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Wang ZR, Fan QX, Wang JL, Zhang S, Wang YX, Zhang ZD, Gao WW, Zhu XQ, Liu Q. Molecular Identification and Survey of Trichomonad Species in Pigs in Shanxi Province, North China. Vet Sci 2024; 11:203. [PMID: 38787175 PMCID: PMC11125679 DOI: 10.3390/vetsci11050203] [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: 02/26/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Several trichomonad species have already been identified in pigs, and their pathogenic potential may not be ruled out. To date, however, no information is available regarding the prevalence of trichomonads in pigs in Shanxi Province, North China. In the present study, a total of 362 fecal samples collected from pigs in three representative counties (Qi, Jishan, and Shanyin) in this province were examined for Tetratrichomonas buttreyi, Tritrichomonas foetus, and Pentatrichomonas hominis using a nested polymerase chain reaction (PCR) with primers targeting the small subunit ribosomal RNA (SSU rRNA) gene. The overall prevalence of T. buttreyi was 49.72%, and region and age were found to be significantly associated with T. buttreyi infection, respectively. Only one pig fecal sample from Qi County was found to be positive for T. foetus, and all samples were negative for P. hominis. Molecular evolutionary analysis revealed that some T. buttreyi isolates showed complete genetic identity with those reported previously, and some T. buttreyi isolates and one T. foetus isolate showed minor allelic variations compared with those reported previously. This is the report of the molecular epidemiology of T. foetus and T. buttreyi in pigs in Shanxi Province, North China. These findings not only enrich the knowledge on the distribution of these trichomonad species in pigs in China but also provide baseline information for planning future research and control strategies.
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Affiliation(s)
- Zi-Rui Wang
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (Z.-R.W.); (Q.-X.F.); (J.-L.W.); (S.Z.); (Y.-X.W.); (Z.-D.Z.); (W.-W.G.); (X.-Q.Z.)
| | - Qing-Xin Fan
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (Z.-R.W.); (Q.-X.F.); (J.-L.W.); (S.Z.); (Y.-X.W.); (Z.-D.Z.); (W.-W.G.); (X.-Q.Z.)
| | - Jin-Long Wang
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (Z.-R.W.); (Q.-X.F.); (J.-L.W.); (S.Z.); (Y.-X.W.); (Z.-D.Z.); (W.-W.G.); (X.-Q.Z.)
| | - Shuo Zhang
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (Z.-R.W.); (Q.-X.F.); (J.-L.W.); (S.Z.); (Y.-X.W.); (Z.-D.Z.); (W.-W.G.); (X.-Q.Z.)
| | - Yu-Xuan Wang
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (Z.-R.W.); (Q.-X.F.); (J.-L.W.); (S.Z.); (Y.-X.W.); (Z.-D.Z.); (W.-W.G.); (X.-Q.Z.)
| | - Ze-Dong Zhang
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (Z.-R.W.); (Q.-X.F.); (J.-L.W.); (S.Z.); (Y.-X.W.); (Z.-D.Z.); (W.-W.G.); (X.-Q.Z.)
| | - Wen-Wei Gao
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (Z.-R.W.); (Q.-X.F.); (J.-L.W.); (S.Z.); (Y.-X.W.); (Z.-D.Z.); (W.-W.G.); (X.-Q.Z.)
| | - Xing-Quan Zhu
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (Z.-R.W.); (Q.-X.F.); (J.-L.W.); (S.Z.); (Y.-X.W.); (Z.-D.Z.); (W.-W.G.); (X.-Q.Z.)
- Key Laboratory of Veterinary Public Health of Higher Education of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Qing Liu
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China; (Z.-R.W.); (Q.-X.F.); (J.-L.W.); (S.Z.); (Y.-X.W.); (Z.-D.Z.); (W.-W.G.); (X.-Q.Z.)
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Kiernan DP, O’Doherty JV, Sweeney T. The Effect of Prebiotic Supplements on the Gastrointestinal Microbiota and Associated Health Parameters in Pigs. Animals (Basel) 2023; 13:3012. [PMID: 37835619 PMCID: PMC10572080 DOI: 10.3390/ani13193012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Establishing a balanced and diverse microbiota in the GIT of pigs is crucial for optimizing health and performance throughout the production cycle. The post-weaning period is a critical phase, as it is often associated with dysbiosis, intestinal dysfunction and poor performance. Traditionally, intestinal dysfunctions associated with weaning have been alleviated using antibiotics and/or antimicrobials. However, increasing concerns regarding the prevalence of antimicrobial-resistant bacteria has prompted an industry-wide drive towards identifying natural sustainable dietary alternatives. Modulating the microbiota through dietary intervention can improve animal health by increasing the production of health-promoting metabolites associated with the improved microbiota, while limiting the establishment and proliferation of pathogenic bacteria. Prebiotics are a class of bioactive compounds that resist digestion by gastrointestinal enzymes, but which can still be utilized by beneficial microbes within the GIT. Prebiotics are a substrate for these beneficial microbes and therefore enhance their proliferation and abundance, leading to the increased production of health-promoting metabolites and suppression of pathogenic proliferation in the GIT. There are a vast range of prebiotics, including carbohydrates such as non-digestible oligosaccharides, beta-glucans, resistant starch, and inulin. Furthermore, the definition of a prebiotic has recently expanded to include novel prebiotics such as peptides and amino acids. A novel class of -biotics, referred to as "stimbiotics", was recently suggested. This bioactive group has microbiota-modulating capabilities and promotes increases in short-chain fatty acid (SCFA) production in a disproportionally greater manner than if they were merely substrates for bacterial fermentation. The aim of this review is to characterize the different prebiotics, detail the current understating of stimbiotics, and outline how supplementation to pigs at different stages of development and production can potentially modulate the GIT microbiota and subsequently improve the health and performance of animals.
