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Xuan B, Park J, Choi S, Kim EB. Postbiotic-based recombinant receptor activator of NF-κB ligand enhanced oral vaccine efficiency in chicken. Appl Microbiol Biotechnol 2024; 108:397. [PMID: 38922350 PMCID: PMC11208263 DOI: 10.1007/s00253-024-13237-9] [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: 12/03/2023] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024]
Abstract
Functional M cells are differentiated by receptor activator of NF-κB ligand (RANKL) and capture of luminal antigens to initiate immune responses. We aimed to use postbiotic-based recombinant chicken RANKL (cRANKL) to promote M cell differentiation and test the efficacy of oral vaccines. Chicks were divided into three groups that were administered phosphate-buffered saline (PBS), cell extracts of wild-type Lactococcus lactis subsp. lactis IL1403 (WT_CE), or cell extracts of recombinant L. lactis expressing cRANKL (cRANKL_CE). The expression of the M cell marker was measured, and the gut microbiome was profiled. The efficiency of the infectious bursal disease (IBD) vaccine was tested after 12 consecutive days of administering cRANKL_CE. The chickens that were administered cRANKL_CE (p = 0.038) had significantly higher Annexin A5 (ANXA5) mRNA expression levels than those in the PBS group (PBS vs. WT_CE, p = 0.657). In the gut microbiome analysis, no significant changes were observed. However, the relative abundance of Escherichia-Shigella was negatively correlated (r = - 0.43, p = 0.019) with ANXA5 mRNA expression in Peyer's patches. cRANKL_CE/IBD (p = 0.018) had significantly higher IBD-specific faecal IgA levels than PBS/IBD (PBS/IBD vs. WT_CE/IBD, p = 0.217). Postbiotic-based recombinant cRANKL effectively improved the expression of M cell markers and the efficiency of oral vaccines. No significant changes were observed in the gut microbiome after administration of postbiotic-based recombinant cRANKL. This strategy can be used for the development of feed additives and adjuvants. KEY POINTS: • Postbiotic-based recombinant cRANKL enhanced the expression of ANXA5 in chicken. • The relative abundance of Escherichia-Shigella was negatively correlated with ANXA5 expression. • Postbiotic-based recombinant cRANKL effectively improved the efficiency of oral vaccine.
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Affiliation(s)
- Biao Xuan
- Department of Animal Science, College of Agriculture, Yanbian University, Yanji, 133002, China
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Kangwon-Do, Chuncheon, 24341, Republic of Korea
| | - Jongbin Park
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Microbiome Convergence Research Center, Daejeon, 34141, South Korea
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Kangwon-Do, Chuncheon, 24341, Republic of Korea
| | - Seojin Choi
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Kangwon-Do, Chuncheon, 24341, Republic of Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Kangwon-Do, Chuncheon, 24341, Republic of Korea.
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König E, Beasley S, Heponiemi P, Kivinen S, Räkköläinen J, Salminen S, Collado MC, Borman T, Lahti L, Piirainen V, Valros A, Heinonen M. Fecal microbiota profiles of growing pigs and their relation to growth performance. PLoS One 2024; 19:e0302724. [PMID: 38709788 PMCID: PMC11073740 DOI: 10.1371/journal.pone.0302724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/10/2024] [Indexed: 05/08/2024] Open
Abstract
The early gut microbiota composition is fundamentally important for piglet health, affecting long-term microbiome development and immunity. In this study, the gut microbiota of postparturient dams was compared with that of their offspring in three Finnish pig farms at three growth phases. The differences in fecal microbiota of three study development groups (Good, Poorly, and PrematureDeath) were analyzed at birth (initial exposure phase), weaning (transitional phase), and before slaughter (stable phase). Dam Lactobacillaceae abundance was lower than in piglets at birth. Limosilactobacillus reuteri and Lactobacillus amylovorus were dominantly expressed in dams and their offspring. Altogether 17 piglets (68%) were identified with Lactobacillaceae at the initial exposure phase, divided unevenly among the development groups: 85% of Good, 37.5% of Poorly, and 75% of PrematureDeath pigs. The development group Good was identified with the highest microbial diversity, whereas the development group PrematureDeath had the lowest diversity. After weaning, the abundance and versatility of Lactobacillaceae in piglets diminished, shifting towards the microbiome of the dam. In conclusion, the fecal microbiota of pigs tends to develop towards a similar alpha and beta diversity despite development group and rearing environment.
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Affiliation(s)
- Emilia König
- Faculty of Veterinary Medicine, Department of Production Animal Medicine, University of Helsinki, Helsinki, Finland
- Faculty of Veterinary Medicine, Department of Production Animal Medicine, Research Centre for Animal Welfare, University of Helsinki, Helsinki, Finland
| | | | | | - Sanni Kivinen
- Functional Foods Forum, University of Turku, Turku, Finland
| | | | - Seppo Salminen
- Functional Foods Forum, University of Turku, Turku, Finland
| | - Maria Carmen Collado
- Functional Foods Forum, University of Turku, Turku, Finland
- Department of Biotechnology, Institute of Agrochemistry and Food Technology–National Research Council (IATA-CSIC), Valencia, Spain
| | - Tuomas Borman
- Department of Computing, University of Turku, Turku, Finland
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Virpi Piirainen
- Faculty of Veterinary Medicine, Department of Production Animal Medicine, University of Helsinki, Helsinki, Finland
- Faculty of Veterinary Medicine, Department of Production Animal Medicine, Research Centre for Animal Welfare, University of Helsinki, Helsinki, Finland
| | - Anna Valros
- Faculty of Veterinary Medicine, Department of Production Animal Medicine, Research Centre for Animal Welfare, University of Helsinki, Helsinki, Finland
| | - Mari Heinonen
- Faculty of Veterinary Medicine, Department of Production Animal Medicine, University of Helsinki, Helsinki, Finland
- Faculty of Veterinary Medicine, Department of Production Animal Medicine, Research Centre for Animal Welfare, University of Helsinki, Helsinki, Finland
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Sarpong N, Seifert J, Bennewitz J, Rodehutscord M, Camarinha-Silva A. Microbial signatures and enterotype clusters in fattening pigs: implications for nitrogen utilization efficiency. Front Microbiol 2024; 15:1354537. [PMID: 38659980 PMCID: PMC11040106 DOI: 10.3389/fmicb.2024.1354537] [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: 12/12/2023] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
As global demand for pork continues to rise, strategies to enhance nitrogen utilization efficiency (NUE) in pig farming have become vital for environmental sustainability. This study explored the relationship between the fecal microbiota, their metabolites, and NUE in crossbreed fattening pigs with a defined family structure. Pigs were kept under standardized conditions and fed in a two-phase feeding regime. In each phase, one fecal sample was collected from each pig. DNA was extracted from a total of 892 fecal samples and subjected to target amplicon sequencing. The results indicated an influence of sire, sampling period (SP), and sex on the fecal microbiota. Streptococcus emerged as a potential biomarker in comparing high and low NUE pigs in SP 1, suggesting a genetic predisposition to NUE regarding the fecal microbiota. All fecal samples were grouped into two enterotype-like clusters named cluster LACTO and cluster CSST. Pigs' affiliation with enterotype-like clusters altered over time and might be sex-dependent. The stable cluster CSST demonstrated the highest NUE despite containing pigs with lower performance characteristics such as average daily gain, dry matter intake, and daily nitrogen retention. This research contributes with valuable insights into the microbiome's role in NUE, paving the way for future strategies to enhance sustainable pig production.
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Affiliation(s)
- Naomi Sarpong
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Markus Rodehutscord
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
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Sebastià C, Folch JM, Ballester M, Estellé J, Passols M, Muñoz M, García-Casco JM, Fernández AI, Castelló A, Sánchez A, Crespo-Piazuelo D. Interrelation between gut microbiota, SCFA, and fatty acid composition in pigs. mSystems 2024; 9:e0104923. [PMID: 38095419 PMCID: PMC10804976 DOI: 10.1128/msystems.01049-23] [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: 10/03/2023] [Accepted: 11/06/2023] [Indexed: 01/24/2024] Open
Abstract
The gut microbiota is a key player in the host metabolism. Some bacteria are able to ferment non-digestible compounds and produce short-chain fatty acids that the host can later transform and accumulate in tissue. In this study, we aimed to better understand the relationships between the microorganisms and the short-chain fatty acid composition of the rectal content, including the possible linkage with the fatty acid composition in backfat and muscle of the pig. We studied a Duroc × Iberian crossbred population, and we found significant correlations between different bacterial and archaeal genera and the fatty acid profile. The abundance of n-butyric acid in the rectal content was positively associated with Prevotella spp. and negatively associated with Akkermansia spp., while conversely, the abundance of acetic acid was negatively and positively associated with the levels of Prevotella spp. and Akkermansia spp., respectively. The most abundant genus, Rikenellaceae RC9 gut group, had a positive correlation with palmitic acid in muscle and negative correlations with stearic acid in backfat and oleic acid in muscle. These results suggest the possible role of Prevotella spp. and Akkermansia spp. as biomarkers for acetic and n-butyric acids, and the relationship of Rikenellaceae RC9 gut group with the lipid metabolism, building up the potential, although indirect, role of the microbiota in the modification of the backfat and muscle fatty acid composition of the host.IMPORTANCEThe vital role of the gut microbiota on its host metabolism makes it essential to know how its modulation is mirrored on the fatty acid composition of the host. Our findings suggest Prevotella spp. and Akkermansia spp. as potential biomarkers for the levels of beneficial short-chain fatty acids and the possible influence of Rikenellaceae RC9 gut group in the backfat and muscle fatty acid composition of the pig.
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Affiliation(s)
- Cristina Sebastià
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Josep M. Folch
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Maria Ballester
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, Spain
| | - Jordi Estellé
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Magí Passols
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
| | - María Muñoz
- Departamento de Mejora Genética Animal, INIA-CSIC, Madrid, Spain
| | | | - Ana I. Fernández
- Departamento de Mejora Genética Animal, INIA-CSIC, Madrid, Spain
| | - Anna Castelló
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Armand Sánchez
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Daniel Crespo-Piazuelo
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, Spain
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Yi L, Zhu J, Li Q, Guan X, Cheng W, Xie Y, Zhao Y, Zhao S. Panax notoginseng stems and leaves affect microbial community and function in cecum of duzang pigs. Transl Anim Sci 2024; 8:txad142. [PMID: 38425544 PMCID: PMC10904106 DOI: 10.1093/tas/txad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/09/2024] [Indexed: 03/02/2024] Open
Abstract
Panax notoginseng is a Chinese medicine with a long history in which stems and leaves are the wastes of processing Panax notoginseng and have not been effectively utilized. The effects of diets containing Panax notoginseng stems and leaves on the cecal short-chain fatty acid (SCFA) concentration and microbiome of independent pigs were studied. Diets containing Panax notoginseng stems and leaves did not affect the concentration of SCFA in the cecal contents of Duzang pigs but affected the microbial composition and diversity. Firmicutes, Proteobacteria, and Bacteroidetes dominate in the cecal of Duzang pigs. Feeding Duzang pigs with a 10% Panax notoginseng stems and leaves diet increases the abundance of Lactobacillus, Christensenellaceae R-7 group, and Akkermansia in the cecal. We found 14 genera positively associated with acetate, and they were Lactobacillus, Ruminococcaceae UCG 005, Ruminiclostridium 6; Escherichia Shigella and Family XIII AD3011 group showed negative correlations. Solobacterium, Desulfovibrio, and Erysipelatoclostridium were positively associated with propionate. Campylobacter, Clostridium sensu stricto 11, and Angelakisella were positively associated with butyrate. In conclusion, Panax notoginseng stems and leaves could affect the cecal microbial community and functional composition of Duzang pigs. Panax notoginseng stems and leaves reduce the enrichment of lipopolysaccharide biosynthetic pathway of the cecal microbiome, which may have a positive effect on intestinal health. The higher abundance of GH25 family in Duzang pig's cecal microbiome of fed Panax notoginseng stems and leaves diet. This increase may be the reason for the microbial diversity decrease.
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Affiliation(s)
- Lanlan Yi
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
| | - Junhong Zhu
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
| | - Qiuyan Li
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
| | - Xuancheng Guan
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
| | - Wenjie Cheng
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
| | - Yuxiao Xie
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
- College of Biology and Agriculture, Zunyi Normal University, Guizhou 563006, China
| | - Yanguang Zhao
- Shanghai Academy of Science Technology, Shanghai Lab. Animal Research Center, Shanghai 201203, China
| | - Sumei Zhao
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Yunnan 650201, China
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6
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Dong W, Ricker N, Holman DB, Johnson TA. Meta-analysis reveals the predictable dynamic development of the gut microbiota in commercial pigs. Microbiol Spectr 2023; 11:e0172223. [PMID: 37815394 PMCID: PMC10715009 DOI: 10.1128/spectrum.01722-23] [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: 05/10/2023] [Accepted: 08/24/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE The swine gut microbiome undergoes an age-dependent assembly pattern with a developmental phase at early ages and a stabilization phase at later ages. Shorter time intervals and a wider range of data sources provided a clearer understanding of the gut microbiota colonization and succession and their associations with pig growth and development. The rapidly changing microbiota of suckling and weaning pigs implies potential time targets for growth and health regulation through gut microbiota manipulation. Since swine gut microbiota development is predictable, swine microbiota age can be calculated and compared between animal treatment groups rather than relying only on static time-matched comparisons.
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Affiliation(s)
- Wenxuan Dong
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Nicole Ricker
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Timothy A. Johnson
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
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Beretta S, Apparicio M, Toniollo GH, Cardozo MV. The importance of the intestinal microbiota in humans and dogs in the neonatal period. Anim Reprod 2023; 20:e20230082. [PMID: 38026003 PMCID: PMC10681130 DOI: 10.1590/1984-3143-ar2023-0082] [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: 05/29/2023] [Accepted: 09/01/2023] [Indexed: 12/01/2023] Open
Abstract
The neonatal period represents a critical stage for the establishment and development of the gut microbiota, which profoundly influences the future health trajectory of individuals. This review examines the importance of intestinal microbiota in humans and dogs, aiming to elucidate the distinct characteristics and variations in the composition between these two species. In humans, the intestinal microbiota contributes to several crucial physiological processes, including digestion, nutrient absorption, immune system development, and modulation of host metabolism. Dysbiosis, an imbalance or disruption of the gut microbial community, has been linked to various disorders, such as inflammatory bowel disease, obesity, and even neurological conditions. Furthermore, recent research has unveiled the profound influence of the gut-brain axis, emphasizing the bidirectional communication between the gut microbiota and the central nervous system, impacting cognitive function and mental health. Similarly, alterations in the canine intestinal microbiota have been associated with gastrointestinal disorders, including chronic enteropathy, such as inflammatory bowel disease, food allergies, and ulcerative histiocytic colitis. However, our understanding of the intricacies and functional significance of the intestinal microbiota in dogs remains limited. Understanding the complex dynamics of the intestinal microbiota in both humans and dogs is crucial for devising effective strategies to promote health and manage disease. Moreover, exploring the similarities and differences in the gut microbial composition between these two species can facilitate translational research, potentially leading to innovative therapeutic interventions and strategies to enhance the well-being of both humans and dogs.
