abundance of Lachnospiraceae in the rumen of sheep was highly enriched, and the decreasing of propionate might be one of the factors affecting the immunity of the animals, the sheep did not suffer from oxidative damage during the experiment.
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45
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Host genetics exerts lifelong effects upon hindgut microbiota and its association with bovine growth and immunity. ISME JOURNAL 2021; 15:2306-2321. [PMID: 33649551 PMCID: PMC8319427 DOI: 10.1038/s41396-021-00925-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/26/2021] [Accepted: 02/03/2021] [Indexed: 12/22/2022]
Abstract
The gut microbiota is a complex ecological community that plays multiple critical roles within a host. Known intrinsic and extrinsic factors affect gut microbiota structure, but the influence of host genetics is understudied. To investigate the role of host genetics upon the gut microbiota structure, we performed a longitudinal study in which we evaluated the hindgut microbiota and its association with animal growth and immunity across life. We evaluated three different growth stages in an Angus-Brahman multibreed population with a graduated spectrum of genetic variation, raised under variable environmental conditions and diets. We found the gut microbiota structure was changed significantly during growth when preweaning, and fattening calves experienced large variations in diet and environmental changes. However, regardless of the growth stage, we found gut microbiota is significantly influenced by breed composition throughout life. Host genetics explained the relative abundances of 52.2%, 40.0%, and 37.3% of core bacterial taxa at the genus level in preweaning, postweaning, and fattening calves, respectively. Sutterella, Oscillospira, and Roseburia were consistently associated with breed composition at these three growth stages. Especially, butyrate-producing bacteria, Roseburia and Oscillospira, were associated with nine single-nucleotide polymorphisms (SNPs) located in genes involved in the regulation of host immunity and metabolism in the hindgut. Furthermore, minor allele frequency analysis found breed-associated SNPs in the short-chain fatty acids (SCFAs) receptor genes that promote anti-inflammation and enhance intestinal epithelial barrier functions. Our findings provide evidence of dynamic and lifelong host genetic effects upon gut microbiota, regardless of growth stages. We propose that diet, environmental changes, and genetic components may explain observed variation in critical hindgut microbiota throughout life.
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46
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Zou Y, Xue W, Lin X, Hu T, Liu SW, Sun CH, Luo G, Lv M, Dai Y, Kristiansen K, Xiao L. Taxonomic Description and Genome Sequence of Christensenella intestinihominis sp. nov., a Novel Cholesterol-Lowering Bacterium Isolated From Human Gut. Front Microbiol 2021; 12:632361. [PMID: 33692769 PMCID: PMC7937921 DOI: 10.3389/fmicb.2021.632361] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/20/2021] [Indexed: 01/29/2023] Open
Abstract
A Gram-staining-negative, non-spore-forming, short, straight rod, non-motile, and obligate anaerobic bacterial strain, AF73-05CM02T, was isolated from a fecal sample of a 30 years old healthy male living in Shenzhen, China. Colonies were approximately 0.2 mm in diameter, beige, and circular after 4 days of incubation on PYG agar under anaerobic conditions at 37°C. Strain AF73-05CM02T grew in a temperature range between 30 and 42°C and a pH range from 6.0 to 8.5, with optimum growth at 37–42°C and pH 7.0. 16S rRNA gene sequence analysis demonstrated that strain AF73-05CM02T belongs to the genus Christensenella and showed the highest level of sequence similarity (98.68%) with Christensenella minuta DSM 22607T. The predominant fatty acids of strain AF73-05CM02T were C10:0 (7.5%), iso-C11:0 (5.6%), C12:0 (7.2%), C14:0 (46.6%), iso-C15:0 (7.4%), C16:0 (9.7%), and C18:1 ω9c (6.9%). Acetic acid, formic acid, butyric acid, and lactic acid were the end products of glucose fermentation. The strain was negative for catalase, indole production, and hydrolysis of gelatin. Genomic relatedness analyses based on average nucleotide identity (ANI) indicated that strain AF73-05CM02T significantly differed from other species of the genus Christensenella, showing ANI values less than 82.89% with the phylogenetically closest species. The G + C content of the genomic DNA was 52.07 mol% from the genome sequence, which differs from that of Christensenella minuta. Several physiological, biochemical, and genotypic properties differentiated the novel bacterial strain from the related species, indicating that the strain represents a new species of the genus Christensenella for which the name Christensenella intestinihominis sp. nov. is proposed, with strain AF73-05CM02T ( = CGMCC 1.5207T = DSM 103477T ) being the type strain. The following study explored the cholesterol-lowering function of strains AF73-05CM02T and Christensenella minuta DSM 22067T and revealed that the two strains exhibit the capacity for removing cholesterol with efficiency rates of 36.6 and 54.3% and produce exopolysaccharide of 234 and 271 mg/L, respectively.