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Affiliation(s)
- Dillon P. Kiernan
- School of Veterinary Medicine, University College Dublin, Belfield, D04 W6F6 Dublin, Ireland;
| | - John V. O’Doherty
- School of Agriculture and Food Science, University College Dublin, Belfield, D04 W6F6 Dublin, Ireland;
| | - Torres Sweeney
- School of Veterinary Medicine, University College Dublin, Belfield, D04 W6F6 Dublin, Ireland;
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Ramayo-Caldas Y, Crespo-Piazuelo D, Morata J, González-Rodríguez O, Sebastià C, Castello A, Dalmau A, Ramos-Onsins S, Alexiou KG, Folch JM, Quintanilla R, Ballester M. Copy Number Variation on ABCC2-DNMBP Loci Affects the Diversity and Composition of the Fecal Microbiota in Pigs. Microbiol Spectr 2023; 11:e0527122. [PMID: 37255458 PMCID: PMC10433821 DOI: 10.1128/spectrum.05271-22] [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: 01/05/2023] [Accepted: 05/16/2023] [Indexed: 06/01/2023] Open
Abstract
Genetic variation in the pig genome partially modulates the composition of porcine gut microbial communities. Previous studies have been focused on the association between single nucleotide polymorphisms (SNPs) and the gut microbiota, but little is known about the relationship between structural variants and fecal microbial traits. The main goal of this study was to explore the association between porcine genome copy number variants (CNVs) and the diversity and composition of pig fecal microbiota. For this purpose, we used whole-genome sequencing data to undertake a comprehensive identification of CNVs followed by a genome-wide association analysis between the estimated CNV status and the fecal bacterial diversity in a commercial Duroc pig population. A CNV predicted as gain (DUP) partially harboring ABCC2-DNMBP loci was associated with richness (P = 5.41 × 10-5, false discovery rate [FDR] = 0.022) and Shannon α-diversity (P = 1.42 × 10-4, FDR = 0.057). The in silico predicted gain of copies was validated by real-time quantitative PCR (qPCR), and its segregation, and positive association with the richness and Shannon α-diversity of the porcine fecal bacterial ecosystem was confirmed in an unrelated F1 (Duroc × Iberian) cross. Our results advise the relevance of considering the role of host-genome structural variants as potential modulators of microbial ecosystems and suggest the ABCC2-DNMBP CNV as a host-genetic factor for the modulation of the diversity and composition of the fecal microbiota in pigs. IMPORTANCE A better understanding of the environmental and host factors modulating gut microbiomes is a topic of greatest interest. Recent evidence suggests that genetic variation in the pig genome partially controls the composition of porcine gut microbiota. However, since previous studies have been focused on the association between single nucleotide polymorphisms and the fecal microbiota, little is known about the relationship between other sources of genetic variation, like the structural variants and microbial traits. Here, we identified, experimentally validated, and replicated in an independent population a positive link between the gain of copies of ABCC2-DNMBP loci and the diversity and composition of pig fecal microbiota. Our results advise the relevance of considering the role of host-genome structural variants as putative modulators of microbial ecosystems and open the possibility of implementing novel holobiont-based management strategies in breeding programs for the simultaneous improvement of microbial traits and host performance.
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Affiliation(s)
- Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology, Caldes de Montbui, Spain
| | - Daniel Crespo-Piazuelo
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology, Caldes de Montbui, Spain
| | - Jordi Morata
- Centro Nacional de Análisis Genómico, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Olga González-Rodríguez
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology, Caldes de Montbui, Spain
| | - Cristina Sebastià
- Plant and Animal Genomics Program, Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas (CSIC)-Institute of Agrifood Research and Technology-Autonomous University of Barcelona-UB, Bellaterra, Spain
- Animal and Food Science Department, Autonomous University of Barcelona, Bellaterra, Spain
| | - Anna Castello
- Plant and Animal Genomics Program, Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas (CSIC)-Institute of Agrifood Research and Technology-Autonomous University of Barcelona-UB, Bellaterra, Spain
- Animal and Food Science Department, Autonomous University of Barcelona, Bellaterra, Spain
| | - Antoni Dalmau
- Animal Welfare Program, Institute of Agrifood Research and Technology, Girona, Spain
| | - Sebastian Ramos-Onsins
- Plant and Animal Genomics Program, Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas (CSIC)-Institute of Agrifood Research and Technology-Autonomous University of Barcelona-UB, Bellaterra, Spain
| | - Konstantinos G. Alexiou
- Plant and Animal Genomics Program, Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas (CSIC)-Institute of Agrifood Research and Technology-Autonomous University of Barcelona-UB, Bellaterra, Spain
| | - Josep M. Folch
- Plant and Animal Genomics Program, Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas (CSIC)-Institute of Agrifood Research and Technology-Autonomous University of Barcelona-UB, Bellaterra, Spain
- Animal and Food Science Department, Autonomous University of Barcelona, Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology, Caldes de Montbui, Spain
| | - Maria Ballester
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology, Caldes de Montbui, Spain
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Calle-García J, Ramayo-Caldas Y, Zingaretti LM, Quintanilla R, Ballester M, Pérez-Enciso M. On the holobiont 'predictome' of immunocompetence in pigs. Genet Sel Evol 2023; 55:29. [PMID: 37127575 PMCID: PMC10150480 DOI: 10.1186/s12711-023-00803-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/07/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex traits, although methods to optimize this are still largely unexplored. In this paper, we assess the impact of different modelling strategies on the predictive capacity for six porcine immunocompetence traits when both genotype and microbiota data are available. METHODS We used phenotypic data on six immunity traits and the relative abundance of gut bacterial communities on 400 Duroc pigs that were genotyped for 70 k SNPs. We compared the predictive accuracy, defined as the correlation between predicted and observed phenotypes, of a wide catalogue of models: reproducing kernel Hilbert space (RKHS), Bayes C, and an ensemble method, using a range of priors and microbial clustering strategies. Combined (holobiont) models that include both genotype and microbiome data were compared with partial models that use one source of variation only. RESULTS Overall, holobiont models performed better than partial models. Host genotype was especially relevant for predicting adaptive immunity traits (i.e., concentration of immunoglobulins M and G), whereas microbial composition was important for predicting innate immunity traits (i.e., concentration of haptoglobin and C-reactive protein and lymphocyte phagocytic capacity). None of the models was uniformly best across all traits. We observed a greater variability in predictive accuracies across models when microbiability (the variance explained by the microbiome) was high. Clustering microbial abundances did not necessarily increase predictive accuracy. CONCLUSIONS Gut microbiota information is useful for predicting immunocompetence traits, especially those related to innate immunity. Modelling microbiome abundances deserves special attention when microbiability is high. Clustering microbial data for prediction is not recommended by default.