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Affiliation(s)
- Samara Beretta
- Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brasil
| | - Maricy Apparicio
- Departamento de Cirurgia Veterinária e Reprodução Animal, Faculdade de Medicina Veterinária e Zootecnia (FMVZ), Universidade Estadual Paulista (UNESP), Botucatu, SP, Brasil
| | - Gilson Hélio Toniollo
- Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brasil
| | - Marita Vedovelli Cardozo
- Laboratório de Fisiologia de Microorganismos, Departamento de Ciências Biomédicas e Saúde, Universidade do Estado de Minas Gerais (UEMG), Passos, MG, Brasil
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Choi S, Kim EB. A comprehensive longitudinal study of gut microbiota dynamic changes in laying hens at four growth stages prior to egg production. Anim Biosci 2023; 36:1727-1737. [PMID: 37871901 PMCID: PMC10623045 DOI: 10.5713/ab.23.0271] [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: 07/18/2023] [Revised: 08/14/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023] Open
Abstract
OBJECTIVE The poultry industry is a primary source of animal protein worldwide. The gut microbiota of poultry birds, such as chickens and ducks, is critical in maintaining their health, growth, and productivity. This study aimed to identify longitudinal changes in the gut microbiota of laying hens from birth to the pre-laying stage. METHODS From a total of 80 Hy-Line Brown laying hens, birds were selected based on weight at equal intervals to collect feces (n = 20 per growth) and ileal contents (n = 10 per growth) for each growth stage (days 10, 21, 58, and 101). The V4 regions of the 16S rRNA gene were amplified after extracting DNA from feces and ileal contents. Amplicon sequencing was performed using Illumina, followed by analysis. RESULTS Microbial diversity increased with growth stages, regardless of sampling sites. Microbial community analysis indicated that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla in the feces and ileal. The abundance of Lactobacillus was highest on day 10, and that of Escherichia-shigella was higher on day 21 than those at the other stages at the genus level (for the feces and ileal contents; p<0.05). Furthermore, Turicibacter was the most abundant genus after changing feed (for the feces and ileal contents; p<0.05). The fecal Ruminococcus torques and ileal Lysinibacillus were negatively correlated with the body weights of chickens (p<0.05). CONCLUSION The gut microbiota of laying hens changes during the four growth stages, and interactions between microbiota and feed may be present. Our findings provide valuable data for understanding the gut microbiota of laying hens at various growth stages and future applied studies.
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Affiliation(s)
- Seojin Choi
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341,
Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341,
Korea
- Institute of Animal Life Science, Kangwon National University, Chuncheon, 24341,
Korea
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9
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Schokker D, Kar SK, Willems E, Bossers A, Dekker RA, Jansman AJM. Dietary supplementation of zinc oxide modulates intestinal functionality during the post-weaning period in clinically healthy piglets. J Anim Sci Biotechnol 2023; 14:122. [PMID: 37789352 PMCID: PMC10548679 DOI: 10.1186/s40104-023-00925-1] [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: 04/21/2023] [Accepted: 08/01/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND To improve our understanding of host and intestinal microbiome interaction, this research investigated the effects of a high-level zinc oxide in the diet as model intervention on the intestinal microbiome and small intestinal functionality in clinically healthy post-weaning piglets. In study 1, piglets received either a high concentration of zinc (Zn) as zinc oxide (ZnO, Zn, 2,690 mg/kg) or a low Zn concentration (100 mg/kg) in the diet during the post weaning period (d 14-23). The effects on the piglet's small intestinal microbiome and functionality of intestinal tissue were investigated. In study 2, the impact of timing of the dietary zinc intervention was investigated, i.e., between d 0-14 and/or d 14-23 post weaning, and the consecutive effects on the piglet's intestinal functionality, here referring to microbiota composition and diversity and gene expression profiles. RESULTS Differences in the small intestinal functionality were observed during the post weaning period between piglets receiving a diet with a low or high concentration ZnO content. A shift in the microbiota composition in the small intestine was observed that could be characterized as a non-pathological change, where mainly the commensals inter-changed. In the immediate post weaning period, i.e., d 0-14, the highest number of differentially expressed genes (DEGs) in intestinal tissue were observed between animals receiving a diet with a low or high concentration ZnO content, i.e., 23 DEGs in jejunal tissue and 11 DEGs in ileal tissue. These genes are involved in biological processes related to immunity and inflammatory responses. For example, genes CD59 and REG3G were downregulated in the animals receiving a diet with a high concentration ZnO content compared to low ZnO content in both jejunum and ileum tissue. In the second study, a similar result was obtained regarding the expression of genes in intestinal tissue related to immune pathways when comparing piglets receiving a diet with a high concentration ZnO content compared to low ZnO content. CONCLUSIONS Supplementing a diet with a pharmaceutical level of Zn as ZnO for clinically healthy post weaning piglets influences various aspects intestinal functionality, in particular in the first two weeks post-weaning. The model intervention increased both the alpha diversity of the intestinal microbiome and the expression of a limited number of genes linked to the local immune system in intestinal tissue. The effects do not seem related to a direct antimicrobial effect of ZnO.
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Affiliation(s)
| | - Soumya K Kar
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Els Willems
- Royal Agrifirm Group, Apeldoorn, The Netherlands
| | - Alex Bossers
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Ruud A Dekker
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Alfons J M Jansman
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
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10
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Kim S, Kwak J, Song M, Cho J, Kim ES, Keum GB, Doo H, Pandey S, Cho JH, Ryu S, Kim S, Im YM, Kim HB. Effects of Lacticaseibacillus casei ( Lactobacillus casei) and Saccharomyces cerevisiae mixture on growth performance, hematological parameters, immunological responses, and intestinal microbiome in weaned pigs. Front Vet Sci 2023; 10:1140718. [PMID: 37383354 PMCID: PMC10296769 DOI: 10.3389/fvets.2023.1140718] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/16/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction This study was conducted to evaluate the effects of Lacticaseibacillus casei (Lactobacillus casei) and Saccharomyces cerevisiae mixture on growth performance, hematological parameters, immunological responses, and gut microbiome in weaned pigs. Methods A total of 300 crossbred pigs [(Landrace × Yorkshire] × Duroc; 8.87 ± 0.34 kg of average initial body weight [BW]; 4 weeks of age) were divided into two dietary treatments (15 pigs/pen, 10 replicates/treatment) using a randomized complete block design (block = BW): control (CON) and the effective microorganism (MEM). The CON was not treated, while the MEM was treated with the mixture of L. casei (1 × 107 CFU/mL) and S. cerevisiae (1 × 107 CFU/mL) at 3 mL/pig/day for 4 weeks via the drinking water supply. Two feces and one blood sample from the randomly selected pigs in each pen were collected on D1 and D28 after weaning. Pigs were individually weighed, and pen feed intakes were recorded to evaluate pig growth performance. For the gut microbiome analysis, 16S rRNA gene hypervariable regions (V5 to V6) were sequenced using the Illumina MiSeq platform, and Quantitative Insight into Microbial Ecology (QIIME) and Microbiome Helper pipeline were used for 16S rRNA gene sequence analysis. Results and Discussion The daily weight gain and feed efficiency of MEM were significantly higher than those of CON (p < 0.001). There were no significant differences in hematological parameters and immune responses between CON and MEM. However, MEM had significantly lower Treponema genus, whereas significantly higher Lactobacillus and Roseburia genera compared to CON. Overall, our data showed that L. casei and S. cerevisiae mixture could promote growth performance through the modulation of gut microbiota in pigs. This study will help to understand the correlation between the growth performance and the gut microbiome.
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Affiliation(s)
- Sheena Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Jinok Kwak
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Minho Song
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Republic of Korea
| | - Jinho Cho
- Division of Food and Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Eun Sol Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Gi Beom Keum
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Hyunok Doo
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Sriniwas Pandey
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Jae Hyoung Cho
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Sumin Ryu
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - San Kim
- BRD Korea Corp., Hwaseong, Republic of Korea
| | - Yu-Mi Im
- Department of Nursing, Dankook University, Cheonan, Republic of Korea
| | - Hyeun Bum Kim
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
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Rutjens S, Vereecke N, Sauer J, Croubels S, Devreese M. Cefquinome shows a higher impact on the pig gut microbiome and resistome compared to ceftiofur. Vet Res 2023; 54:45. [PMID: 37280708 DOI: 10.1186/s13567-023-01176-8] [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: 02/17/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
Cephalosporins are licensed for treatment of severe bacterial infections in different species. However, the effect of these antimicrobials on the fecal microbiome and potential spread of resistance-associated genes causes great concern. This highlights the need to understand the impact of cephalosporins on the porcine fecal microbiome and resistome. A combination of long-read 16S rRNA gene and shotgun metagenomic sequencing was applied to investigate the effect of conventional treatment with either ceftiofur (3 mg.kg-1 intramuscular, 3 consecutive days) or cefquinome (2 mg.kg-1 intramuscular, 5 consecutive days) on the porcine microbiome and resistome. Fecal samples were collected from 17 pigs (6 ceftiofur treated, 6 cefquinome treated, 5 control pigs) at four different timepoints. Treatment with ceftiofur resulted in an increase in Proteobacteria members on microbiome level, while on resistome level selection in TetQ containing Bacteroides, CfxA6 containing Prevotella and blaTEM-1 containing Escherichia coli was observed. Cefquinome treatment resulted in a decline in overall species richness (α-diversity) and increase in Proteobacteria members. On genus level, administration of cefquinome significantly affected more genera than ceftiofur (18 vs 8). On resistome level, cefquinome resulted in a significant increase of six antimicrobial resistance genes, with no clear correlation with certain genera. For both antimicrobials, the resistome levels returned back to the control levels 21 days post-treatment. Overall, our study provides novel insights on the effect of specific cephalosporins on the porcine gut microbiome and resistome after conventional intramuscular treatment. These results might contribute to better tailoring of the most ideal treatment strategy for some bacterial infections.
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Affiliation(s)
- Sofie Rutjens
- Department of Pathobiology, Pharmacology and Zoological Medicine, Laboratory of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium
| | - Nick Vereecke
- PathoSense BV, 2500, Lier, Belgium
- Department of Translational Physiology, Infectiology and Public Health, Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium
| | | | - Siska Croubels
- Department of Pathobiology, Pharmacology and Zoological Medicine, Laboratory of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium
| | - Mathias Devreese
- Department of Pathobiology, Pharmacology and Zoological Medicine, Laboratory of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium.
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12
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Paganin ACL, Monzani PS, Carazzolle MF, Araujo RB, Gonzalez-Esquerra R, Haese D, Kill JL, Rezende GS, de Lima CG, Malavazi I, de Melo Freire CC, da Cunha AF. Assessment of cecal microbiota modulation from piglet dietary supplementation with copper. BMC Microbiol 2023; 23:92. [PMID: 37003969 PMCID: PMC10064724 DOI: 10.1186/s12866-023-02826-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Swine production expanded in the last decades. Efforts have been made to improve meat production and to understand its relationship to pig gut microbiota. Copper (Cu) is a usual supplement to growth performance in animal production. Here, two performance studies were conducted to investigate the effects of three different sources of Cu on the microbiota of piglets. A total of 256 weaned piglets were randomly allocated into 4 treatments (10 replicates per treatment of 4 piglets per pen in Trial 1 and 8 replicates of 3 piglets per pen in Trial 2). Treatments included a control group (fed 10 mg/kg of Cu from CuSO4), a group fed at 160 mg/kg of Copper (II) sulfate (CuSO4) or tri-basic copper chloride (TBCC), and a group fed with Cu methionine hydroxy analogue chelated (Cu-MHAC) at 150, 80, and 50 mg/kg in Phases 1 (24-35 d), 2 (36-49 d), and 3 (50-70 d), respectively. At 70 d, the cecum luminal contents from one pig per pen were collected and polled for 16 S rRNA sequencing (V3/V4 regions). Parameters were analyzed in a completely randomized block design, in which each experiment was considered as a block. RESULTS A total of 1337 Operational Taxonomic Units (OTUs) were identified. Dominance and Simpson ecological metrics were statistically different between control and treated groups (P < 0.10) showing that different Cu sources altered the gut microbiota composition with the proliferation of some bacteria that improve gut health. A high abundance of Prevotella was observed in all treatments while other genera were enriched and differentially modulated, according to the Cu source and dosage. The supplementation with Cu-MHAC can modify a group of bacteria involved in feed efficiency (FE) and short chain fatty acids (SCFA) production (Clostridium XIVa, Desulfovibrio, and Megasphera). These bacteria are also important players in the activation of ghrelin and growth hormones that were previously reported to correlate with Cu-MHAC supplementation. CONCLUSIONS These results indicated that some genera seem to be directly affected by the Cu source offered to the animals. TBCC and Cu-MHAC (even in low doses) can promote healthy modifications in the gut bacterial composition, being a promising source of supplementation for piglets.
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Affiliation(s)
| | - Paulo Sérgio Monzani
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Universidade de São Paulo, Pirassununga, SP, Brasil
| | | | | | | | - Douglas Haese
- Centro de Tecnologia Animal Ltda, Espirito Santo - ES, Domingos Martins, Brasil
| | - João L Kill
- Centro de Tecnologia Animal Ltda, Espirito Santo - ES, Domingos Martins, Brasil
| | - Graziela Silva Rezende
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
| | - César Gonçalves de Lima
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Universidade de São Paulo, Pirassununga, SP, Brasil
| | - Iran Malavazi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
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Tardiolo G, Romeo O, Zumbo A, Di Marsico M, Sutera AM, Cigliano RA, Paytuví A, D’Alessandro E. Characterization of the Nero Siciliano Pig Fecal Microbiota after a Liquid Whey-Supplemented Diet. Animals (Basel) 2023; 13:642. [PMID: 36830429 PMCID: PMC9951753 DOI: 10.3390/ani13040642] [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: 01/04/2023] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
The utilization of dairy by-products as animal feed, especially in swine production, is a strategy to provide functional ingredients to improve gut health. This study explored the potential effect of a liquid whey-supplemented diet on the fecal microbiota of eleven pigs belonging to the Nero Siciliano breed. Five pigs were assigned to the control group and fed with a standard formulation feed, whereas six pigs were assigned to the experimental group and fed with the same feed supplemented with liquid whey. Fecal samples were collected from each individual before the experimental diet (T0), and one (T1) and two (T2) months after the beginning of the co-feed supplementation. Taxonomic analysis, based on the V3-V4 region of the bacterial 16S rRNA, showed that pig feces were populated by a complex microbial community with a remarkable abundance of Firmicutes, Bacteroidetes, and Spirochaetes phyla and Prevotella, Lactobacillus, Clostridium, and Treponema genera. Alpha and beta diversity values suggested that the experimental diet did not significantly affect the overall fecal microbiota diversity. However, analysis of abundance at different time points revealed significant variation in several bacterial genera, suggesting that the experimental diet potentially affected some genera of the microbial community.
