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Kavanova K, Kostovova I, Moravkova M, Kubasova T, Babak V, Crhanova M. Comparative Genome Analysis and Characterization of the Probiotic Properties of Lactic Acid Bacteria Isolated from the Gastrointestinal Tract of Wild Boars in the Czech Republic. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10259-7. [PMID: 38652229 DOI: 10.1007/s12602-024-10259-7] [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] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Probiotics are crucial components for maintaining a healthy gut microbiota in pigs, especially during the weaning period. Lactic acid bacteria (LAB) derived from the gastrointestinal tract of wild boars can serve as an abundant source of beneficial probiotic strains with suitable properties for use in pig husbandry. In this study, we analyzed and characterized 15 strains of Limosilactobacillus mucosae obtained from the gut contents of wild boars to assess their safety and suitability as probiotic candidates. The strains were compared using pan-genomic analysis with 49 L. mucosae strains obtained from the NCBI database. All isolated strains demonstrated their safety by showing an absence of transferrable antimicrobial resistance genes and hemolysin activity. Based on the presence of beneficial genes, five candidates with probiotic properties were selected and subjected to phenotypic profiling. These five selected isolates exhibited the ability to survive conditions mimicking passage through the host's digestive tract, such as low pH and the presence of bile salts. Furthermore, five selected strains demonstrated the presence of corresponding carbohydrate-active enzymes and the ability to utilize various carbohydrate substrates. These strains can enhance the digestibility of oligosaccharide or polysaccharide substrates found in food or feed, specifically resistant starch, α-galactosides, cellobiose, gentiobiose, and arabinoxylans. Based on the results obtained, the L. mucosae isolates tested in this study appear to be promising candidates for use as probiotics in pigs.
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Affiliation(s)
- Katerina Kavanova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic.
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.
| | - Iveta Kostovova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic
| | - Monika Moravkova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic
| | - Tereza Kubasova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic
| | - Vladimir Babak
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic
| | - Magdalena Crhanova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic
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Kuthyar S, Diaz J, Avalos-Villatoro F, Maltecca C, Tiezzi F, Dunn RR, Reese AT. Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population. J Evol Biol 2023; 36:1695-1711. [PMID: 37885134 DOI: 10.1111/jeb.14227] [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: 01/24/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 10/28/2023]
Abstract
Animal ecology and evolution have long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between animal ecology and evolution and health. The gut microbiome has been shown to differ between wild and domestic animals, but the role of these differences for domestic animal evolution remains unknown. Gut microbiome responses to new animal genotypes and local environmental change during domestication may promote specific host phenotypes that are adaptive (or not) to the domestic environment. Because the gut microbiome supports host immune function, understanding the effects of animal ecology and evolution on the gut microbiome and immune phenotypes is critical. We investigated how domestication affects the gut microbiome and host immune state in multiple pig populations across five domestication contexts representing domestication status and current living conditions: free-ranging wild, captive wild, free-ranging domestic, captive domestic in research or industrial settings. We observed that domestication context explained much of the variation in gut microbiome composition, pathogen abundances and immune markers, yet the main differences in the repertoire of metabolic genes found in the gut microbiome were between the wild and domestic genetic lineages. We also documented population-level effects within domestication contexts, demonstrating that fine scale environmental variation also shaped host and microbe features. Our findings highlight that understanding which gut microbiome and immune traits respond to host genetic lineage and/or scales of local ecology could inform targeted interventions that manipulate the gut microbiome to achieve beneficial health outcomes.