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Affiliation(s)
- Joan Calle-García
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, 08193, Bellaterra, Spain
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, 08140, Barcelona, Spain
| | - Laura M Zingaretti
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, 08193, Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, 08140, Barcelona, Spain
| | - María Ballester
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, 08140, Barcelona, Spain
| | - Miguel Pérez-Enciso
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, 08193, Bellaterra, Spain.
- ICREA, Passeig Lluis Companys 23, 08010, Barcelona, Spain.
- Corteva Agriscience, Virtual Location, Bergen op Zoom, Indianapolis, 4611 BB, Netherlands.
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Vargas-Albores F, Garibay-Valdez E, Medina-Félix D, Martínez-Porchas M. The micro-eukaryotic community: An underrated component of the mammalian gut microbiota? Front Microbiol 2023; 14:1123513. [PMID: 37007497 PMCID: PMC10060968 DOI: 10.3389/fmicb.2023.1123513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Affiliation(s)
- Francisco Vargas-Albores
- Centro de Investigación en Alimentación y Desarrollo, A.C. Biología de Organismos Acuáticos, Hermosillo, Sonora, Mexico
| | - Estefanía Garibay-Valdez
- Centro de Investigación en Alimentación y Desarrollo, A.C. Biología de Organismos Acuáticos, Hermosillo, Sonora, Mexico
| | - Diana Medina-Félix
- Departamento de Ecología, Universidad Estatal de Sonora, Hermosillo, Sonora, Mexico
| | - Marcel Martínez-Porchas
- Centro de Investigación en Alimentación y Desarrollo, A.C. Biología de Organismos Acuáticos, Hermosillo, Sonora, Mexico
- *Correspondence: Marcel Martínez-Porchas
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Hu J, Chen J, Hou Q, Xu X, Ren J, Ma L, Yan X. Core-predominant gut fungus Kazachstania slooffiae promotes intestinal epithelial glycolysis via lysine desuccinylation in pigs. MICROBIOME 2023; 11:31. [PMID: 36814349 PMCID: PMC9948344 DOI: 10.1186/s40168-023-01468-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Gut fungi are increasingly recognized as important contributors to host physiology, although most studies have focused on gut bacteria. Post-translational modifications (PTMs) of proteins play vital roles in cell metabolism. However, the contribution of gut fungi to host protein PTMs remains unclear. Mining gut fungi that mediate host protein PTMs and dissecting their mechanism are urgently needed. RESULTS We studied the gut fungal communities of 56 weaned piglets and 56 finishing pigs from seven pig breeds using internal transcribed spacer (ITS) gene amplicon sequencing and metagenomics. The results showed that Kazachstania slooffiae was the most abundant gut fungal species in the seven breeds of weaned piglets. K. slooffiae decreased intestinal epithelial lysine succinylation levels, and these proteins were especially enriched in the glycolysis pathway. We demonstrated that K. slooffiae promoted intestinal epithelial glycolysis by decreasing lysine succinylation by activating sirtuin 5 (SIRT5). Furthermore, K. slooffiae-derived 5'-methylthioadenosine metabolite promoted the SIRT5 activity. CONCLUSIONS These findings provide a landscape of gut fungal communities of pigs and suggest that K. slooffiae plays a crucial role in intestinal glycolysis metabolism through lysine desuccinylation. Our data also suggest a potential protective strategy for pigs with an insufficient intestinal energy supply. Video Abstract.
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Affiliation(s)
- Jun Hu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Jianwei Chen
- BGI Research-Qingdao, BGI, Qingdao, 266555, China
| | - Qiliang Hou
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Xiaojian Xu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Jing Ren
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Libao Ma
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China
| | - Xianghua Yan
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, 430070, Hubei, China.