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Affiliation(s)
- Giuseppe Tardiolo
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell’Annunziata, Via Palatucci snc, 98168 Messina, Italy
| | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Alessandro Zumbo
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell’Annunziata, Via Palatucci snc, 98168 Messina, Italy
| | - Marco Di Marsico
- Sequentia Biotech SL, Carrer del Dr. Trueta 179, 08005 Barcelona, Spain
| | - Anna Maria Sutera
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell’Annunziata, Via Palatucci snc, 98168 Messina, Italy
| | | | - Andreu Paytuví
- Sequentia Biotech SL, Carrer del Dr. Trueta 179, 08005 Barcelona, Spain
| | - Enrico D’Alessandro
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell’Annunziata, Via Palatucci snc, 98168 Messina, Italy
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14
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Bak JE, Oh BS, Ryu SW, Yu SY, Choi WJ, Kim JS, Lee JS, Park SH, Kang SW, Lee J, Lee MK, Yun CS, Jung WY, Kim JE, Cho ES, Kim HB, Kim JK, Lee JH, Lee JH. Parabacteroides faecalis sp. nov. Isolated from Swine Faeces. Curr Microbiol 2023; 80:91. [PMID: 36725751 DOI: 10.1007/s00284-023-03190-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/13/2023] [Indexed: 02/03/2023]
Abstract
A Gram-negative, obligate anaerobic, non-motile, non-spore-forming, rod-shaped bacterial strain designated AGMB00274T was isolated from swine faeces. An 16S rRNA gene analysis indicated that strain AGMB00274T belonged to the genus Parabacteroides, with the highest similarity to Parabacteroides johnsonii (P. johnsonii) DSM 18315T (sequence similarity of 94.9%). The genome size of strain AGMB00274T was 4,308,683 bp, with a DNA G+C content of 42.5 mol%. The biochemical analysis of strain AGMB00274T showed that it was positive for gelatin hydrolysis and α-fucosidase, but negative for the acid production from D-glucose, D-mannitol, D-maltose, salicin, glycerol, D-cellobiose, D-mannose, D-melezitose, D-sorbitol, D-trehalose, and negative for α-arabinosidase, glutamic acid decarboxylase, and pyroglutamic acid arylamidase. The dominant cellular fatty acids (> 10%) of the isolate were anteiso-C15: 0 (23.2%), iso-C15: 0 (16.6%), C18: 1 ω9c (16.4%), summed feature 11 (iso-C17: 0 3-OH and/or C18: 2 DMA) (12.5%), and C16: 0 (11.3%). The major respiratory quinones of strain AGMB00274T were MK-9 (55.4%) and MK-10 (44.6%). The major polar lipid was phosphatidylethanolamine. Based on phylogenetic, genetic, physiological, and chemotaxonomic analyses, as a novel species of the genus Parabacteroides, strain AGMB00274T was proposed with the name Parabacteroides faecalis sp. nov. The type strain used was AGMB00274T (= KCTC 25286T = GDMCC 1.2742T).
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Affiliation(s)
- Jeong Eun Bak
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Byeong Seob Oh
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Seoung Woo Ryu
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Seung Yeob Yu
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Won Jung Choi
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Se Won Kang
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Jiyoung Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Mi-Kyung Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Chan Seok Yun
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Won Yong Jung
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Jo Eun Kim
- National Institute of Animal Science, Cheonan, 31000, Republic of Korea
| | - Eun Seok Cho
- National Institute of Animal Science, Cheonan, 31000, Republic of Korea
| | - Hyeun Bum Kim
- Department of Animal Resources Science, Dankook University, Cheonan, 31116, Republic of Korea
| | - Jae-Kyung Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Ju-Hoon Lee
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea.
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15
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Li L, Yin F, Wang X, Yang C, Yu H, Lepp D, Wang Q, Lessard M, Lo Verso L, Mondor M, Yang C, Nie S, Gong J. Microencapsulation protected Lactobacillus viability and its activity in modulating the intestinal microbiota in newly weaned piglets. J Anim Sci 2023; 101:skad193. [PMID: 37403537 PMCID: PMC10516462 DOI: 10.1093/jas/skad193] [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: 03/07/2023] [Accepted: 06/27/2023] [Indexed: 07/06/2023] Open
Abstract
Lactobacilli are sensitive to heat, which limits their application as probiotics in livestock production. Lactobacillus rhamnosus LB1 was previously shown to reduce enterotoxigenic Escherichia coli (ETEC) and Salmonella infections in pigs. To investigate its potential in the application, the bacterium was microencapsulated and examined for its survival from feed pelleting and long-term storage as well as its function in modulating pig intestinal microbiota. The in vitro studies showed that freshly microencapsulated Lactobacillus rhamnosus LB1 had viable counts of 9.03 ± 0.049 log10 colony-forming units/g, of which only 0.06 and 0.87 Log of viable counts were reduced after storage at 4 and 22 °C for 427 d. The viable counts of encapsulated Lactobacillus rhamnosus LB1 were 1.06 and 1.54 Log higher in the pelleted and mash feed, respectively, than the non-encapsulated form stored at 22 °C for 30 d. In the in vivo studies, 80 piglets (weaned at 21 d of age) were allocated to five dietary treatments for a 10-d growth trial. The dietary treatments were the basal diet (CTL) and basal diet combined with either non-encapsulated LB1 (NEP), encapsulated LB1 (EP), bovine colostrum (BC), or a combination of encapsulated LB1 and bovine colostrum (EP-BC). The results demonstrated that weaning depressed feed intake and reduced growth rates in pigs of all the treatments during 21 to 25 d of age; however, the body weight gain was improved during 25 to 31 d of age in all groups with the numerically highest increase in the EP-BC-fed pigs during 21 to 31 d of age. Dietary treatments with EP, particularly in combination with BC, modulated pig intestinal microbiota, including an increase in Lactobacillus relative abundance. These results suggest that microencapsulation can protect Lactobacillus rhamnosus LB1 against cell damage from a high temperature during processing and storage and there are possible complementary effects between EP and BC.
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Affiliation(s)
- Linyan Li
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi, China
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
| | - Fugui Yin
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
| | - Xiaoyin Wang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi, China
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
| | - Chongwu Yang
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
| | - Hai Yu
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
| | - Dion Lepp
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
| | - Qi Wang
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
| | - Martin Lessard
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
| | - Luca Lo Verso
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
| | - Martin Mondor
- St-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, St-Hyacinthe, Quebec, Canada
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi, China
| | - Joshua Gong
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
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16
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Xu D, Cheng J, Zhang D, Huang K, Zhang Y, Li X, Zhao Y, Zhao L, Wang J, Lin C, Yang X, Zhai R, Cui P, Zeng X, Huang Y, Ma Z, Liu J, Han K, Liu X, Yang F, Tian H, Weng X, Zhang X, Wang W. Relationship between hindgut microbes and feed conversion ratio in Hu sheep and microbial longitudinal development. J Anim Sci 2023; 101:skad322. [PMID: 37742310 PMCID: PMC10576521 DOI: 10.1093/jas/skad322] [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: 04/25/2023] [Accepted: 09/22/2023] [Indexed: 09/26/2023] Open
Abstract
Feed efficiency is an important indicator in the sheep production process, which plays an important role in improving economic benefits and strengthening energy conservation and emission reduction. Compared with the rumen, the fermentation of the hindgut microorganisms can also provide part of the energy for the host, and the composition of the hindgut microorganisms will affect the feed efficiency. Therefore, we hope to find new ways to regulate sheep feed efficiency by studying the sheep gut microbes. In this study, male Hu sheep with the same birth date were raised under the same conditions until 180 d old. The sheep were divided into high and low groups according to the feed conversion ratio (FCR) at 80 to 180 d old, and the differences in rectal microorganisms between the two groups were compared. The permutational multivariate analysis (PERMANOVA) test showed that there were differences in microorganisms between the two groups (P < 0.05). Combined with linear fitting analysis, a total of six biomarkers were identified, including Ruminobacter, Eubacterium_xylanophilum_group, Romboutsia, etc. Functional enrichment analysis showed that microorganisms may affect FCR through volatile fatty acids synthesis and inflammatory response. At the same time, we conducted a longitudinal analysis of the hindgut microbes, sampling nine-time points throughout the sheep birth to market stages. The microbiota is clearly divided into two parts: before weaning and after weaning, and after weaning microbes are less affected by before weaning microbial composition.
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Affiliation(s)
- Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Kai Huang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Yukun Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Kunchao Han
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaoqiang Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Fan Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Huibin Tian
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiuxiu Weng
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
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He J, Zhang Y, Li H, Xie Y, Huang G, Peng C, Zhao P, Wang Z. Hybridization alters the gut microbial and metabolic profile concurrent with modifying intestinal functions in Tunchang pigs. Front Microbiol 2023; 14:1159653. [PMID: 37152756 PMCID: PMC10157192 DOI: 10.3389/fmicb.2023.1159653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/15/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction Hybridization has been widely used among Chinese wild boars to improve their growth performance and maintain meat quality. Most studies have focused on the genetic basis for such variation. However, the differences in the gut environment between hybrid and purebred boars, which can have significant impacts on their health and productivity, have been poorly understood. Methods In the current study, metagenomics was used to detect the gut microbial diversity and composition in hybrid Batun (BT, Berkshire × Tunchang) pigs and purebred Tunchang (TC) pigs. Additionally, untargeted metabolomic analysis was used to detect differences in gut metabolic pathways. Furthermore, multiple molecular experiments were conducted to demonstrate differences in intestinal functions. Results As a result of hybridization in TC pigs, a microbial change was observed, especially in Prevotella and Lactobacillus. Significant differences were found in gut metabolites, including fatty acyls, steroids, and steroid derivatives. Furthermore, the function of the intestinal barrier was decreased by hybridization, while the function of nutrient metabolism was increased. Discussion Evidences were shown that hybridization changed the gut microbiome, gut metabolome, and intestinal functions of TC pigs. These findings supported our hypothesis that hybridization altered the gut microbial composition, thereby modifying the intestinal functions, even the host phenotypes. Overall, our study highlights the importance of considering the gut microbiome as a key factor in the evaluation of animal health and productivity, particularly in the context of genetic selection and breeding programs.
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Affiliation(s)
- Jiayi He
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yunchao Zhang
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Hui Li
- Long Jian Animal Husbandry Company, Haikou, China
| | - Yanshe Xie
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Guiqing Huang
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Chen Peng
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Pengju Zhao
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
- *Correspondence: Pengju Zhao,
| | - Zhengguang Wang
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
- Zhengguang Wang,
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Wang W, Dang G, Khan I, Ye X, Liu L, Zhong R, Chen L, Ma T, Zhang H. Bacterial Community Characteristics Shaped by Artificial Environmental PM2.5 Control in Intensive Broiler Houses. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 20:723. [PMID: 36613044 PMCID: PMC9819255 DOI: 10.3390/ijerph20010723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
Multilayer cage-houses for broiler rearing have been widely used in intensive Chinese farming in the last decade. This study investigated the characteristics and influencing factors of bacterial communities in the PM2.5 of broiler cage-houses. The PM2.5 samples and environmental variables were collected inside and outside of three parallel broiler houses at the early, middle, and late rearing stages; broiler manure was also gathered simultaneously. The bacterial 16S rRNA sequencing results indicated that indoor bacterial communities were different from the outdoor atmosphere and manure. Furthermore, the variations in airborne bacterial composition and structure were highly influenced by the environmental control variables at different growth stages. The db-RDA results showed that temperature and wind speed, which were artificially modified according to managing the needs for broiler growth, were the main factors affecting the diversity of dominant taxa. Indoor airborne and manurial samples shared numerous common genera, which contained high abundances of manure-origin bacteria. Additionally, the airborne bacterial community tended to stabilize in the middle and late stages, but the population of potentially pathogenic bacteria grew gradually. Overall, this study enhances the understanding of airborne bacteria variations and highlighted the potential role of environmental control measures in intensive farming.
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Affiliation(s)
- Wenxing Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guoqi Dang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Imran Khan
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaobin Ye
- Bureau of Agriculture and Rural Affairs of Luanping County, Chengde 068250, China
| | - Lei Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ruqing Zhong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Liang Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Teng Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Saladrigas-García M, Durán M, D’Angelo M, Coma J, Pérez JF, Martín-Orúe SM. An insight into the commercial piglet's microbial gut colonization: from birth towards weaning. Anim Microbiome 2022; 4:68. [PMID: 36572944 PMCID: PMC9791761 DOI: 10.1186/s42523-022-00221-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 12/18/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The establishment of the gut microbiota can be influenced by several perinatal factors, including, most importantly, the maternal microbiota. Moreover, early-life environmental variation affects gut microbial colonization and the intestinal health of offspring throughout life. The present study aimed to explore the development of piglet gut microbiota from birth to weaning in the commercial practice and also to assess how different farm environments could condition this process. Although it is possible to find in the literature other studies with similar objectives this work probably represents one of the few studies that make a systematic evaluation of such differential factors under a real scenario. To achieve this objective, we performed two trials. In a first Trial, we selected 2 farms in which we performed an intensive sampling (5 samples /animal) to characterize the gut colonization pattern during the first days of life and to identify the time window with the greatest impact. Both farms differed in their health status and the use of antimicrobials in the piglets. In a second Trial, we selected 4 additional farms with variable rearing conditions and a distinctive use of antimicrobials in the sows with a simplified sampling pattern (2 samples/animal). Faecal samples were obtained with swabs and DNA was extracted by using the PSP® Spin Stool DNA Kit and sequencing of the 16S rRNA gene (V3-V4 region) performed by Illumina MiSeq Platform. RESULTS The present study contributes to a better understanding of microbiome development during the transition from birth to weaning in commercial conditions. Alpha diversity was strongly affected by age, with an increased richness of species through time. Beta diversity decreased after weaning, suggesting a convergent evolvement among individuals. We pinpointed the early intestinal colonizers belonging to Bacteroides, Escherichia-Shigella, Clostridium sensu stricto 1, and Fusobacterium genera. During lactation(d7-d21 of life), the higher relative abundances of Bacteroides and Lactobacillus genera were correlated with a milk-oriented microbiome. As the piglets aged and after weaning (d36 of life), increasing abundances of genera such as Prevotella, Butyricimonas, Christensenellaceae R-7 group, Dorea, Phascolarctobacterium, Rikenellaceae RC9 gut group, Subdoligranulum, and Ruminococcaceae UCG-002 were observed. These changes indicate the adaptation of the piglets to a cereal-based diet rich in oligosaccharides and starch. Our results also show that the farm can have a significant impact in such a process, evidencing the influence of different environments and rearing systems on the gut microbiota development of the young piglet. Differences between farms were more noticeable after weaning than during lactation with changes in alpha and beta biodiversity and specific taxa. The analysis of such differences suggests that piglets receiving intramuscular amoxicillin (days 2-5 of life) and being offered an acidifying rehydrating solution (Alpha farm in Trial 1) have a greater alpha diversity and more abundant Lactobacillus population. Moreover, the only farm that did not offer any rehydrating solution (Foxtrot farm in Trial 2) showed a lower alpha diversity (day 2 of life) and increased abundance of Enterobacteriaceae (both at 2 and 21 days). The use of in-feed antibiotics in the sows was also associated with structural changes in the piglets' gut ecosystem although without changes in richness or diversity. Significant shifts could be registered in different microbial groups, particularly lower abundances of Fusobacterium in those piglets from medicated sows. CONCLUSIONS In conclusion, during the first weeks of life, the pig microbiota showed a relevant succession of microbial groups towards a more homogeneous and stable ecosystem better adapted to the solid dry feed. In this relevant early-age process, the rearing conditions, the farm environment, and particularly the antimicrobial use in piglets and mothers determine changes that could have a relevant impact on gut microbiota maturation. More research is needed to elucidate the relative impact of these farm-induced early life-long changes in the growing pig.