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Affiliation(s)
- Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
| | | | - Xiaoqian Lin
- BGI-Shenzhen, Shenzhen, China.,School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China
| | | | - Shao-Wei Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cheng-Hang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Mei Lv
- BGI-Shenzhen, Shenzhen, China
| | | | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China.,BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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47
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Ngowi EE, Wang YZ, Khattak S, Khan NH, Mahmoud SSM, Helmy YASH, Jiang QY, Li T, Duan SF, Ji XY, Wu DD. Impact of the factors shaping gut microbiota on obesity. J Appl Microbiol 2021; 131:2131-2147. [PMID: 33570819 DOI: 10.1111/jam.15036] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/01/2021] [Accepted: 02/08/2021] [Indexed: 12/12/2022]
Abstract
Obesity is considered as a risk factor for chronic health diseases such as heart diseases, cancer and diabetes 2. Reduced physical activities, lifestyle, poor nutritional diet and genetics are among the risk factors associated with the development of obesity. In recent years, several studies have explored the link between the gut microbiome and the progression of diseases including obesity, with the shift in microbiome abundance and composition being the main focus. The alteration of gut microbiome composition affects both nutrients metabolism and specific gene expressions, thereby disturbing body physiology. Specifically, the abundance of fibre-metabolizing microbes is associated with weight loss and that of protein and fat-metabolizing bacteria with weight gain. Various internal and external factors such as genetics, maternal obesity, mode of delivery, breastfeeding, nutrition, antibiotic use and the chemical compounds present in the environment are known to interfere with the richness of the gut microbiota (GM), thus influencing weight gain/loss and ultimately the development of obesity. However, the effectiveness of each factor in potentiating the shift in microbes' abundance to result in significant changes that can lead to obesity is not yet clear. In this review, we will highlight the factors involved in shaping GM, their influence on obesity and possible interventions. Understanding the influence of these factors on the diversity of the GM and how to improve their effectiveness on disease conditions could be keys in the treatment of metabolic diseases.
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Affiliation(s)
- Ebenezeri Erasto Ngowi
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China.,Department of Biological Sciences, Faculty of Science, Dares Salaam University College of Education, Dares Salaam, Tanzania
| | - Yi-Zhen Wang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Saadullah Khattak
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Nazeer Hussain Khan
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Salma Sayed Mohamed Mahmoud
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Yasmeen Ahmed Saleheldin Hassan Helmy
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Qi-Ying Jiang
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Tao Li
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Municipal Key Laboratory of Cell Signal Transduction, Henan Provincial Engineering Centre for Tumor Molecular Medicine, Henan University, Kaifeng, Henan, China
| | - Shao-Feng Duan
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Institute for Innovative Drug Design and Evaluation, School of Pharmacy, Henan University, Kaifeng, Henan, China
| | - Xin-Ying Ji
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,Kaifeng Key Laboratory of Infection and Biological Safety, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China
| | - Dong-Dong Wu
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan, China.,School of Stomatology, Henan University, Kaifeng, Henan, China
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48
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Amin N, Seifert J. Dynamic progression of the calf's microbiome and its influence on host health. Comput Struct Biotechnol J 2021; 19:989-1001. [PMID: 33613865 PMCID: PMC7868804 DOI: 10.1016/j.csbj.2021.01.035] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/20/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
The first year of a calf's life is a critical phase as its digestive system and immunity are underdeveloped. A high level of stress caused by separation from mothers, transportation, antibiotic treatments, dietary shifts, and weaning can have long-lasting health effects, which can reduce future production parameters, such as milk yield and reproduction, or even increase the mortality of calves. The early succession of microbes throughout the gastrointestinal tract of neonatal calves follows a sequential pattern of colonisation and is greatly influenced by their physiological state, age, diet, and environmental factors; this leads to the establishment of region- and site-specific microbial communities. This review summarises the current information on the various potential factors that may affect the early life microbial colonisation pattern in the gastrointestinal tract of calves. The possible role of host-microbe interactions in the development and maturation of host gut, immune system, and health are described. Additionally, the possibility of improving the health of calves through gut microbiome modulation and using antimicrobial alternatives is discussed. Finally, the trends, challenges, and limitations of the current research are summarised and prospective directions for future studies are highlighted.