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Xu R, Li Q, Wang H, Su Y, Zhu W. Reduction of Redox Potential Exerts a Key Role in Modulating Gut Microbial Taxa and Function by Dietary Supplementation of Pectin in a Pig Model. Microbiol Spectr 2023; 11:e0328322. [PMID: 36475916 PMCID: PMC9927287 DOI: 10.1128/spectrum.03283-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Pectin exists in a vast range of plants and has a long history of acting as a functional food additive with potential prebiotic effects on intestinal health. However, knowledge of how pectin regulates gut microbial communities is still insufficient and limited. Here, metatranscriptome sequencing revealed that a pectin-enriched diet (PEC) decreased the abundances of fungal keystone taxa (e.g., amino acid-producing Kazachstania spp.) and their genes involved in oxidative phosphorylation, while it increased the abundance of sulfate-reducing Desulfovibrio spp., and methane-producing Methanobrevibacter spp. in colon microbiomes. Furthermore, we first confirmed that PEC decreased fecal redox potential in a fistula pig model, which could be supported by the enrichment of antioxidants (e.g., inosine) in feces. Fecal metagenome analysis disclosed that certain microbial taxa promoted inosine biosynthesis from pectin degradation, including Prevotella, which plays an essential role in pectin biodegradation. Overall, these results demonstrate that pectin decreases the redox potential in pig hindgut to modulate microbial composition and functions, and specific microorganisms generate reducing agents in the course of pectin degradation to decrease redox potential of microbial ecosystem. IMPORTANCE Collective studies indicate that pectin degradation promotes extensive microorganisms that can be involved in pectin degradation directly or indirectly, or benefit from the altered physiological conditions caused by pectin ingestions. Our study focuses on effects of pectin on gut microbial taxa and functions, as well as its interactions with altered environmental features. Our results demonstrate pectin-induced proreducing shifts on colon microbial taxa and functions, and first confirm that pectin decreases hindgut redox potential, which is an important environmental feature that can modulate microbial communities. These results infer that there is bidirectional regulation between microbiota and redox potential during pectin degradation. In general, this investigation proposes new insights into the pectin-modulating gut microbial ecosystem and also provides new perspectives for targeting modulation of gut microbiota.
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Affiliation(s)
- Rongying Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Qiuke Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Hongyu Wang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Yong Su
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China
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West AG, Digby A, Taylor MW. The mycobiota of faeces from the critically endangered kākāpō and associated nest litter. NEW ZEALAND JOURNAL OF ZOOLOGY 2023. [DOI: 10.1080/03014223.2023.2170428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Annie G. West
- Te Kura Mātauranga Koiora School of Biological Sciences, Waipapa Taumata Rau University of Auckland, Auckland, New Zealand
| | - Andrew Digby
- Te Papa Atawhai Department of Conservation, Kākāpō Recovery Programme, Invercargill, New Zealand
| | - Michael W. Taylor
- Te Kura Mātauranga Koiora School of Biological Sciences, Waipapa Taumata Rau University of Auckland, Auckland, New Zealand
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Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives. Animals (Basel) 2022; 12:ani12233375. [PMID: 36496896 PMCID: PMC9736591 DOI: 10.3390/ani12233375] [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: 09/13/2022] [Revised: 11/16/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available.
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Li J, Chen D, Yu B, He J, Huang Z, Zheng P, Mao X, Li H, Yu J, Luo J, Yan H, Luo Y. Batch and sampling time exert a larger influence on the fungal community than gastrointestinal location in model animals: A meaningful case study. Front Nutr 2022; 9:1021215. [PMID: 36419550 PMCID: PMC9676510 DOI: 10.3389/fnut.2022.1021215] [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: 08/17/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022] Open
Abstract
Fungi play a fundamental role in the intestinal ecosystem and health, but our knowledge of fungal composition and distribution in the whole gastrointestinal tract (GIT) is very limited. The physiological similarity between humans and pigs in terms of digestive and associated metabolic processes places, the pig in a superior position over other non-primate models. Here, we aimed to characterize the diversity and composition of fungi in the GIT of pigs. Using high-throughput sequencing, we evaluated the fungal community in different locations of GIT of 11 pigs with 128.41 ± 1.25 kg body weight acquired successively. Among them, five pigs are sacrificed in April 2019 (Batch 1) and the other six are sacrificed in January 2020 (Batch 2). All subjects with similar genetic backgrounds, housing, management, and diet. Finally, no significant difference is found in the α-diversity (Richness) of the fungal community among all intestinal segments. Basidiomycota and Ascomycota are the two predominant fungal phyla, but Batch 1 harbored a notably high abundance of Basidiomycota and Batch 2 harbored a high abundance of Ascomycota. Moreover, the two batches harbored completely different fungal compositions and core fungal genera. FUNGuild (Fungal Functional Guild) analysis revealed that most of the fungal species present in the GIT are saprotroph, plant pathogen, and animal endosymbiont. Our study is the first to report that even under the same condition, large variations in fungal composition in the host GIT still occur from batch-to-batch and sampling time. The implications of our observations serve as references to the development of better models of the human gut.