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Affiliation(s)
- Mireia Saladrigas-García
- grid.7080.f0000 0001 2296 0625Servicio de Nutrición Y Bienestar Animal. Departamento de Ciencia Animal Y de los Alimentos, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | | | - Matilde D’Angelo
- grid.7080.f0000 0001 2296 0625Servicio de Nutrición Y Bienestar Animal. Departamento de Ciencia Animal Y de los Alimentos, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Jaume Coma
- Grupo Vall Companys, 25191 Lleida, Spain
| | - José Francisco Pérez
- grid.7080.f0000 0001 2296 0625Servicio de Nutrición Y Bienestar Animal. Departamento de Ciencia Animal Y de los Alimentos, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Susana María Martín-Orúe
- grid.7080.f0000 0001 2296 0625Servicio de Nutrición Y Bienestar Animal. Departamento de Ciencia Animal Y de los Alimentos, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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Springer A, Wagner L, Koehler S, Klinger S, Breves G, Brüggemann DA, Strube C. Modulation of the porcine intestinal microbiota in the course of Ascaris suum infection. Parasit Vectors 2022; 15:433. [PMID: 36397169 PMCID: PMC9673396 DOI: 10.1186/s13071-022-05535-w] [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: 07/28/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022] Open
Abstract
Background The porcine roundworm Ascaris suum impairs feed conversion and weight gain, but its effects on intestinal microbiota remain largely unexplored. Methods Modulation of the intestinal microbiota was assessed in pigs that were infected once with 10,000 A. suum eggs and pigs that received a trickle infection (1000 eggs/day over 10 days), compared with a non-infected control group. Six pigs each were sacrificed per group at days 21, 35 and 49 post-infection (p.i.). Faecal samples taken weekly until slaughter and ingesta samples from different intestinal compartments were subjected to next-generation sequencing of the bacterial 16S rRNA gene. Results The results revealed marked differences between the single- and the trickle-infected group. Single infection caused a remarkable but transient decrease in microbial diversity in the caecum, which was not observed in the trickle-infected group. However, an increase in short-chain fatty acid-producing genera in the caecum on day 21 p.i., which shifted to a decrease on day 35 p.i., was common to both groups, possibly related to changes in excretory–secretory products following the parasite’s final moult. Faecal microbial interaction networks were more similar between the single-infected and control group than the trickle-infected group. In addition, a lower degree of similarity over time indicated that A. suum trickle infection prevented microbiota stabilization. Conclusions These different patterns may have important implications regarding the comparability of experimental infections with natural scenarios characterized by continuous exposure, and should be confirmed by further studies. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05535-w.
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de Carvalho FM, Valiatti TB, Santos FF, Silveira ACDO, Guimarães APC, Gerber AL, Souza CDO, Cassu Corsi D, Brasiliense DM, Castelo-Branco DDSCM, Anzai EK, Bessa-Neto FO, Guedes GMDM, de Souza GHDA, Lemos LN, Ferraz LFC, Bahia MDNM, Vaz MSM, da Silva RGB, Veiga R, Simionatto S, Monteiro WAP, Lima WADO, Kiffer CRV, Campos Pignatari AC, Cayô R, de Vasconcelos ATR, Gales AC. Exploring the Bacteriome and Resistome of Humans and Food-Producing Animals in Brazil. Microbiol Spectr 2022; 10:e0056522. [PMID: 35993730 PMCID: PMC9602611 DOI: 10.1128/spectrum.00565-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/03/2022] [Indexed: 12/30/2022] Open
Abstract
The epidemiology of antimicrobial resistance (AMR) is complex, with multiple interfaces (human-animal-environment). In this context, One Health surveillance is essential for understanding the distribution of microorganisms and antimicrobial resistance genes (ARGs). This report describes a multicentric study undertaken to evaluate the bacterial communities and resistomes of food-producing animals (cattle, poultry, and swine) and healthy humans sampled simultaneously from five Brazilian regions. Metagenomic analysis showed that a total of 21,029 unique species were identified in 107 rectal swabs collected from distinct hosts, the highest numbers of which belonged to the domain Bacteria, mainly Ruminiclostridium spp. and Bacteroides spp., and the order Enterobacterales. We detected 405 ARGs for 12 distinct antimicrobial classes. Genes encoding antibiotic-modifying enzymes were the most frequent, followed by genes related to target alteration and efflux systems. Interestingly, carbapenemase-encoding genes such as blaAIM-1, blaCAM-1, blaGIM-2, and blaHMB-1 were identified in distinct hosts. Our results revealed that, in general, the bacterial communities from humans were present in isolated clusters, except for the Northeastern region, where an overlap of the bacterial species from humans and food-producing animals was observed. Additionally, a large resistome was observed among all analyzed hosts, with emphasis on the presence of carbapenemase-encoding genes not previously reported in Latin America. IMPORTANCE Humans and food production animals have been reported to be important reservoirs of antimicrobial resistance (AMR) genes (ARGs). The frequency of these multidrug-resistant (MDR) bacteria tends to be higher in low- and middle-income countries (LMICs), due mainly to a lack of public health policies. Although studies on AMR in humans or animals have been carried out in Brazil, this is the first multicenter study that simultaneously collected rectal swabs from humans and food-producing animals for metagenomics. Our results indicate high microbial diversity among all analyzed hosts, and several ARGs for different antimicrobial classes were also found. As far as we know, we have detected for the first time ARGs encoding carbapenemases, such as blaAIM-1, blaCAM-1, blaGIM-2, and blaHMB-1, in Latin America. Thus, our results support the importance of metagenomics as a tool to track the colonization of food-producing animals and humans by antimicrobial-resistant bacteria. In addition, a network surveillance system called GUARANI, created for this study, is ready to be expanded and to collect additional data.
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Affiliation(s)
- Fabíola Marques de Carvalho
- Bioinformatics Laboratory, National Laboratory of Scientific Computing (LNCC), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tiago Barcelos Valiatti
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, Brazil
| | - Fernanda Fernandes Santos
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, Brazil
| | | | - Ana Paula C. Guimarães
- Bioinformatics Laboratory, National Laboratory of Scientific Computing (LNCC), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandra Lehmkuhl Gerber
- Bioinformatics Laboratory, National Laboratory of Scientific Computing (LNCC), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cintya de Oliveira Souza
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Secretaria de Vigilância em Saúde (SVS), Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Dandara Cassu Corsi
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, Brazil
| | - Danielle Murici Brasiliense
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Secretaria de Vigilância em Saúde (SVS), Ministério da Saúde, Ananindeua, Pará, Brazil
| | | | | | - Francisco Ozório Bessa-Neto
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, Brazil
- Universidade Federal de São Paulo (UNIFESP), Laboratório de Imunologia e Bacteriologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia, Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema, São Paulo, Brazil
| | - Glaucia Morgana de Melo Guedes
- Postgraduate Program in Medical Microbiology, Group of Applied Medical Microbiology, Federal University of Ceará (UFC), Fortaleza, Ceará, Brazil
| | | | - Leandro Nascimento Lemos
- Bioinformatics Laboratory, National Laboratory of Scientific Computing (LNCC), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lúcio Fábio Caldas Ferraz
- Laboratory of Molecular Biology of Microorganisms, University São Francisco (USF), Bragança Paulista, São Paulo, Brazil
| | - Márcia de Nazaré Miranda Bahia
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Secretaria de Vigilância em Saúde (SVS), Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Márcia Soares Mattos Vaz
- Universidade Federal da Grande Dourados (UFGD), Laboratório de Pesquisa em Ciências da Saúde, Dourados, Mato Grosso do Sul, Brazil
| | - Ramon Giovani Brandão da Silva
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, Brazil
- Universidade Federal de São Paulo (UNIFESP), Laboratório de Imunologia e Bacteriologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia, Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema, São Paulo, Brazil
| | - Ruanita Veiga
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, Brazil
| | - Simone Simionatto
- Universidade Federal da Grande Dourados (UFGD), Laboratório de Pesquisa em Ciências da Saúde, Dourados, Mato Grosso do Sul, Brazil
| | | | - William Alencar de Oliveira Lima
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Secretaria de Vigilância em Saúde (SVS), Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Carlos Roberto Veiga Kiffer
- Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, Brazil
| | - Antonio Carlos Campos Pignatari
- Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, Brazil
| | - Rodrigo Cayô
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, Brazil
- Universidade Federal de São Paulo (UNIFESP), Laboratório de Imunologia e Bacteriologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia, Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema, São Paulo, Brazil
| | | | - Ana Cristina Gales
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, Brazil
- Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, São Paulo, Brazil
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Le Bon M, Tötemeyer S, Emes RD, Mellits KH. Gut transcriptome reveals differential gene expression and enriched pathways linked to immune activation in response to weaning in pigs. Front Genet 2022; 13:961474. [DOI: 10.3389/fgene.2022.961474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Weaning represents one of the most critical periods in pig production associated with increase in disease risk, reduction in performance and economic loss. Physiological changes faced by piglets during the weaning period have been well characterised, however little is currently known about the underlying molecular pathways involved in these processes. As pig meat remains one of the most consumed sources of protein worldwide, understanding how these changes are mediated is critical to improve pig production and consequently sustainable food production globally. In this study, we evaluated the effect of weaning on transcriptomic changes in the colon of healthy piglets over time using an RNA-sequencing approach. The findings revealed a complex and coordinated response to weaning with the majority of genes found to be rapidly differentially expressed within 1 day post weaning. Multiple genes and pathways affected by weaning in the colon were associated with immune regulation, cell signalling and bacterial defence. NOD-like receptors, Toll-like receptor and JAK-STAT signalling pathways were amongst the pathways significantly enriched. Immune activation was evidenced by the enrichment of pathways involved in interferon response, cytokines interactions, oxidoreductase activities and response to microbial invasion. Biosynthesis of amino acids, in particular arginine, was also amongst the most enriched KEGG pathways in weaned pigs, reinforcing the critical role of arginine in gut homeostasis under stress conditions. Overall, transcriptomic and physiological results suggest that pigs going through the weaning transition undergo a transient period of inflammatory state with a temporary breakdown of barrier functions in the gut. These findings could provide valuable tools to monitor host response post weaning, and may be of particular relevance for the investigation and development of intervention strategies aimed to reduce antibiotic use and improve pig health and performance.
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Kumar A, Sakhare K, Bhattacharya D, Chattopadhyay R, Parikh P, Narayan KP, Mukherjee A. Communication in non-communicable diseases (NCDs) and role of immunomodulatory nutraceuticals in their management. Front Nutr 2022; 9:966152. [PMID: 36211513 PMCID: PMC9532975 DOI: 10.3389/fnut.2022.966152] [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: 06/13/2022] [Accepted: 08/11/2022] [Indexed: 12/24/2022] Open
Abstract
Conveyance of pathogens between organisms causes communicable diseases. On the other hand, a non-communicable disease (NCD) was always thought to have no causative transmissible infective agents. Today, this clear distinction is increasingly getting blurred and NCDs are found to be associated with some transmissible components. The human microbiota carries a congregation of microbes, the majority and the most widely studied being bacteria in the gut. The adult human gut harbors ginormous inhabitant microbes, and the microbiome accommodates 150-fold more genes than the host genome. Microbial communities share a mutually beneficial relationship with the host, especially with respect to host physiology including digestion, immune responses, and metabolism. This review delineates the connection between environmental factors such as infections leading to gut dysbiosis and NCDs and explores the evidence regarding possible causal link between them. We also discuss the evidence regarding the value of appropriate therapeutic immunomodulatory nutritional interventions to reduce the development of such diseases. We behold such immunomodulatory effects have the potential to influence in various NCDs and restore homeostasis. We believe that the beginning of the era of microbiota-oriented personalized treatment modalities is not far away.
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Affiliation(s)
- Abhiram Kumar
- Esperer Onco Nutrition Pvt. Ltd., Mumbai, India
- Department of Biological Sciences, Birla Institute of Technology and Science – Pilani, Hyderabad, India
| | - Kalyani Sakhare
- Department of Biological Sciences, Birla Institute of Technology and Science – Pilani, Hyderabad, India
| | - Dwaipayan Bhattacharya
- Department of Biological Sciences, Birla Institute of Technology and Science – Pilani, Hyderabad, India
| | | | - Purvish Parikh
- Department of Clinical Haematology, Mahatma Gandhi Medical College and Hospital, Jaipur, India
| | - Kumar P. Narayan
- Department of Biological Sciences, Birla Institute of Technology and Science – Pilani, Hyderabad, India
- *Correspondence: Kumar P. Narayan,
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Van de Vliet M, Joossens M. The Resemblance between Bacterial Gut Colonization in Pigs and Humans. Microorganisms 2022; 10:1831. [PMID: 36144433 PMCID: PMC9500663 DOI: 10.3390/microorganisms10091831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/02/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Thorough understanding of the initial colonization process of human intestines is important to optimize the prevention of microbiota-associated diseases, and also to further improve the current microbial therapies. In recent years, therefore, colonization of the human gut has gained renewed interest. However, due to a lack of standardization of life events that might influence this early colonization process in humans, many generally accepted insights are based on deduction and assumption. In our review, we compare knowledge on colonization in humans with research in piglets, because the intestinal tract of pigs is remarkably similar to that of humans and the early-life events are more standardized. We assess potential similarities and challenge some concepts that have been widely accepted in human microbiota research. Bacterial colonization of the human gut is characterized by successive waves in a progressive process, to a complex gut microbiota community. After re-analyzing available data from piglets, we found that the bacterial colonization process is very similar in terms of the wave sequence and functionality of each wave. Moreover, based on the piglet data, we found that, in addition to external factors such as suckling and nutrition, the bacterial community itself appears to have a major influence on the colonization success of additional bacteria in the intestine. Thus, the colonization process in piglets might rely, at least in part, on niche dependency, an ecological principle to be considered in the intestinal colonization process in humans.
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Affiliation(s)
| | - Marie Joossens
- Laboratory of Microbiology, Department of Biochemistry and Microbiology (WE10), Faculty of Sciences, Ghent University, 9000 Ghent, Belgium
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Garrigues Q, Apper E, Chastant S, Mila H. Gut microbiota development in the growing dog: A dynamic process influenced by maternal, environmental and host factors. Front Vet Sci 2022; 9:964649. [PMID: 36118341 PMCID: PMC9478664 DOI: 10.3389/fvets.2022.964649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms of the gastrointestinal tract play a crucial role in the health, metabolism and development of their host by modulating vital functions such as digestion, production of key metabolites or stimulation of the immune system. This review aims to provide an overview on the current knowledge of factors shaping the gut microbiota of young dogs. The composition of the gut microbiota is modulated by many intrinsic (i.e., age, physiology, pathology) and extrinsic factors (i.e., nutrition, environment, medication) which can cause both beneficial and harmful effects depending on the nature of the changes. The composition of the gut microbiota is quickly evolving during the early development of the dog, and some crucial bacteria, mostly anaerobic, progressively colonize the gut before the puppy reaches adulthood. Those bacterial communities are of paramount importance for the host health, with disturbance in their composition potentially leading to altered metabolic states such as acute diarrhea or inflammatory bowel disease. While many studies focused on the microbiota of young children, there is still a lack of knowledge concerning the development of gut microbiota in puppies. Understanding this early evolution is becoming a key aspect to improve dogs' short and long-term health and wellbeing.