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Affiliation(s)
- Nida Amin
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
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49
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Tang J, Wu X, Mou M, Wang C, Wang L, Li F, Guo M, Yin J, Xie W, Wang X, Wang Y, Ding Y, Xue W, Zhu F. GIMICA: host genetic and immune factors shaping human microbiota. Nucleic Acids Res 2021; 49:D715-D722. [PMID: 33045729 PMCID: PMC7779047 DOI: 10.1093/nar/gkaa851] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/09/2020] [Accepted: 10/08/2020] [Indexed: 01/09/2023] Open
Abstract
Besides the environmental factors having tremendous impacts on the composition of microbial community, the host factors have recently gained extensive attentions on their roles in shaping human microbiota. There are two major types of host factors: host genetic factors (HGFs) and host immune factors (HIFs). These factors of each type are essential for defining the chemical and physical landscapes inhabited by microbiota, and the collective consideration of both types have great implication to serve comprehensive health management. However, no database was available to provide the comprehensive factors of both types. Herein, a database entitled 'Host Genetic and Immune Factors Shaping Human Microbiota (GIMICA)' was constructed. Based on the 4257 microbes confirmed to inhabit nine sites of human body, 2851 HGFs (1368 single nucleotide polymorphisms (SNPs), 186 copy number variations (CNVs), and 1297 non-coding ribonucleic acids (RNAs)) modulating the expression of 370 microbes were collected, and 549 HIFs (126 lymphocytes and phagocytes, 387 immune proteins, and 36 immune pathways) regulating the abundance of 455 microbes were also provided. All in all, GIMICA enabled the collective consideration not only between different types of host factor but also between the host and environmental ones, which is freely accessible without login requirement at: https://idrblab.org/gimica/.
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Affiliation(s)
- Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xianglu Wu
- Joint International Research Lab of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chuan Wang
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Lidan Wang
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Maiyuan Guo
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenqin Xie
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaona Wang
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yingxiong Wang
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China.,Joint International Research Lab of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Yubin Ding
- Joint International Research Lab of Reproductive and Development, Department of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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50
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Baghbani T, Nikzad H, Azadbakht J, Izadpanah F, Haddad Kashani H. Dual and mutual interaction between microbiota and viral infections: a possible treat for COVID-19. Microb Cell Fact 2020; 19:217. [PMID: 33243230 PMCID: PMC7689646 DOI: 10.1186/s12934-020-01483-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/20/2020] [Indexed: 02/07/2023] Open
Abstract
All of humans and other mammalian species are colonized by some types of microorganisms such as bacteria, archaea, unicellular eukaryotes like fungi and protozoa, multicellular eukaryotes like helminths, and viruses, which in whole are called microbiota. These microorganisms have multiple different types of interaction with each other. A plethora of evidence suggests that they can regulate immune and digestive systems and also play roles in various diseases, such as mental, cardiovascular, metabolic and some skin diseases. In addition, they take-part in some current health problems like diabetes mellitus, obesity, cancers and infections. Viral infection is one of the most common and problematic health care issues, particularly in recent years that pandemics like SARS and COVID-19 caused a lot of financial and physical damage to the world. There are plenty of articles investigating the interaction between microbiota and infectious diseases. We focused on stimulatory to suppressive effects of microbiota on viral infections, hoping to find a solution to overcome this current pandemic. Then we reviewed mechanistically the effects of both microbiota and probiotics on most of the viruses. But unlike previous studies which concentrated on intestinal microbiota and infection, our focus is on respiratory system's microbiota and respiratory viral infection, bearing in mind that respiratory system is a proper entry site and residence for viruses, and whereby infection, can lead to asymptomatic, mild, self-limiting, severe or even fatal infection. Finally, we overgeneralize the effects of microbiota on COVID-19 infection. In addition, we reviewed the articles about effects of the microbiota on coronaviruses and suggest some new therapeutic measures.
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Affiliation(s)
- Taha Baghbani
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Hossein Nikzad
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Javid Azadbakht
- Department of Radiology, Faculty of Medicin, Kashan University of Medical Sciences, Kashan, Iran
| | - Fatemeh Izadpanah
- Food and Drug Laboratory Research Center and Food and Drug Reference Control Laboratories Center, Food & Drug Administration of Iran, MOH & ME, Tehran, Iran
| | - Hamed Haddad Kashani
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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