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Velasco-Galilea M, Piles M, Ramayo-Caldas Y, Varona L, Sánchez JP. Use of Bayes factors to evaluate the effects of host genetics, litter and cage on the rabbit cecal microbiota. Genet Sel Evol 2022; 54:46. [PMID: 35761200 PMCID: PMC9235133 DOI: 10.1186/s12711-022-00738-2] [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: 09/30/2021] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Background The rabbit cecum hosts and interacts with a complex microbial ecosystem that contributes to the variation of traits of economic interest. Although the influence of host genetics on microbial diversity and specific microbial taxa has been studied in several species (e.g., humans, pigs, or cattle), it has not been investigated in rabbits. Using a Bayes factor approach, the aim of this study was to dissect the effects of host genetics, litter and cage on 984 microbial traits that are representative of the rabbit microbiota. Results Analysis of 16S rDNA sequences of cecal microbiota from 425 rabbits resulted in the relative abundances of 29 genera, 951 operational taxonomic units (OTU), and four microbial alpha-diversity indices. Each of these microbial traits was adjusted with mixed linear and zero-inflated Poisson (ZIP) models, which all included additive genetic, litter and cage effects, and body weight at weaning and batch as systematic factors. The marginal posterior distributions of the model parameters were estimated using MCMC Bayesian procedures. The deviance information criterion (DIC) was used for model comparison regarding the statistical distribution of the data (normal or ZIP), and the Bayes factor was computed as a measure of the strength of evidence in favor of the host genetics, litter, and cage effects on microbial traits. According to DIC, all microbial traits were better adjusted with the linear model except for the OTU present in less than 10% of the animals, and for 25 of the 43 OTU with a frequency between 10 and 25%. On a global scale, the Bayes factor revealed substantial evidence in favor of the genetic control of the number of observed OTU and Shannon indices. At the taxon-specific level, significant proportions of the OTU and relative abundances of genera were influenced by additive genetic, litter, and cage effects. Several members of the genera Bacteroides and Parabacteroides were strongly influenced by the host genetics and nursing environment, whereas the family S24-7 and the genus Ruminococcus were strongly influenced by cage effects. Conclusions This study demonstrates that host genetics shapes the overall rabbit cecal microbial diversity and that a significant proportion of the taxa is influenced either by host genetics or environmental factors, such as litter and/or cage. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00738-2.
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Affiliation(s)
- María Velasco-Galilea
- Institute of Agrifood Research and Technology (IRTA)-Animal Breeding and Genetics, Caldes de Montbui, Barcelona, Spain. .,Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona, Spain.
| | - Miriam Piles
- Institute of Agrifood Research and Technology (IRTA)-Animal Breeding and Genetics, Caldes de Montbui, Barcelona, Spain
| | - Yuliaxis Ramayo-Caldas
- Institute of Agrifood Research and Technology (IRTA)-Animal Breeding and Genetics, Caldes de Montbui, Barcelona, Spain
| | - Luis Varona
- Veterinary Faculty, University of Zaragoza, Saragossa, Spain
| | - Juan Pablo Sánchez
- Institute of Agrifood Research and Technology (IRTA)-Animal Breeding and Genetics, Caldes de Montbui, Barcelona, Spain
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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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13
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Amplicon-based next-generation sequencing of eukaryotic nuclear ribosomal genes (metabarcoding) for the detection of single-celled parasites in human faecal samples. Parasite Epidemiol Control 2022; 17:e00242. [PMID: 35146142 PMCID: PMC8819130 DOI: 10.1016/j.parepi.2022.e00242] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 01/12/2023] Open
Abstract
Comprehensive detection and differentiation of intestinal protists mostly rely on DNA-based methods. Here, we evaluated next-generation sequencing of eukaryotic nuclear ribosomal genes (metabarcoding) for the detection and differentiation of intestinal eukaryotic protists in the stool of healthy Tunisian individuals. Thirty-six faecal DNA samples previously evaluated by microscopy and ameboid species-specific PCRs were tested. The hypervariable regions V3-V4 and V3-V5 of the 18S rRNA gene were amplified using three universal eukaryotic primer sets and sequenced using Illumina®MiSeq sequencing. In addition, real-time PCR assays were used to detect Dientamoeba fragilis, Giardia duodenalis, and Cryptosporidium spp. The metabarcoding assay detected Blastocystis (subtypes 1, 2, and 3) and archamoebid species and subtypes (Entamoeba dispar, Entamoeba hartmanni, Entamoeba coli RL1 and RL2, Endolimax nana, Iodamoeba bütschlii RL1) in 27 (75%) and 22 (61%) of the 36 stool samples, respectively. Meanwhile, the assay had limited sensitivity for flagellates as evidenced by the fact that no Giardia-specific reads were found in any of the five Giardia-positive samples included, and Dientamoeba-specific reads were observed only in 3/13 D. fragilis-positive samples. None of the samples were positive for Cryptosporidium by any of the methods. In conclusion, a large variety of intestinal eukaryotic protists were detected and differentiated at species and subtype level; however, limited sensitivity for common flagellates was observed.