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Affiliation(s)
- Quentin Garrigues
- NeoCare, ENVT, Université de Toulouse, Toulouse, France
- *Correspondence: Quentin Garrigues
| | | | | | - Hanna Mila
- NeoCare, ENVT, Université de Toulouse, Toulouse, France
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Gaire TN, Odland C, Zhang B, Ray T, Doster E, Nerem J, Dee S, Davies P, Noyes N. The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs. MICROBIOME 2022; 10:118. [PMID: 35922873 PMCID: PMC9351240 DOI: 10.1186/s40168-022-01312-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Antimicrobials are used in food-producing animals for purposes of preventing, controlling, and/or treating infections. In swine, a major driver of antimicrobial use is porcine reproductive and respiratory syndrome (PRRS), which is caused by a virus that predisposes infected animals to secondary bacterial infections. Numerous antimicrobial protocols are used to treat PRRS, but we have little insight into how these treatment schemes impact antimicrobial resistance (AMR) dynamics within the fecal microbiome of commercial swine. The aim of this study was to determine whether different PRRS-relevant antimicrobial treatment protocols were associated with differences in the fecal microbiome and resistome of growing pigs. To accomplish this, we used a metagenomics approach to characterize and compare the longitudinal wean-to-market resistome and microbiome of pigs challenged with PRRS virus and then exposed to different antimicrobial treatments, and a group of control pigs not challenged with PRRS virus and having minimal antimicrobial exposure. Genomic DNA was extracted from pen-level composite fecal samples from each treatment group and subjected to metagenomic sequencing and microbiome-resistome bioinformatic and statistical analysis. Microbiome-resistome profiles were compared over time and between treatment groups. RESULTS Fecal microbiome and resistome compositions both changed significantly over time, with a dramatic and stereotypic shift between weaning and 9 days post-weaning (dpw). Antimicrobial resistance gene (ARG) richness and diversity were significantly higher at earlier time points, while microbiome richness and diversity were significantly lower. The post-weaning shift was characterized by transition from a Bacteroides-dominated enterotype to Lactobacillus- and Streptococcus-dominated enterotypes. Both the microbiome and resistome stabilized by 44 dpw, at which point the trajectory of microbiome-resistome maturation began to diverge slightly between the treatment groups, potentially due to physical clustering of the pigs. Challenge with PRRS virus seemed to correspond to the re-appearance of many very rare and low-abundance ARGs within the feces of challenged pigs. Despite very different antimicrobial exposures after challenge with PRRS virus, resistome composition remained largely similar between the treatment groups. Differences in ARG abundance between the groups were mostly driven by temporal changes in abundance that occurred prior to antimicrobial exposures, with the exception of ermG, which increased in the feces of treated pigs, and was significantly more abundant in the feces of these pigs compared to the pigs that did not receive post-PRRS antimicrobials. CONCLUSIONS The fecal microbiome-resistome of growing pigs exhibited a stereotypic trajectory driven largely by weaning and physiologic aging of the pigs. Events such as viral illness, antimicrobial exposures, and physical grouping of the pigs exerted significant yet relatively minor influence over this trajectory. Therefore, the AMR profile of market-age pigs is the culmination of the life history of the individual pigs and the populations to which they belong. Disease status alone may be a significant driver of AMR in market-age pigs, and understanding the interaction between disease processes and antimicrobial exposures on the swine microbiome-resistome is crucial to developing effective, robust, and reproducible interventions to control AMR. Video Abstract.
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Affiliation(s)
- Tara N Gaire
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Carissa Odland
- Pipestone Veterinary Services, Pipestone, Minnesota, USA
| | - Bingzhou Zhang
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tui Ray
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Enrique Doster
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Joel Nerem
- Pipestone Applied Research, Pipestone, Minnesota, USA
| | - Scott Dee
- Pipestone Applied Research, Pipestone, Minnesota, USA
| | - Peter Davies
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Noelle Noyes
- Department of Veterinary Population Medicine (VPM), College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA.
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Pu G, Hou L, Du T, Wang B, Liu H, Li K, Niu P, Zhou W, Huang R, Li P. Effects of short-term feeding with high fiber diets on growth, utilization of dietary fiber, and microbiota in pigs. Front Microbiol 2022; 13:963917. [PMID: 35966661 PMCID: PMC9363921 DOI: 10.3389/fmicb.2022.963917] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/30/2022] [Indexed: 01/10/2023] Open
Abstract
Finishing pigs can adapt to high-fiber diet smoothly according to the production performance and their intestinal microbiota through a 28-day trial or longer. However, it is unclear, at which stage during the experimental period, the adaptation occurred. Here we studied the dosage effects of dietary fiber (Total dietary fiber (TDF) from 16.70 to 24.11%) on growth performance, fiber digestibility, fecal microbiota, and microbial fermentation of finishing pigs during a 14-day feeding period. The results showed that the average daily feed intake (ADFI) and feed/gain (F/G) of pigs were not affected as the dietary fiber increased. Apparent total tract digestibility (ATTD) of cellulose, hemicellulose, insoluble dietary fiber (IDF), soluble dietary fiber (SDF), and TDF of pigs remained unchanged when TDF was between 16.70 and 17.75%, while strikingly decreased when TDF increased from 17.75 to 24.11%. It is worth noting that increasing fiber intake seemed to favor hemicellulose digestion. In addition, the increase in fiber intake increased fecal microbial diversity, especially improved the proportion of the members of the family Prevotellaceae, Ruminococcaceae, and Lachnospiraceae, and decreased the abundance of the genus Streptococcus. Moreover, the increase in fiber intake promoted the digestion of fiber, production of short chain fatty acids (SCFAs), and enhanced microbial pyruvate metabolism and butanoate metabolism. In conclusion, short-term high fiber feeding has no adverse effects on the growth performance of finishing pigs. ATTD of dietary fiber of finishing pigs was maintained when TDF was at 17.75%. And short-term high fiber feeding improved microbial diversity and fiber degradation functions of finishing pigs.
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Affiliation(s)
- Guang Pu
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Intestinal Microbiology, Huaian Academy, Nanjing Agricultural University, Nanjing, China
| | - Liming Hou
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Intestinal Microbiology, Huaian Academy, Nanjing Agricultural University, Nanjing, China
| | - Taoran Du
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Intestinal Microbiology, Huaian Academy, Nanjing Agricultural University, Nanjing, China
| | - Binbin Wang
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Intestinal Microbiology, Huaian Academy, Nanjing Agricultural University, Nanjing, China
| | - Hang Liu
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Intestinal Microbiology, Huaian Academy, Nanjing Agricultural University, Nanjing, China
| | - Kaijun Li
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Intestinal Microbiology, Huaian Academy, Nanjing Agricultural University, Nanjing, China
| | - Peipei Niu
- Laboratory of Intestinal Microbiology, Huaian Academy, Nanjing Agricultural University, Nanjing, China
| | - Wuduo Zhou
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Industrial Technology System Integration Innovation Center of Jiangsu Modern Agriculture (PIG), Nanjing, China
| | - Ruihua Huang
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Industrial Technology System Integration Innovation Center of Jiangsu Modern Agriculture (PIG), Nanjing, China
| | - Pinghua Li
- Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Intestinal Microbiology, Huaian Academy, Nanjing Agricultural University, Nanjing, China
- Industrial Technology System Integration Innovation Center of Jiangsu Modern Agriculture (PIG), Nanjing, China
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Effects of the Probiotic, Lactobacillus delbrueckii subsp. bulgaricus, as a Substitute for Antibiotics on the Gastrointestinal Tract Microbiota and Metabolomics Profile of Female Growing-Finishing Pigs. Animals (Basel) 2022; 12:ani12141778. [PMID: 35883325 PMCID: PMC9311557 DOI: 10.3390/ani12141778] [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: 05/21/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022] Open
Abstract
Lactobacillus delbrueckii subsp. bulgaricus (LDB) is an approved feed additive on the Chinese ‘Approved Feed Additives’ list. However, the possibility of LDB as an antibiotic replacement remains unclear. Particularly, the effect of LDB on microbiota and metabolites in the gastrointestinal tract (GIT) requires further explanation. This study aimed to identify the microbiota and metabolites present in fecal samples and investigate the relationship between the microbiota and metabolites to evaluate the potential of LDB as an antibiotic replacement in pig production. A total of 42 female growing-finishing pigs were randomly allocated into the antibiotic group (basal diet + 75 mg/kg aureomycin) and LDB (basal diet + 3.0 × 109 cfu/kg LDB) groups. Fecal samples were collected on days 0 and 30. Growth performance was recorded and assessed. 16S rRNA sequencing and liquid chromatography-mass spectrometry-based non-targeted metabolomics approaches were used to analyze the differences in microbiota and metabolites. Associations between the differences were calculated using Spearman correlations with the Benjamini−Hochberg adjustment. The LDB diet had no adverse effect on feed efficiency but slightly enhanced the average daily weight gain and average daily feed intake (p > 0.05). The diet supplemented with LDB increased Lactobacillus abundance and decreased that of Prevotellaceae_NK3B31_group spp. Dietary-supplemented LDB enhanced the concentrations of pyridoxine, tyramine, D-(+)-pyroglutamic acid, hypoxanthine, putrescine and 5-hydroxyindole-3-acetic acid and decreased the lithocholic acid concentration. The Lactobacillus networks (Lactobacillus, Peptococcus, Ruminococcaceae_UCG-004, Escherichia-Shigella, acetophenone, tyramine, putrescine, N-methylisopelletierine, N1-acetylspermine) and Prevotellaceae_NK3B31_group networks (Prevotellaceae_NK3B31_group, Treponema_2, monolaurin, penciclovir, N-(5-acetamidopentyl)acetamide, glycerol 3-phosphate) were the most important in the LDB effect on pig GIT health in our study. These findings indicate that LDB may regulate GIT function through the Lactobacillus and Prevotellaceae_NK3B31_group networks. However, our results were restrained to fecal samples of female growing-finishing pigs; gender, growth stages, breeds and other factors should be considered to comprehensively assess LDB as an antibiotic replacement in pig production.
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Ma J, Chen J, Gan M, Chen L, Zhao Y, Zhu Y, Niu L, Zhang S, Zhu L, Shen L. Gut Microbiota Composition and Diversity in Different Commercial Swine Breeds in Early and Finishing Growth Stages. Animals (Basel) 2022; 12:1607. [PMID: 35804507 PMCID: PMC9264831 DOI: 10.3390/ani12131607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/19/2022] [Accepted: 06/20/2022] [Indexed: 11/22/2022] Open
Abstract
The gut microbiota affects the metabolism, health and growth rate of pigs. Understanding the characteristics of gut microbiota of different pig breeds at each growth stage will enable the design of individualized feeding strategies. The present study aimed to compare the growth curves and development patterns of pigs of three different breeds (Duroc, Landrace and Yorkshire) using the mathematical models Gompertz, Logistic, Von Bertalanffy and Richards. For Duroc pigs, the Gompertz model showed the highest prediction accuracy (R2 = 0.9974). In contrast, the best models for Landrace and Yorkshire pigs were Richards (R2 = 0.9986) and Von Bertalanffy (R2 = 0.9977), respectively. Path analysis showed that body length (path coefficient = 0.507) and chest circumference (path coefficient = 0.532) contributed more significantly to the body weight of pigs at the early growth stage, while hip circumference (path coefficient = 0.312) had a greater influence on pig body weight in the late growth stage. Moreover, the composition of the gut microbiota of pigs at two growth stages (60 kg of body weight in the early growth stage and 120 kg in the finishing stage) was studied using 16S rRNA sequencing technology. Variations in gut microbiota composition of pigs at different growth stages were observed. KEGG pathway enrichment analysis of annotated metagenomes revealed that protein synthesis and amino acid metabolism pathways were significantly enriched in pigs at the early growth stage, which may be related to nutritional requirements of pigs during this stage. This study confirmed longitudinal variation in the gut microbiota of pigs pertaining to age as well as lateral variation related to pig breed. The present findings expand the current understanding of the variations in swine gut microbiota during production stages.
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Affiliation(s)
- Jianfeng Ma
- Department of Animal Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.M.); (J.C.); (M.G.); (L.C.); (Y.Z.); (L.N.); (S.Z.)
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingyun Chen
- Department of Animal Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.M.); (J.C.); (M.G.); (L.C.); (Y.Z.); (L.N.); (S.Z.)
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Mailin Gan
- Department of Animal Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.M.); (J.C.); (M.G.); (L.C.); (Y.Z.); (L.N.); (S.Z.)
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Chen
- Department of Animal Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.M.); (J.C.); (M.G.); (L.C.); (Y.Z.); (L.N.); (S.Z.)
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ye Zhao
- Department of Animal Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.M.); (J.C.); (M.G.); (L.C.); (Y.Z.); (L.N.); (S.Z.)
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Zhu
- College of Life Science, China West Normal University, Nanchong 637009, China;
| | - Lili Niu
- Department of Animal Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.M.); (J.C.); (M.G.); (L.C.); (Y.Z.); (L.N.); (S.Z.)
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- Department of Animal Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.M.); (J.C.); (M.G.); (L.C.); (Y.Z.); (L.N.); (S.Z.)
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- Department of Animal Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.M.); (J.C.); (M.G.); (L.C.); (Y.Z.); (L.N.); (S.Z.)
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Linyuan Shen
- Department of Animal Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.M.); (J.C.); (M.G.); (L.C.); (Y.Z.); (L.N.); (S.Z.)
- Farm Animal Genetic Resource Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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Oral Immunization of Mice with Cell Extracts from Recombinant Lactococcus lactis Expressing SARS-CoV-2 Spike Protein. Curr Microbiol 2022; 79:167. [PMID: 35460453 PMCID: PMC9034443 DOI: 10.1007/s00284-022-02866-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 04/05/2022] [Indexed: 12/22/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread all over the world and became a pandemic that named coronavirus disease-2019 (COVID-19). At present, several intramuscular vaccines have been successfully developed and mass vaccination has progressed in many countries. The aim of the study is to develop and examine an oral vaccine against COVID-19 with recombinant Lactococcus lactis IL1403, a strain of lactic acid bacteria, expressing SARS-CoV-2 spike (S) protein receptor-binding domain (RBD) S1 subunit as an immunizing antigen. PBS or cell extracts from recombinant L. lactis were orally administered into mice (control VS treatment), and formation of antigen-specific antibodies and changes in the gut microbiome were analyzed. Intracellular antigen was detected, but its secretion was not successful. After immunization, antigen-specific serum IgG and fecal IgA levels were 1.5-fold (P = 0.002) and 1.4-fold (P = 0.016) higher in the immunized mice (treatment) than control, respectively. Gut microbiome profiles were clearly separated between the two groups when analyzed for beta diversity with overall similarity. At the genus level, while Coprococcus (P = 0.036) and unclassified genus of Ruminococcaceae (P = 0.037) in treatment were more abundant than control, rc4-4 (P = 0.013) and Stenotrophomonas (P = 0.021) were less abundant. Our results indicate that cell extract containing SARS-CoV-2 antigen can induce mice to produce antigen-specific antibodies without overall changes in the gut microbiome. This strategy may be useful for the development of other oral viral vaccines.