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Perlman D, Martínez-Álvaro M, Moraïs S, Altshuler I, Hagen LH, Jami E, Roehe R, Pope PB, Mizrahi I. Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development. Annu Rev Anim Biosci 2021; 10:177-201. [PMID: 34941382 DOI: 10.1146/annurev-animal-013020-020412] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Animal microbiomes are occasionally considered as an extension of host anatomy, physiology, and even their genomic architecture. Their compositions encompass variable and constant portions when examined across multiple hosts. The latter, termed the core microbiome, is viewed as more accommodated to its host environment and suggested to benefit host fitness. Nevertheless, discrepancies in its definitions, characteristics, and importance to its hosts exist across studies. We survey studies that characterize the core microbiome, detail its current definitions and available methods to identify it, and emphasize the crucial need to upgrade and standardize the methodologies among studies. We highlight ruminants as a case study and discuss the link between the core microbiome and host physiology and genetics, as well as potential factors that shape it. We conclude with main directives of action to better understand the host-core microbiome axis and acquire the necessary insights into its controlled modulation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Daphne Perlman
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel;
| | - Marina Martínez-Álvaro
- Department of Agriculture, Horticulture and Engineering Sciences, SRUC (Scotland's Rural College), Edinburgh, Scotland, United Kingdom
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel;
| | - Ianina Altshuler
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway;
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Elie Jami
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Rainer Roehe
- Department of Agriculture, Horticulture and Engineering Sciences, SRUC (Scotland's Rural College), Edinburgh, Scotland, United Kingdom
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway; .,Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel;
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15
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Ramayo-Caldas Y, Zingaretti LM, Pérez-Pascual D, Alexandre PA, Reverter A, Dalmau A, Quintanilla R, Ballester M. Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs. Anim Microbiome 2021; 3:74. [PMID: 34689834 PMCID: PMC8543910 DOI: 10.1186/s42523-021-00138-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/12/2021] [Indexed: 01/13/2023] Open
Abstract
Background The gut microbiota influences host performance playing a relevant role in homeostasis and function of the immune system. The aim of the present work was to identify microbial signatures linked to immunity traits and to characterize the contribution of host-genome and gut microbiota to the immunocompetence in healthy pigs. Results To achieve this goal, we undertook a combination of network, mixed model and microbial-wide association studies (MWAS) for 21 immunity traits and the relative abundance of gut bacterial communities in 389 pigs genotyped for 70K SNPs. The heritability (h2; proportion of phenotypic variance explained by the host genetics) and microbiability (m2; proportion of variance explained by the microbial composition) showed similar values for most of the analyzed immunity traits, except for both IgM and IgG in plasma that was dominated by the host genetics, and the haptoglobin in serum which was the trait with larger m2 (0.275) compared to h2 (0.138). Results from the MWAS suggested a polymicrobial nature of the immunocompetence in pigs and revealed associations between pigs gut microbiota composition and 15 of the analyzed traits. The lymphocytes phagocytic capacity (quantified as mean fluorescence) and the total number of monocytes in blood were the traits associated with the largest number of taxa (6 taxa). Among the associations identified by MWAS, 30% were confirmed by an information theory network approach. The strongest confirmed associations were between Fibrobacter and phagocytic capacity of lymphocytes (r = 0.37), followed by correlations between Streptococcus and the percentage of phagocytic lymphocytes (r = -0.34) and between Megasphaera and serum concentration of haptoglobin (r = 0.26). In the interaction network, Streptococcus and percentage of phagocytic lymphocytes were the keystone bacterial and immune-trait, respectively. Conclusions Overall, our findings reveal an important connection between gut microbiota composition and immunity traits in pigs, and highlight the need to consider both sources of information, host genome and microbial levels, to accurately characterize immunocompetence in pigs. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00138-9.
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Affiliation(s)
- Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, IRTA, Torre Marimón, 08140, Caldes de Montbui, Barcelona, Spain.
| | - Laura M Zingaretti
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - David Pérez-Pascual
- Unité de Génétique des Biofilms, Institut Pasteur, UMR CNRS2001, Paris, France
| | | | - Antonio Reverter
- CSIRO Agriculture and Food, St. Lucia, Brisbane, QLD, 4067, Australia
| | - Antoni Dalmau
- Animal Welfare Subprogram, IRTA, 17121, Monells, Girona, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, IRTA, Torre Marimón, 08140, Caldes de Montbui, Barcelona, Spain
| | - Maria Ballester
- Animal Breeding and Genetics Program, IRTA, Torre Marimón, 08140, Caldes de Montbui, Barcelona, Spain.
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16
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Pérez-Enciso M, Zingaretti LM, Ramayo-Caldas Y, de Los Campos G. Opportunities and limits of combining microbiome and genome data for complex trait prediction. Genet Sel Evol 2021; 53:65. [PMID: 34362312 PMCID: PMC8344190 DOI: 10.1186/s12711-021-00658-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Background Analysis and prediction of complex traits using microbiome data combined with host genomic information is a topic of utmost interest. However, numerous questions remain to be answered: how useful can the microbiome be for complex trait prediction? Are estimates of microbiability reliable? Can the underlying biological links between the host’s genome, microbiome, and phenome be recovered? Methods Here, we address these issues by (i) developing a novel simulation strategy that uses real microbiome and genotype data as inputs, and (ii) using variance-component approaches (Bayesian Reproducing Kernel Hilbert Space (RKHS) and Bayesian variable selection methods (Bayes C)) to quantify the proportion of phenotypic variance explained by the genome and the microbiome. The proposed simulation approach can mimic genetic links between the microbiome and genotype data by a permutation procedure that retains the distributional properties of the data. Results Using real genotype and rumen microbiota abundances from dairy cattle, simulation results suggest that microbiome data can significantly improve the accuracy of phenotype predictions, regardless of whether some microbiota abundances are under direct genetic control by the host or not. This improvement depends logically on the microbiome being stable over time. Overall, random-effects linear methods appear robust for variance components estimation, in spite of the typically highly leptokurtic distribution of microbiota abundances. The predictive performance of Bayes C was higher but more sensitive to the number of causative effects than RKHS. Accuracy with Bayes C depended, in part, on the number of microorganisms’ taxa that influence the phenotype. Conclusions While we conclude that, overall, genome-microbiome-links can be characterized using variance component estimates, we are less optimistic about the possibility of identifying the causative host genetic effects that affect microbiota abundances, which would require much larger sample sizes than are typically available for genome-microbiome-phenome studies. The R code to replicate the analyses is in https://github.com/miguelperezenciso/simubiome. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00658-7.