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Effects of Growth Stage and Rearing Pattern on Pig Gut Microbiota. Curr Microbiol 2022; 79:136. [PMID: 35303185 DOI: 10.1007/s00284-022-02828-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/03/2021] [Indexed: 01/03/2023]
Abstract
Understanding the developmental period or the patterns of gut microbiota is important for nutritionists when designing a feed formula or adjusting a feeding strategy. The effects of growth stage or rearing pattern on pig gut microbiota have not been fully investigated. Herein, 39 fecal samples from pigs aged 3-9 months under two rearing patterns were collected to analyze the gut microbiome. Samples were clustered into three distinct groups, namely, early (3 months), middle (5 months), and late (7 and 9 months) stages, using principal coordinate analysis and analysis of similarities test. The rearing-pattern effects were very minimal, and no differences were observed in the alpha diversity [observed operational taxonomic units (OTUs) and Shannon index] of gut microbiota. From early and middle to late stage, Shannon index gradually decreased and OTUs gradually increased. Pigs at early stage were enriched with bacteria from family Prevotellaceae, including the genera Prevotella_9 and Prevotellaceae_NK3B31, whereas pigs at late stage were enriched with family Ruminococcaceae, including genera Ruminococcaceae_UCG-005 and Oscillospira. Pigs in the semi-free-grazing farm group were significantly enriched with bacteria from order Clostridiales. Growth stage better explained the changes in porcine gut microbiota than rearing patterns.
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Intestinal Exposure to Ceftiofur and Cefquinome after Intramuscular Treatment and the Impact of Ceftiofur on the Pig Fecal Microbiome and Resistome. Antibiotics (Basel) 2022; 11:antibiotics11030342. [PMID: 35326805 PMCID: PMC8944603 DOI: 10.3390/antibiotics11030342] [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: 02/07/2022] [Revised: 02/21/2022] [Accepted: 03/02/2022] [Indexed: 11/21/2022] Open
Abstract
Optimization of antimicrobial treatment during a bacterial infection in livestock requires in-depth knowledge of the impact of antimicrobial therapy on the pathogen and commensal microbiota. Once administered antimicrobials and/or their metabolites are excreted either by the kidneys through urine and/or by the intestinal tract through feces, causing antimicrobial pressure and possibly the emergence of resistance in the gastro-intestinal tract. So far, the excretion of ceftiofur and cefquinome in the intestinal tract of pigs has not been described. The objective of this study was to investigate the excretion of ceftiofur and cefquinome in the different segments of the gut and feces after intramuscular administration. Therefore, 16 pigs were treated either with ceftiofur (n = 8) or cefquinome (n = 8), and feces were collected during the entire treatment period. The presence of ceftiofur and desfuroylceftiofuracetamide or cefquinome were quantified via liquid chromatography−tandem mass spectrometry. At the end of the treatment, pigs were euthanized, and samples from the duodenum, jejunum, ileum and cecum were analyzed. In feces, no active antimicrobial residues could be measured, except for one ceftiofur-treated pig. In the gut segments, the concentration of both antimicrobials increased from duodenum toward the ileum, with a maximum in the ileum (187.8 ± 101.7 ng·g−1 ceftiofur-related residues, 57.8 ± 37.5 ng·g−1 cefquinome) and sharply decreased in the cecum (below the limit of quantification for ceftiofur-related residues, 6.4 ± 4.2 ng·g−1 cefquinome). Additionally, long-read Nanopore sequencing and targeted quantitative polymerase chain reaction (qPCR) were performed in an attempt to clarify the discrepancy in fecal excretion of ceftiofur-related residues between pigs. In general, there was an increase in Prevotella, Bacteroides and Faecalibacterium and a decrease in Escherichia and Clostridium after ceftiofur administration (q-value < 0.05). The sequencing and qPCR could not provide an explanation for the unexpected excretion of ceftiofur-related residues in one pig out of eight. Overall, this study provides valuable information on the gut excretion of parenteral administered ceftiofur and cefquinome.
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López-García A, Saborío-Montero A, Gutiérrez-Rivas M, Atxaerandio R, Goiri I, García-Rodríguez A, Jiménez-Montero JA, González C, Tamames J, Puente-Sánchez F, Serrano M, Carrasco R, Óvilo C, González-Recio O. Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle. Gigascience 2022; 11:6514927. [PMID: 35077540 PMCID: PMC8848325 DOI: 10.1093/gigascience/giab088] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/18/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Background Mitigating the effects of global warming has become the main challenge for humanity in recent decades. Livestock farming contributes to greenhouse gas emissions, with an important output of methane from enteric fermentation processes, mostly in ruminants. Because ruminal microbiota is directly involved in digestive fermentation processes and methane biosynthesis, understanding the ecological relationships between rumen microorganisms and their active metabolic pathways is essential for reducing emissions. This study analysed whole rumen metagenome using long reads and considering its compositional nature in order to disentangle the role of rumen microbes in methane emissions. Results The β-diversity analyses suggested a subtle association between methane production and overall microbiota composition (0.01 < R2 < 0.02). Differential abundance analysis identified 36 genera and 279 KEGGs as significantly associated with methane production (Padj < 0.05). Those genera associated with high methane production were Eukaryota from Alveolata and Fungi clades, while Bacteria were associated with low methane emissions. The genus-level association network showed 2 clusters grouping Eukaryota and Bacteria, respectively. Regarding microbial gene functions, 41 KEGGs were found to be differentially abundant between low- and high-emission animals and were mainly involved in metabolic pathways. No KEGGs included in the methane metabolism pathway (ko00680) were detected as associated with high methane emissions. The KEGG network showed 3 clusters grouping KEGGs associated with high emissions, low emissions, and not differentially abundant in either. A deeper analysis of the differentially abundant KEGGs revealed that genes related with anaerobic respiration through nitrate degradation were more abundant in low-emission animals. Conclusions Methane emissions are largely associated with the relative abundance of ciliates and fungi. The role of nitrate electron acceptors can be particularly important because this respiration mechanism directly competes with methanogenesis. Whole metagenome sequencing is necessary to jointly consider the relative abundance of Bacteria, Archaea, and Eukaryota in the statistical analyses. Nutritional and genetic strategies to reduce CH4 emissions should focus on reducing the relative abundance of Alveolata and Fungi in the rumen. This experiment has generated the largest ONT ruminal metagenomic dataset currently available.
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Affiliation(s)
- Adrián López-García
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Alejandro Saborío-Montero
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain.,Escuela de Zootecnia y Centro de Investigación en Nutrición Animal, Universidad de Costa Rica, 11501 San José, Costa Rica
| | - Mónica Gutiérrez-Rivas
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Raquel Atxaerandio
- NEIKER - Instituto Vasco de Investigación y Desarrollo Agrario. Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Idoia Goiri
- NEIKER - Instituto Vasco de Investigación y Desarrollo Agrario. Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Aser García-Rodríguez
- NEIKER - Instituto Vasco de Investigación y Desarrollo Agrario. Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Jose A Jiménez-Montero
- Confederación de Asociaciones de Frisona Española (CONAFE), Ctra. de Andalucía km 23600 Valdemoro, 28340 Madrid, Spain
| | - Carmen González
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Javier Tamames
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, 28049 Madrid, Spain
| | - Fernando Puente-Sánchez
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, 28049 Madrid, Spain
| | - Magdalena Serrano
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Rafael Carrasco
- Departamento de Periodismo y Nuevos Medios, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Cristina Óvilo
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain.,Departamento de Producción Agraria, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
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Han G, Luong H, Vaishnava S. Low abundance members of the gut microbiome exhibit high immunogenicity. Gut Microbes 2022; 14:2104086. [PMID: 35881003 PMCID: PMC9331198 DOI: 10.1080/19490976.2022.2104086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/12/2022] [Indexed: 02/04/2023] Open
Abstract
Studies identifying bacterial members that dictate host phenotype have focused mainly on the dominant members, and the role of low abundance microbes in determining host phenotypes and pathogenesis of diseases remains unexplored. In this study, we compared the gut bacterial community of mice with wide-ranging microbial exposure to determine if low abundance bacteria vary based on microbial exposure or remain consistent. We noted that similar to the high abundance bacterial community, a core community of low abundance bacteria made up a significant portion of the gut microbiome irrespective of microbial exposure. To determine the role of low abundance bacteria in regulating community composition and host gene expression, we devised a microbiome dilution strategy to "delete" out low abundance bacteria and engrafted the diluted microbiomes into germ-free mice. Our approach successfully excluded low abundance bacteria from small and large intestinal bacterial communities and induced global changes in microbial community composition in the large intestine. Gene expression analysis of intestinal tissue revealed that loss of low abundance bacteria resulted in a drastic reduction in expression of multiple genes involved MHCII antigen presentation pathway and T-cell cytokine production in the small intestine. The effect of low abundance bacteria on MHCII expression was found to be specific to the intestinal epithelium at an early timepoint post-colonization and correlated with bacteria belonging to the family Erysipelotrichaceae. We conclude that low abundance bacteria have a significantly higher immuno-stimulatory effect compared to dominant bacteria and are thus potent drivers of early immune education in the gut.
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Affiliation(s)
- Geongoo Han
- Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Hien Luong
- Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Shipra Vaishnava
- Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
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Understanding host-microbiota interactions in the commercial piglet around weaning. Sci Rep 2021; 11:23488. [PMID: 34873196 PMCID: PMC8648723 DOI: 10.1038/s41598-021-02754-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
Weaning is a critical period in the life of pigs with repercussions on their health and welfare and on the economy of the swine industry. This study aimed to assess the effect of the commercial early weaning on gut microbiota, intestinal gene expression and serum metabolomic response via an integrated-omic approach combining 16S rRNA gene sequencing, the OpenArray gene expression technology and 1H-NMR spectroscopy. Fourteen piglets from different litters were sampled for blood, jejunum tissue and caecal content two days before (− 2d), and three days after (+ 3d) weaning. A clearly differential ordination of caecal microbiota was observed. Higher abundances of Roseburia, Ruminococcus, Coprococcus, Dorea and Lachnospira genera in weaned piglets compared to prior to weaning showed the quick microbial changes of the piglets’ gut microbiota. Downregulation of OCLN, CLDN4, MUC2, MUC13, SLC15A1 and SLC13A1 genes, also evidenced the negative impact of weaning on gut barrier and digestive functions. Metabolomic approach pinpointed significant decreases in choline, LDL, triglycerides, fatty acids, alanine and isoleucine and increases in 3-hydroxybutyrate after weaning. Moreover, the correlation between microbiota and metabolome datasets revealed the existence of metabolic clusters interrelated to different bacterial clusters. Our results demonstrate the impact of weaning stress on the piglet and give insights regarding the associations between gut microbiota and the animal gene activity and metabolic response.
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Yan H, Wei W, Hu L, Zhang Y, Zhang H, Liu J. Reduced Feeding Frequency Improves Feed Efficiency Associated With Altered Fecal Microbiota and Bile Acid Composition in Pigs. Front Microbiol 2021; 12:761210. [PMID: 34712219 PMCID: PMC8546368 DOI: 10.3389/fmicb.2021.761210] [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: 08/19/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
A biphasic feeding regimen exerts an improvement effect on feed efficiency of pigs. While gut microbiome and metabolome are known to affect the host phenotype, so far the effects of reduced feeding frequency on fecal microbiota and their metabolism in pigs remain unclear. Here, the combination of 16S rRNA sequencing technique as well as untargeted and targeted metabolome analyses was adopted to investigate the fecal microbiome and metabolome of growing–finishing pigs in response to a biphasic feeding [two meals per day (M2)] pattern. Sixty crossbred barrows were randomly assigned into two groups with 10 replicates (three pigs/pen), namely, the free-access feeding group (FA) and the M2 group. Pigs in the FA group were fed free access while those in the M2 group were fed ad libitum twice daily for 1 h at 8:00 and 18:00. Results showed that pigs fed biphasically exhibited increased feed efficiency compared to FA pigs. The Shannon and Simpson indexes were significantly increased by reducing the feeding frequency. In the biphasic-fed pigs, the relative abundances of Subdoligranulum, Roseburia, Mitsuokella, and Terrisporobacter were significantly increased while the relative abundances of unidentified_Spirochaetaceae, Methanobrevibacter, unidentified_Bacteroidales, Alloprevotella, Parabacteroides, and Bacteroides were significantly decreased compared to FA pigs. Partial least-square discriminant analysis (PLS-DA) analysis revealed an obvious variation between the FA and M2 groups; the differential features were mainly involved in arginine, proline, glycine, serine, threonine, and tryptophan metabolism as well as primary bile acid (BA) biosynthesis. In addition, the changes in the microbial genera were correlated with the differential fecal metabolites. A biphasic feeding regimen significantly increased the abundances of primary BAs and secondary BAs in feces of pigs, and the differentially enriched BAs were positively correlated with some specific genera. Taken together, these results suggest that the improvement effect of a reduced feeding frequency on feed efficiency of pigs might be associated with the altered fecal microbial composition and fecal metabolite profile in particular the enlarged stool BA pool.
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Affiliation(s)
- Honglin Yan
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Wenzhuo Wei
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Luga Hu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Yong Zhang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingbo Liu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
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Law K, Lozinski B, Torres I, Davison S, Hilbrands A, Nelson E, Parra-Suescun J, Johnston L, Gomez A. Disinfection of Maternal Environments Is Associated with Piglet Microbiome Composition from Birth to Weaning. mSphere 2021; 6:e0066321. [PMID: 34494881 PMCID: PMC8550216 DOI: 10.1128/msphere.00663-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
Maternal factors predetermine offspring development and health, including the establishment of offsprings' first microbiomes. Research in swine has shown that early microbial exposures impact microbiome colonization in piglets, but this phenomenon has never been tested in the context of delivery room disinfection. Thus, we exposed gestating sows to two delivery environments (n = 3/environment): stalls cleaned with a broad-spectrum disinfectant (disinfected environment [D]) or stalls cleaned only with hot-water power washing (nondisinfected environment [Nde]), 3 days prior to farrowing. Microbiomes of sows and farrowed piglets (n = 27/environment) were profiled at 4 different time points from birth to weaning via 16S rRNA sequencing. The results show that although vaginal, milk, skin, and gut microbiomes in mothers were minimally affected, sanitation of farrowing stalls impacted piglet microbiome colonization. These effects were mainly characterized by lower bacterial diversity in the gut and nasal cavity, specifically in D piglets at birth, and by distinct taxonomic compositions from birth to weaning depending on the farrowing environment. For instance, environmental bacteria greatly influenced microbiome colonization in Nde piglets, which also harbored significantly higher abundances of gut Lactobacillus and nasal Enhydrobacter at several time points through weaning. Different sanitation strategies at birth also resulted in distinct microbiome assembly patterns, with lower microbial exposures in D piglets being associated with limited interactions between bacterial taxa. However, increasing microbial exposures at birth through the lack of disinfection were also associated with lower piglet weight, highlighting the importance of understanding the trade-offs among optimal microbiome development, health, and growth performance in swine production systems. IMPORTANCE We show that levels of disinfection in farrowing facilities can impact early microbial exposures and colonization by pioneer microbes in piglets. Although previous research has shown a similar effect by raising pigs outdoors or by exposing them to soil, these practices are unattainable in most swine production systems in the United States due to biosecurity practices. Thus, our results underscore the importance of evaluating different disinfection practices in swine production to safely reduce pathogenic risks without limiting early microbial exposures. Allowing early exposure to both beneficial and pathogenic microbes may positively impact immune responses, reduce the stressors of weaning, and potentially reduce the need for dietary antimicrobials. However, the benefits of modified early microbial exposures need to be accomplished along with acceptable growth performance. Thus, our results also provide clues for understanding how disinfection practices in farrowing rooms may impact early microbiome development and assembly.
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Affiliation(s)
- Kayla Law
- Department of Animal Science, University of Minnesotagrid.17635.36, St. Paul, Minnesota, USA
| | - Brigit Lozinski
- Department of Animal Science, University of Minnesotagrid.17635.36, St. Paul, Minnesota, USA
| | - Ivanellis Torres
- Department of Animal Science, University of Minnesotagrid.17635.36, St. Paul, Minnesota, USA
| | - Samuel Davison
- Department of Animal Science, University of Minnesotagrid.17635.36, St. Paul, Minnesota, USA
| | - Adrienne Hilbrands
- Department of Animal Science, University of Minnesotagrid.17635.36, St. Paul, Minnesota, USA
- University of Minnesotagrid.17635.36, West Central Research and Outreach Center, Morris, Minnesota, USA
| | - Emma Nelson
- Department of Animal Science, University of Minnesotagrid.17635.36, St. Paul, Minnesota, USA
- University of Minnesotagrid.17635.36, West Central Research and Outreach Center, Morris, Minnesota, USA
| | | | - Lee Johnston
- Department of Animal Science, University of Minnesotagrid.17635.36, St. Paul, Minnesota, USA
- University of Minnesotagrid.17635.36, West Central Research and Outreach Center, Morris, Minnesota, USA
| | - Andres Gomez
- Department of Animal Science, University of Minnesotagrid.17635.36, St. Paul, Minnesota, USA
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Effect of functional oils or probiotics on performance and microbiota profile of newly weaned piglets. Sci Rep 2021; 11:19457. [PMID: 34593866 PMCID: PMC8484476 DOI: 10.1038/s41598-021-98549-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 09/06/2021] [Indexed: 11/16/2022] Open
Abstract
The study aimed to evaluate a commercial blend of functional oils based on liquid from the cashew nutshell and castor oil as a growth promoter in newly weaned piglets. A total of 225 piglets, castrated males and females with 28 days of age were randomly distributed in pens with 15 animals composing three treatments and five repetitions. The treatments were: control (without the inclusion of additives), probiotics, or functional oils. The performance was evaluated. At 50 days of age, a pool of fresh feces from 3 animals/repetition was collected to perform the sequencing of microbiota using the Illumina MiSeq platform. Supplementation with functional oils improved the piglets' daily weight gain and feed conversion ratio (P < 0.05) in the first weeks of the experiment, which resulted in higher final live weight (P < 0.05) in the phase when compared to the control treatment (24.34 kg and 21.55 kg, respectively). The animals that received probiotics showed an intermediate performance (23.66 kg final live weight) at the end of the 38 experimental days. Both additives were effective in increasing groups essential for intestinal health, such as Ruminococcaceae and Lachnospiraceae. The functional oils were more effective in reducing pathogenic bacteria, such as Campylobacter and Escherichia coli. In conclusion, the use of functional oils optimized performance and effectively modulated the microbiota of newly weaned piglets.
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Sarri L, Costa-Roura S, Balcells J, Seradj AR, de la Fuente G. The Impact of Genetics on Gut Microbiota of Growing and Fattening Pigs under Moderate N Restriction. Animals (Basel) 2021; 11:ani11102846. [PMID: 34679867 PMCID: PMC8532768 DOI: 10.3390/ani11102846] [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: 09/01/2021] [Revised: 09/25/2021] [Accepted: 09/26/2021] [Indexed: 11/16/2022] Open
Abstract
Characterization of intestinal microbiota is of great interest due to its relevant impact on growth, feed efficiency and pig carcass quality. Microbial composition shifts along the gut, but it also depends on the host (i.e., age, genetic background), diet composition and environmental conditions. To simultaneously study the effects of producing type (PT), production phase (PP) and dietary crude protein (CP) content on microbial populations, 20 Duroc pigs and 16 crossbred pigs (F2), belonging to growing and fattening phases, were used. Half of the pigs of each PT were fed a moderate CP restriction (2%). After sacrifice, contents of ileum, cecum and distal colon were collected for sequencing procedure. Fattening pigs presented higher microbial richness than growing pigs because of higher maturity and stability of the community. The F2 pigs showed higher bacterial alpha diversity and microbial network complexity (cecum and colon), especially in the fattening phase, while Duroc pigs tended to have higher Firmicutes/Bacteroidetes ratio in cecum segment. Lactobacillus was the predominant genus, and along with Streptococcus and Clostridium, their relative abundance decreased throughout the intestine. Although low CP diet did not alter the microbial diversity, it increased interaction network complexity. These results have revealed that the moderate CP restriction had lower impact on intestinal microbiota than PP and PT of pigs.
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Mazgaj R, Lipiński P, Szudzik M, Jończy A, Kopeć Z, Stankiewicz AM, Kamyczek M, Swinkels D, Żelazowska B, Starzyński RR. Comparative Evaluation of Sucrosomial Iron and Iron Oxide Nanoparticles as Oral Supplements in Iron Deficiency Anemia in Piglets. Int J Mol Sci 2021; 22:9930. [PMID: 34576090 PMCID: PMC8466487 DOI: 10.3390/ijms22189930] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/06/2021] [Accepted: 09/11/2021] [Indexed: 12/15/2022] Open
Abstract
Iron deficiency is the most common mammalian nutritional disorder. However, among mammalian species iron deficiency anemia (IDA), occurs regularly only in pigs. To cure IDA, piglets are routinely injected with high amounts of iron dextran (FeDex), which can lead to perturbations in iron homeostasis. Here, we evaluate the therapeutic efficacy of non-invasive supplementation with Sucrosomial iron (SI), a highly bioavailable iron supplement preventing IDA in humans and mice and various iron oxide nanoparticles (IONPs). Analysis of red blood cell indices and plasma iron parameters shows that not all iron preparations used in the study efficiently counteracted IDA comparable to FeDex-based supplementation. We found no signs of iron toxicity of any tested iron compounds, as evaluated based on the measurement of several toxicological markers that could indicate the occurrence of oxidative stress or inflammation. Neither SI nor IONPs increased hepcidin expression with alterations in ferroportin (FPN) protein level. Finally, the analysis of the piglet gut microbiota indicates the individual pattern of bacterial diversity across taxonomic levels, independent of the type of supplementation. In light of our results, SI but not IONPs used in the experiment emerges as a promising nutritional iron supplement, with a high potential to correct IDA in piglets.
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Affiliation(s)
- Rafał Mazgaj
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology PAS, 28-130 Jastrzębiec, Poland; (R.M.); (M.S.); (A.J.); (Z.K.); (A.M.S.); (B.Ż.)
| | - Paweł Lipiński
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology PAS, 28-130 Jastrzębiec, Poland; (R.M.); (M.S.); (A.J.); (Z.K.); (A.M.S.); (B.Ż.)
| | - Mateusz Szudzik
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology PAS, 28-130 Jastrzębiec, Poland; (R.M.); (M.S.); (A.J.); (Z.K.); (A.M.S.); (B.Ż.)
| | - Aneta Jończy
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology PAS, 28-130 Jastrzębiec, Poland; (R.M.); (M.S.); (A.J.); (Z.K.); (A.M.S.); (B.Ż.)
| | - Zuzanna Kopeć
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology PAS, 28-130 Jastrzębiec, Poland; (R.M.); (M.S.); (A.J.); (Z.K.); (A.M.S.); (B.Ż.)
| | - Adrian M. Stankiewicz
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology PAS, 28-130 Jastrzębiec, Poland; (R.M.); (M.S.); (A.J.); (Z.K.); (A.M.S.); (B.Ż.)
| | - Marian Kamyczek
- Pig Hybridization Centre, National Research Institute of Animal Production, 43-246 Pawłowice, Poland;
| | - Dorine Swinkels
- Department of Laboratory Medicine (TLM 830), Radboud University Nijmegen Medical Center, 6525 GA Nijmegen, The Netherlands;
- Hepcidin Analysis, Department of Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Beata Żelazowska
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology PAS, 28-130 Jastrzębiec, Poland; (R.M.); (M.S.); (A.J.); (Z.K.); (A.M.S.); (B.Ż.)
| | - Rafał R. Starzyński
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology PAS, 28-130 Jastrzębiec, Poland; (R.M.); (M.S.); (A.J.); (Z.K.); (A.M.S.); (B.Ż.)
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Wen C, van Dixhoorn I, Schokker D, Woelders H, Stockhofe-Zurwieden N, Rebel JMJ, Smidt H. Environmentally enriched housing conditions affect pig welfare, immune system and gut microbiota in early life. Anim Microbiome 2021; 3:52. [PMID: 34321110 PMCID: PMC8320228 DOI: 10.1186/s42523-021-00115-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/16/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Conventional pig housing and management conditions are associated with gastrointestinal pathophysiology and disease susceptibility in early life. Developing new strategies to reduce both therapeutic and prophylactic antibiotic use is urgent for the sustainable swine production globally. To this end, housing methodology providing effective environmental enrichment could be a promising alternative approach to reduce antibiotic usage, as it has been proven to positively influence pig welfare and immune status and reduce susceptibility to infections. It is, however, poorly understood how this enriched housing affects systemic and local pulmonary immune status and gut microbiota colonization during early life. In the present study, we compared the effects of two housing conditions, i.e., conventional housing: (CH) versus enriched housing (EH), on immune status and gut microbiota from birth until 61 days of age. RESULTS The expected benefits of enrichment on pig welfare were confirmed as EH pigs showed more positive behaviour, less aggression behaviour during the weaning transition and better human animal relation during the post weaning phase. Regarding the pigs' immune status, EH pigs had higher values of haemoglobin and mean corpuscular volume in haematological profiles and higher percentages of T cells and cytotoxic T cells in peripheral blood. Furthermore, EH pigs showed higher ex vivo secretion of IL1ß and TNF-α after lipopolysaccharide stimulation of whole blood than CH pigs. The structure of the developing faecal microbiota of CH and EH pigs significantly differed as early as day 12 with an increase in the relative abundance of several bacterial groups known to be involved in the production of short chain fatty acids, such as Prevotella_2, Christensenellaceae_R_7_group and Ruminococcus gauvreauii group. Furthermore, the main difference between both housing conditions post weaning was that on day 61, CH pigs had significantly larger inter-individual variation of ileal and colonic microbiota than EH pigs. In addition to housing, other intrinsic factors (e.g., sex) were associated with gut microbiota development and immune competence. CONCLUSIONS In addition to the known welfare benefits for pigs, environmentally enriched housing also positively drives important aspects of the development of the immune system and the establishment of gut microbiota in early life. Consequently, EH may contribute to increasing productivity of pigs and reducing antibiotic use.
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Affiliation(s)
- Caifang Wen
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ingrid van Dixhoorn
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Dirkjan Schokker
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Henri Woelders
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Johanna M. J. Rebel
- Wageningen Livestock Research, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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Comprehensive Cultivation of the Swine Gut Microbiome Reveals High Bacterial Diversity and Guides Bacterial Isolation in Pigs. mSystems 2021; 6:e0047721. [PMID: 34282935 PMCID: PMC8407297 DOI: 10.1128/msystems.00477-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite the substantial progress made in human gut culturomics, little is known about the culturability of the swine gut microbiota. In this study, we cultured swine gut microbiota using 53 bacterial cultivation methods with different medium and gas combinations from three pigs at four different growth stages. Both culture-dependent (CD; colony mixtures from each method) and culture-independent (CI; original fecal suspensions) samples were subjected to 16S rRNA gene amplicon sequencing. Increasing microbial diversities were observed in both CI and CD samples from successive growth stages. While a total of 378, 482, 565, and 555 bacterial amplicon sequence variants (ASVs) were observed in the CI samples, higher microbial diversities (415, 675, 808, and 823 observed ASVs) were detected using the CD methods at the lactation, nursery, growing, and finishing stages, respectively. We constructed reference culture maps showing the preferred cultivation conditions for specific bacterial taxa and examined the effects of culturing factors such as oxygen, medium, donor pig age, antibiotics, and blood culture preincubation on swine gut microbiota cultivation. We focused on a wide range of beneficial bacteria, chose 1,299 colonies based on the reference map, and Sanger sequenced their 16S rRNA genes. These isolates clustered into 148 different bacterial taxa covering 28 genera. We observed 11, 19, 33, and 25 pairs of cooccurring ASVs in both CD and CI samples at four successive growth stages. This study provides guidance in culturing the swine gut microbiota of interest, which is critical when characterizing their functions in this important animal species. IMPORTANCE The swine gut microbiome has been the focus of many investigations due to the fact that pigs serve as both an excellent biomedical model for human diseases and an important protein source. Substantial progress has been made in swine gut microbiome studies using next-generation sequencing-based culture-independent approaches, but little is known about the culturability of the swine gut microbiota. To understand their roles in swine production, it is critical to culture bacterial strains of interest. In this study, we cultured the gut microbiota from pigs at different growth stages using 53 bacterial cultivation methods with different medium and gas combinations. This study provides evidence that the swine gut microbiota is much more diverse based on a culture-dependent approach than previously known. It provides preliminary guidance for isolating certain bacteria of interest from pigs, which is critical in establishing causal relationships between the gut microbiota and the health status of pigs.
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Yang Y, Liu Y, Liu J, Wang H, Guo Y, Du M, Cai C, Zhao Y, Lu C, Guo X, Cao G, Duan Z, Li B, Gao P. Composition of the Fecal Microbiota of Piglets at Various Growth Stages. Front Vet Sci 2021; 8:661671. [PMID: 34336969 PMCID: PMC8319241 DOI: 10.3389/fvets.2021.661671] [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: 02/09/2021] [Accepted: 06/15/2021] [Indexed: 11/24/2022] Open
Abstract
Gastrointestinal (GI) microbiota play an important role in promoting growth in piglets. However, studies on microbiota composition at various growth stages are lacking. We measured body weights of Jinfen White and Mashen piglets every 7 days and collected their fecal samples by rectal swabbing at nine time points during suckling (1-28 days) and nursery (35-70 days) stages to gain insight into microbiota variability during piglet growth. The fecal microbiota were characterized via 16S rRNA gene sequencing to analyze the effects of microbial diversity on piglet growth and development preliminarily. The results showed that although the two breeds of piglets have similar body weights at birth, weaned Jinfen White piglets demonstrated a significantly greater body weight and daily weight gain than weaned Mashen piglets (P < 0.01). A total of 1,976 operational taxonomic units (OTUs) belonging to 27 phyla and 489 genera were uncovered, in which the highest numbers of OTUs belong to the phyla Firmicutes and Bacteroidetes. Lactobacillus, Bacteroides, and Prevotellaceae NK3B31 groups accounting for 12.4, 8.8, and 5.8% of OTUs, respectively, showed relatively high abundance at the genus level. Nine sampling time points were divided into three growth stages, namely, immediate postfarrowing (1 day old), suckling (7, 14, and 21 days old), and nursery (28, 35, 49, 63, and 70 days old), on the basis of the results of microbial diversity, principal coordinate, and co-occurrence network analyses. In addition, it identified 54 discriminative features in the microbiota between two breeds of piglets by LEfSe analysis, in which 17 genera enriched the microbiota community of Jinfen White piglets. Finally, abundances of 29 genera showed significant positive correlations with body weights and daily weight gain of piglets. Conversely, abundances of 12 genera demonstrated significant negative correlations with body weights of piglets. The results of our study will provide a theoretical basis for succession patterns in fecal microbiota of piglets and suggest the need for meticulous management of piglets in pig production.