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Affiliation(s)
- Miguel Pérez-Enciso
- ICREA, Passeig de Lluís Companys 23, 08010, Barcelona, Spain. .,Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain. .,Dept. of Epidemiology & Biostatistics, and Dept. of Statistics & Probability, Michigan State University, East Lansing, MI, 48824, USA.
| | - Laura M Zingaretti
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193, Bellaterra, Barcelona, Spain.,Dept. of Epidemiology & Biostatistics, and Dept. of Statistics & Probability, Michigan State University, East Lansing, MI, 48824, USA
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Barcelona, Spain
| | - Gustavo de Los Campos
- Dept. of Epidemiology & Biostatistics, and Dept. of Statistics & Probability, Michigan State University, East Lansing, MI, 48824, USA
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17
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Assessment of Biolog Ecoplate TM method for functional metabolic diversity of aerotolerant pig fecal microbiota. Appl Microbiol Biotechnol 2021; 105:6033-6045. [PMID: 34296337 PMCID: PMC8390420 DOI: 10.1007/s00253-021-11449-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 01/04/2023]
Abstract
Abstract In the last decades, gut microbiota and its role in mammal host development and health have been increasingly investigated. Metabolites produced by gut microbiota can affect intestinal homeostasis and immune system maturity and activation, and in turn, they can influence the health and growth performance of livestock. Therefore, a better understanding of the functional metabolic capability of the gut microbiota would be appreciated by the scientific community. In this study, the BiologTM Ecoplates technology was applied for studying the metabolic potential of the aerotolerant microbial community of pig fecal samples, evaluating the interference of different storage conditions and cell concentrations. The length of time for which a fecal sample maintained detectable and unchanged microbial metabolic activity was also investigated. Two assays aimed to evaluate differences in the metabolic activities between fresh and snap-frozen fecal samples at different dilutions and at different lengths of times of preservation at −80°C were carried out. The biodiversity and the predicted functionality of the entire bacterial community through a targeted metagenomic approach were also explored. The results highlighted that snap freezing of fecal samples preserved the metabolic activity of the microbial community when compared to fresh feces. Sample storage at −80 °C did not significantly affect the metabolic activity of the microbial community, which was stable for 150 days. Furthermore, the highest metabolic activity was detected with 1:2 to 1:5 dilutions of the stock suspension. BiologTM Ecoplates technology is a rapid and useful method to explore microbial communities’ metabolism in animal fecal samples contributing to investigate host animal physiology. Key points • Freezing of samples can preserve the functional activity of the aerotolerant microbial community for 150 days. • The concentration of microbial cells strongly influences metabolic activity detection. • Sequencing coupled with the BiologTMEcoplates could be a strategy to evaluate the metabolic potential of the microbiota of the fecal sample. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11449-x.
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Stensvold CR, Jirků-Pomajbíková K, Tams KW, Jokelainen P, Berg RPKD, Marving E, Petersen RF, Andersen LO, Angen Ø, Nielsen HV. Parasitic Intestinal Protists of Zoonotic Relevance Detected in Pigs by Metabarcoding and Real-Time PCR. Microorganisms 2021; 9:microorganisms9061189. [PMID: 34073014 PMCID: PMC8229027 DOI: 10.3390/microorganisms9061189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022] Open
Abstract
Several parasite species are shared between humans and pigs. We explored the application of next-generation sequencing-based metabarcoding supplemented with real-time PCR to fecal DNAs from 259 samples from 116 pigs in Denmark to detect and differentiate single-celled intestinal parasites of zoonotic relevance. Enterocytozoon bieneusi, Balantioides coli, and Giardia duodenalis were observed in 34/37 (92%), 148/259 (57%), and 86/259 (33%) samples, respectively. Entamoeba polecki ST1, E. polecki ST3, and Entamoeba hartmanni were detected in 104/259 (40%), 161/259 (62%), and 8/259 (3%) samples, respectively. Metabarcoding and real-time PCR detected Cryptosporidium in 90/259 (35%) and 239/259 (92%) of the samples, respectively, with Cryptosporidium suis and Cryptosporidium scrofarum observed in nearly equal proportions. Blastocystis subtypes 1, 3, 5, and 15 were found in 72 (28%), 6 (2%), 176 (68%), and 36 (14%) of 259 samples, respectively. Iodamoeba was identified in 1/259 samples (<1%), while none of 37 tested samples was positive for Dientamoeba fragilis. Our results illustrate how metabarcoding exemplifies a 'one-fits-many' approach to detecting intestinal single-celled parasites in feces supplemented with real-time PCR for selected parasites. Using metabarcoding with pathogen-specific assays may help detect emerging and previously underdetected pathogens and further elucidate the role of micro-eukaryotic parasites in human and animal health and disease.
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Affiliation(s)
- Christen Rune Stensvold
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark; (P.J.); (R.P.K.D.B.); (R.F.P.); (L.O.A.); (Ø.A.); (H.V.N.)
- Correspondence:
| | - Kateřina Jirků-Pomajbíková
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - Katrine Wegener Tams
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Bygning 221, DK-2800 Kongens Lyngby, Denmark;
| | - Pikka Jokelainen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark; (P.J.); (R.P.K.D.B.); (R.F.P.); (L.O.A.); (Ø.A.); (H.V.N.)
| | - Rebecca P. K. D. Berg
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark; (P.J.); (R.P.K.D.B.); (R.F.P.); (L.O.A.); (Ø.A.); (H.V.N.)
| | - Ellinor Marving
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark;
| | - Randi Føns Petersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark; (P.J.); (R.P.K.D.B.); (R.F.P.); (L.O.A.); (Ø.A.); (H.V.N.)
| | - Lee O’Brien Andersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark; (P.J.); (R.P.K.D.B.); (R.F.P.); (L.O.A.); (Ø.A.); (H.V.N.)
| | - Øystein Angen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark; (P.J.); (R.P.K.D.B.); (R.F.P.); (L.O.A.); (Ø.A.); (H.V.N.)
| | - Henrik Vedel Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark; (P.J.); (R.P.K.D.B.); (R.F.P.); (L.O.A.); (Ø.A.); (H.V.N.)