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Affiliation(s)
- Yang Yang
- College of Animal Sciences, Shanxi Agricultural University, Taigu County, China
| | - Yadan Liu
- College of Animal Sciences, Shanxi Agricultural University, Taigu County, China
| | - Juan Liu
- College of Animal Sciences, Shanxi Agricultural University, Taigu County, China
| | - Haizhen Wang
- College of Animal Sciences, Shanxi Agricultural University, Taigu County, China
| | - Yulong Guo
- College of Animal Sciences, Shanxi Agricultural University, Taigu County, China
| | - Min Du
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Chunbo Cai
- College of Animal Sciences, Shanxi Agricultural University, Taigu County, China
| | - Yan Zhao
- College of Animal Sciences, Shanxi Agricultural University, Taigu County, China
| | - Chang Lu
- College of Animal Sciences, Shanxi Agricultural University, Taigu County, China
| | - Xiaohong Guo
- College of Animal Sciences, Shanxi Agricultural University, Taigu County, China
| | - Guoqing Cao
- College of Animal Sciences, Shanxi Agricultural University, Taigu County, China
| | - Zhibian Duan
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu County, China
| | - Bugao Li
- College of Animal Sciences, Shanxi Agricultural University, Taigu County, China
| | - Pengfei Gao
- College of Animal Sciences, Shanxi Agricultural University, Taigu County, China
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Hashimoto-Hill S, Alenghat T. Inflammation-Associated Microbiota Composition Across Domestic Animals. Front Genet 2021; 12:649599. [PMID: 34239536 PMCID: PMC8257562 DOI: 10.3389/fgene.2021.649599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/27/2021] [Indexed: 12/26/2022] Open
Abstract
Domestic animals represent important resources for understanding shared mechanisms underlying complex natural diseases that arise due to both genetic and environmental factors. Intestinal inflammation, particularly inflammatory bowel disease (IBD), is a significant health challenge in humans and domestic animals. While the etiology of IBD is multifactorial, imbalance of symbiotic gut microbiota has been hypothesized to play a central role in disease pathophysiology. Advances in genomic sequencing and analytical pipelines have enabled researchers to decipher the composition of the intestinal microbiota during health and in the context of naturally occurring diseases. This review compiles microbiome genomic data across domestic species and highlights a common occurrence of gut microbiome dysbiosis during idiopathic intestinal inflammation in multiple species, including dogs, cats, horses, cows, and pigs. Current microbiome data obtained from animals with intestinal inflammation are mostly limited to taxonomical analyses in association with broad clinical phenotype. In general, a pathogen or pathosymbiont were not detected. Rather, functional potential of the altered microbiota has been suggested to be one of the key etiologic factors. Among the domestic species studied, canine analyses are currently the most advanced with incorporation of functional profiling of microbiota. Canine IBD parallels features of the disease in humans, thus canines represent a strong natural model for human IBD. While deeper analyses of metagenomic data, coupled with host molecular analyses are needed, comparative studies across domestic species can reveal shared microbial alterations and regulatory mechanisms that will improve our understanding of intestinal inflammation in both animals and humans.
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Affiliation(s)
| | - Theresa Alenghat
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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Comparative analysis of the gut microbiota of mice fed a diet supplemented with raw and cooked beef loin powder. Sci Rep 2021; 11:11489. [PMID: 34075086 PMCID: PMC8169908 DOI: 10.1038/s41598-021-90461-7] [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: 06/03/2020] [Accepted: 02/05/2021] [Indexed: 02/05/2023] Open
Abstract
We used 16S ribosomal RNA sequencing to evaluate changes in the gut microbiota of mice fed a diet supplemented with either raw or cooked beef loin powder for 9 weeks. Male BALB/c mice (n = 60) were randomly allocated to five groups: mice fed AIN-93G chow (CON), chow containing 5% (5RB) and 10% (10RB) raw beef loin powder, and chow containing 5% (5CB) and 10% (10CB) cooked beef loin powder. Dietary supplementation with both RB and CB increased the relative abundance of Clostridiales compared to the CON diet (p < 0.05). Mice fed 10RB showed a significantly higher relative abundance of Firmicutes (p = 0.018) and Lactobacillus (p = 0.001) than CON mice, and the ratio of Firmicutes/Bacteroidetes showed an increasing trend in the 10RB mice (p > 0.05). Mice fed 10CB showed a higher abundance of Peptostreptococcaceae and a lower abundance of Desulfovibrionaceae compared with the CON mice (p < 0.05). Genes for glycan biosynthesis, which result in short-chain fatty acid synthesis, were enriched in the CB mice compared to the RB mice, which was correlated to a high abundance of Bacteroides. Overall, dietary RB and CB changed the gut microbiota of mice (p < 0.05).
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46
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Saccharomyces cerevisiae boulardii CNCM I-1079 supplementation in finishing male pigs helps to cope with heat stress through feeding behaviour and gut microbiota modulation. Br J Nutr 2021; 127:353-368. [PMID: 34039449 DOI: 10.1017/s0007114521001756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Pigs subjected to heat stress (HS) decrease their feed intake and growth. The objectives of the experiment were to determine the effects of live yeast (LY) supplementation (Saccharomyces cerevisiae var boulardii CNCM I-1079) on feeding behaviour, energy metabolism and faecal microbiota composition of finishing boars (n 10) housed in a respiration chamber at thermoneutrality (7 d at 22°C) or during HS (seven plus six days at 28°C). Dietary LY supplementation increased DM intake (P = 0·01) whatever the ambient temperature, whereas HS decreased feed intake whatever the dietary supplementation (P = 0·01). Dietary LY supplementation increased the number of meals (P = 0·02). Energy retention was higher with dietary LY supplementation (P < 0·01) but decreased during HS (P < 0·01). The skin temperature of the supplemented pigs was lower at thermoneutrality and increased during HS to a lesser extent than that of non-supplemented pigs (P < 0·01). Faecal microbiota composition was determined using 16S rRNA gene sequencing. Treponema, Christensenellaceae R-7, Ruminococcaceae UCG-002, Rikenellaceae RC9, Clostridium sensu stricto 1 and Romboutsia genera and some bacteria belonging to Alloprevotella, Oxalobacter and Anaeroplasma genera were more abundant under HS. LY supplementation attenuated HS effects on Romboutsia abundance, while decreasing the abundance of some bacteria from Ruminoccocus, Coprococcus, Peptococcus and Oxalobacter genera and increasing the abundance of beneficial bacteria from Lactococcus and Subdoligranulum genera. Our results suggest that higher level of the keystone species Ruminococcus bromii at thermoneutrality may be one of the causes for higher energy retention observed under subsequent HS.
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López-García A, Benítez R, Núñez Y, Gómez-Izquierdo E, de Mercado E, García-Casco JM, González-Recio Ó, López-Bote C, Estellé J, Óvilo C. Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs. PLoS One 2021; 16:e0251804. [PMID: 34014992 PMCID: PMC8136687 DOI: 10.1371/journal.pone.0251804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/03/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Phenotypic variability for productive and meat quality traits has been largely studied in Iberian pigs, especially in genetic selection and nutritional experiments. Complex interactions among genetic background, diet composition and gut microbiota hinder the correct assessment of each factor's contribution on phenotypes. In order to disentangle these interactions, we evaluated changes in gut microbiota composition comparing 48 Iberian and Duroc pigs fed diets with different energy source (standard diet with carbohydrates vs sunflower oil-enriched diet with high oleic acid content). RESULTS A higher richness was observed for Iberian pigs (p < 0.05) and compositional analysis was applied for beta-diversity, differential abundance and pairwise log-ratio analyses. We found significant differences in overall microbiota composition between breeds, and also between diets inside breeds, to a lesser extent. Differential abundance analysis revealed that Duroc animals have more proportion of Actinobacteria and Prevotella, while Iberian replace those microorganisms with other more variable taxa. According to dietary differences, high-oleic fed animals were richer in Prevotella. We also found microbial ratios capable of separating animals by breeds and diets, mostly related to Actinobacteria. CONCLUSION This study reveals that both genetic background and diet composition might have a relevant impact in gut microbiota composition. The application of compositional data analysis has facilitated the identification of microorganisms and ratios as possibly related to metabolic changes due to genetic background and, to a lower extent, to dietary changes. This may lead to a relevant progress in the knowledge of interactions between pig genetics, environment and gut microbiota.
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Affiliation(s)
| | - Rita Benítez
- Department of Animal Breeding, INIA, Madrid, Spain
| | | | | | | | | | | | | | - Jordi Estellé
- GABI, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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48
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Metagenomics of antimicrobial and heavy metal resistance in the cecal microbiome of fattening pigs raised without antibiotics. Appl Environ Microbiol 2021; 87:AEM.02684-20. [PMID: 33547058 PMCID: PMC8091117 DOI: 10.1128/aem.02684-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study aimed to detect the cecal microbiome, antimicrobial resistance (AMR) and heavy metal resistance genes (MRGs) in fattening pigs raised under antibiotic-free (ABF) conditions compared with ordinary industrial pigs (control, C) using whole-genome shotgun sequencing. ABF pigs showed the enrichment of Prevotella (33%) and Lactobacillus (13%), whereas Escherichia coli (40%), Fusobacterium and Bacteroides (each at 4%) were notably observed in the C group. Distinct clusters of cecal microbiota of ABF and C pigs were revealed; however, microbiota of some C pigs (C1) appeared in the same cluster as ABF and were totally separated from the remaining C pigs (C2). For AMR genes, the highest abundance tet(Q) (35.7%) and mef(A) (12.7%) were markedly observed in the ABF group whereas tet(Q) (26.2%) and tet(W) (10.4%) were shown in the C group. tet(Q) was positively correlated to Prevotella in ABF and C1 samples. In the C2 group, the prominent tet(W) was positively correlated to Fusobacterium and Bacteroides Pigs have never received tetracycline but pregnant sows used chlortetracycline once 7 d before parturition. Chromosomal Cu and Zn resistance genes were also shown in both groups regardless the received Cu and Zn feed additives. A higher abundance of multi-metal resistance genes was observed in the C group (44%) compared with the ABF group (41%). In conclusion, the microbiome clusters in some C pigs were similar to that in ABF pigs. High abundant tetracycline resistance genes interrelated to major bacteria were observed in both ABF and C pigs. MRGs were also observed.IMPORTANCE: Owing to the increased problem of AMR in farm animals, raising farm animals without antibiotics is one method that could solve this problem. Our study showed that only some tetracycline and macrolide resistance genes, tet(Q), tet(W) and mef(A), were markedly abundant in ABF and C groups. The tet(Q) and tet(W) genes interrelated to different predominant bacteria in each group, showing the potential role of major bacteria as reservoirs of AMR genes. In addition, chromosomal Cu and Zn resistance genes were also observed in both pig groups, not depending on the use of Cu and Zn additives in both farms. The association of MRGs and AMR genotypes and phenotypes together with the method to re-sensitize bacteria to antibiotics should be studied further to unveil the cause of high resistance genes and solve the problems.
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Moturi J, Kim KY, Hosseindoust A, Lee JH, Xuan B, Park J, Kim EB, Kim JS, Chae BJ. Effects of Lactobacillus salivarius isolated from feces of fast-growing pigs on intestinal microbiota and morphology of suckling piglets. Sci Rep 2021; 11:6757. [PMID: 33762614 PMCID: PMC7990948 DOI: 10.1038/s41598-021-85630-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 02/15/2021] [Indexed: 12/17/2022] Open
Abstract
The study determined the effects of Lactobacillus salivarius (LS) administered early in the life of suckling piglets on their growth performance, gut morphology, and gut microbiota. Thirty litters of 3-day-old crossbreed piglets were randomly assigned to one of the three treatments, and treatments were commenced on day 3 after birth. During the whole period of the experiment, the piglets were kept with their mothers and left to suckle ad libitum while being supplemented with a milk formula with or without the bacterial probiotic supplemented. The control group (CON) was not treated with probiotics, the HLS group was treated with LS144 (HLS) screened from feces of fast-growing pigs with high body mass index (BMI) while the NLS group was supplemented with LS160 (NLS) screened from feces obtained from pigs of normal BMI. At the weaning time, a higher abundance of Actinobacteria, Lentisphaerae, and Elusimicrobia phyla were observed in NLS piglets, whereas the abundance of Fibrobacteres phylum was significantly reduced in NLS and HLS piglets compared with the CON. A greater abundance of Lactobacillus was detected in the HLS treatment compared with the CON. The abundance of Bacteroides and Fibrobacter was higher in the CON piglets compared with the HLS and NLS piglets. Compared with the CON group, the oral administration of LS significantly increased the number of Lactobacillus and villus height in the duodenum, jejunum, and ileum. Moreover, the villus height of the duodenum was significantly improved in the HLS treatment compared with the NLS treatment. Based on the findings in the neonatal piglet model, we suggest that oral supplementation of LS, particularly LS isolated from high BMI pigs, could be beneficial by improving the intestinal villus height.
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Affiliation(s)
- Joseph Moturi
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea.,Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Kwang Yeol Kim
- Poultry Research Institute, National Institute of Animal Science, Pyeongchang, 25342, Republic of Korea
| | - Abdolreza Hosseindoust
- Department of Animal Resource Science, College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Jun Hyung Lee
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Biao Xuan
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
| | - Jongbin Park
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
| | - Eun Bae Kim
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon, Kangwon-do, Republic of Korea
| | - Jin Soo Kim
- Department of Animal Industry Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea. .,Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Byung Jo Chae
- Department of Animal Resource Science, College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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Ramon E, Belanche-Muñoz L, Molist F, Quintanilla R, Perez-Enciso M, Ramayo-Caldas Y. kernInt: A Kernel Framework for Integrating Supervised and Unsupervised Analyses in Spatio-Temporal Metagenomic Datasets. Front Microbiol 2021; 12:609048. [PMID: 33584612 PMCID: PMC7876079 DOI: 10.3389/fmicb.2021.609048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/07/2021] [Indexed: 12/20/2022] Open
Abstract
The advent of next-generation sequencing technologies allowed relative quantification of microbiome communities and their spatial and temporal variation. In recent years, supervised learning (i.e., prediction of a phenotype of interest) from taxonomic abundances has become increasingly common in the microbiome field. However, a gap exists between supervised and classical unsupervised analyses, based on computing ecological dissimilarities for visualization or clustering. Despite this, both approaches face common challenges, like the compositional nature of next-generation sequencing data or the integration of the spatial and temporal dimensions. Here we propose a kernel framework to place on a common ground the unsupervised and supervised microbiome analyses, including the retrieval of microbial signatures (taxa importances). We define two compositional kernels (Aitchison-RBF and compositional linear) and discuss how to transform non-compositional beta-dissimilarity measures into kernels. Spatial data is integrated with multiple kernel learning, while longitudinal data is evaluated by specific kernels. We illustrate our framework through a single point soil dataset, a human dataset with a spatial component, and a previously unpublished longitudinal dataset concerning pig production. The proposed framework and the case studies are freely available in the kernInt package at https://github.com/elies-ramon/kernInt.
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Affiliation(s)
- Elies Ramon
- Plant and Animal Genomics, Statistical and Population Genomics Group, CSIC-IRTA-UAB-UB Consortium, Centre for Research in Agricultural Genomics (CRAG), Bellaterra, Spain
| | - Lluís Belanche-Muñoz
- Department of Computer Science, Polytechnic University of Catalonia, Barcelona, Spain
| | | | | | - Miguel Perez-Enciso
- Plant and Animal Genomics, Statistical and Population Genomics Group, CSIC-IRTA-UAB-UB Consortium, Centre for Research in Agricultural Genomics (CRAG), Bellaterra, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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