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Reverter A, Ballester M, Alexandre PA, Mármol-Sánchez E, Dalmau A, Quintanilla R, Ramayo-Caldas Y. A gene co-association network regulating gut microbial communities in a Duroc pig population. MICROBIOME 2021; 9:52. [PMID: 33612109 PMCID: PMC7898758 DOI: 10.1186/s40168-020-00994-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/29/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Analyses of gut microbiome composition in livestock species have shown its potential to contribute to the regulation of complex phenotypes. However, little is known about the host genetic control over the gut microbial communities. In pigs, previous studies are based on classical "single-gene-single-trait" approaches and have evaluated the role of host genome controlling gut prokaryote and eukaryote communities separately. RESULTS In order to determine the ability of the host genome to control the diversity and composition of microbial communities in healthy pigs, we undertook genome-wide association studies (GWAS) for 39 microbial phenotypes that included 2 diversity indexes, and the relative abundance of 31 bacterial and six commensal protist genera in 390 pigs genotyped for 70 K SNPs. The GWAS results were processed through a 3-step analytical pipeline comprised of (1) association weight matrix; (2) regulatory impact factor; and (3) partial correlation and information theory. The inferred gene regulatory network comprised 3561 genes (within a 5 kb distance from a relevant SNP-P < 0.05) and 738,913 connections (SNP-to-SNP co-associations). Our findings highlight the complexity and polygenic nature of the pig gut microbial ecosystem. Prominent within the network were 5 regulators, PRDM15, STAT1, ssc-mir-371, SOX9 and RUNX2 which gathered 942, 607, 588, 284 and 273 connections, respectively. PRDM15 modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency and regulates the production of Th1- and Th2-type immune response. The signal transducer STAT1 has long been associated with immune processes and was recently identified as a potential regulator of vaccine response to porcine reproductive and respiratory syndrome. The list of regulators was enriched for immune-related pathways, and the list of predicted targets includes candidate genes previously reported as associated with microbiota profile in pigs, mice and human, such as SLIT3, SLC39A8, NOS1, IL1R2, DAB1, TOX3, SPP1, THSD7B, ELF2, PIANP, A2ML1, and IFNAR1. Moreover, we show the existence of host-genetic variants jointly associated with the relative abundance of butyrate producer bacteria and host performance. CONCLUSIONS Taken together, our results identified regulators, candidate genes, and mechanisms linked with microbiome modulation by the host. They further highlight the value of the proposed analytical pipeline to exploit pleiotropy and the crosstalk between bacteria and protists as significant contributors to host-microbiome interactions and identify genetic markers and candidate genes that can be incorporated in breeding program to improve host-performance and microbial traits. Video Abstract.
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Affiliation(s)
- Antonio Reverter
- CSIRO Agriculture and Food, St. Lucia, Brisbane, Queensland 4067 Australia
| | - Maria Ballester
- Animal Breeding and Genetics Program, IRTA, Torre Marimón, 08140 Caldes de Montbui, Barcelona, Spain
| | | | - Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Antoni Dalmau
- Animal Welfare Subprogram, IRTA, 17121 Monells, Girona, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, IRTA, Torre Marimón, 08140 Caldes de Montbui, Barcelona, Spain
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, IRTA, Torre Marimón, 08140 Caldes de Montbui, Barcelona, Spain
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Arfken AM, Frey JF, Summers KL. Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig. Microorganisms 2020; 8:E868. [PMID: 32526857 PMCID: PMC7356342 DOI: 10.3390/microorganisms8060868] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/22/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
Weaning is a period of environmental changes and stress that results in significant alterations to the piglet gut microbiome and is associated with a predisposition to disease, making potential interventions of interest to the swine industry. In other animals, interactions between the bacteriome and mycobiome can result in altered nutrient absorption and susceptibility to disease, but these interactions remain poorly understood in pigs. Recently, we assessed the colonization dynamics of fungi and bacteria in the gastrointestinal tract of piglets at a single time point post-weaning (day 35) and inferred interactions were found between fungal and bacterial members of the porcine gut ecosystem. In this study, we performed a longitudinal assessment of the fecal bacteriome and mycobiome of piglets from birth through the weaning transition. Piglet feces in this study showed a dramatic shift over time in the bacterial and fungal communities, as well as an increase in network connectivity between the two kingdoms. The piglet fecal bacteriome showed a relatively stable and predictable pattern of development from Bacteroidaceae to Prevotellaceae, as seen in other studies, while the mycobiome demonstrated a loss in diversity over time with a post-weaning population dominated by Saccharomycetaceae. The mycobiome demonstrated a more transient community that is likely driven by factors such as diet or environmental exposure rather than an organized pattern of colonization and succession evidenced by fecal sample taxonomic clustering with nursey feed samples post-weaning. Due to the potential tractability of the community, the mycobiome may be a viable candidate for potential microbial interventions that will alter piglet health and growth during the weaning transition.
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Affiliation(s)
| | | | - Katie Lynn Summers
- Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA; (A.M.A.); (J.F.F.)
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