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Affiliation(s)
- Sahana Kuthyar
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Jessica Diaz
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | | | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Francesco Tiezzi
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Aspen T Reese
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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Liu W, Huang Z, Zhang Y, Zhang S, Cui Z, Liu W, Li L, Xia J, Zou Y, Qi Z. ASMT determines gut microbiota and increases neurobehavioral adaptability to exercise in female mice. Commun Biol 2023; 6:1126. [PMID: 37935873 PMCID: PMC10630421 DOI: 10.1038/s42003-023-05520-8] [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: 03/23/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
N-acetylserotonin O-methyltransferase (ASMT) is responsible for melatonin biosynthesis. The Asmt gene is located on the X chromosome, and its genetic polymorphism is associated with depression in humans. However, the underlying mechanism remains unclear. Here, we use CRISPR/Cas9 to delete 20 bp of exon 2 of Asmt, and construct C57BL/6J mouse strain with Asmt frameshift mutation (Asmtft/ft). We show that female Asmtft/ft mice exhibit anxiety- and depression-like behaviors, accompanied by an obvious structural remodeling of gut microbiota. These behavioral abnormalities are not observed in male. Moreover, female Asmtft/ft mice show a lower neurobehavioral adaptability to exercise, while wild-type shows a "higher resilience". Cross-sectional and longitudinal analysis indicates that the structure of gut microbiota in Asmtft/ft mice is less affected by exercise. These results suggests that Asmt maintains the plasticity of gut microbiota in female, thereby enhancing the neurobehavioral adaptability to exercise.
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Affiliation(s)
- Weina Liu
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention (Ministry of Education), East China Normal University, Shanghai, 200241, China.
- College of Physical Education and Health, East China Normal University, Shanghai, 200241, China.
| | - Zhuochun Huang
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention (Ministry of Education), East China Normal University, Shanghai, 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai, 200241, China
| | - Ye Zhang
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention (Ministry of Education), East China Normal University, Shanghai, 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai, 200241, China
| | - Sen Zhang
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention (Ministry of Education), East China Normal University, Shanghai, 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai, 200241, China
| | - Zhiming Cui
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention (Ministry of Education), East China Normal University, Shanghai, 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai, 200241, China
| | - Wenbin Liu
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention (Ministry of Education), East China Normal University, Shanghai, 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai, 200241, China
| | - Lingxia Li
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention (Ministry of Education), East China Normal University, Shanghai, 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai, 200241, China
| | - Jie Xia
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention (Ministry of Education), East China Normal University, Shanghai, 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai, 200241, China
| | - Yong Zou
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention (Ministry of Education), East China Normal University, Shanghai, 200241, China
- College of Physical Education and Health, East China Normal University, Shanghai, 200241, China
| | - Zhengtang Qi
- The Key Laboratory of Adolescent Health Assessment and Exercise Intervention (Ministry of Education), East China Normal University, Shanghai, 200241, China.
- College of Physical Education and Health, East China Normal University, Shanghai, 200241, China.
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Sharma S, Kumari M, Vakhlu J. Metatranscriptomic insight into the possible role of clay microbiome in skin disease management. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2023; 67:1803-1811. [PMID: 37584759 DOI: 10.1007/s00484-023-02540-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/28/2023] [Accepted: 08/04/2023] [Indexed: 08/17/2023]
Abstract
Even though the scientific documentation is limited, microbiome of healing clay is gradually gaining attention of the scientific community, as a therapeutic force playing an indispensable role in skin disease management. The present study explores the metatranscriptome profile of the Chamliyal clay, widely known for its efficacy in managing various skin problems, using Illumina NextSeq sequencing technology. The gene expression profile of the clay microbial community was analyzed through SEED subsystems of the MG-RAST server. Due to the unavailability of metatranscriptomic data on other therapeutic clays, Chamliyal's profile was compared to non-therapeutic soils, as well as healthy and diseased human skin microbiomes. The study identified Firmicutes, Proteobacteria, and Actinobacteria as the primary active microbial phyla in Chamliyal clay. These resemble those abundant in a healthy human skin microbiome. This is significant as lower levels of these phyla in the skin are linked to inflammatory skin conditions like psoriasis. Interestingly, pathogenic microbes actively metabolizing in the clay were absent. Importantly, 6% of the transcripts annotated to sulfur and iron metabolism, which are known to play a major role in skin disease management. This study provides the most comprehensive and a novel overview of the metatranscriptome of any of the healing clay available worldwide. The findings offer valuable insights into the clay microbiome's potential in managing skin disorders, inspiring future endeavors to harness these insights for medical applications.
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Affiliation(s)
- Sakshi Sharma
- School of Biotechnology, University of Jammu, J&K, 180006, India
| | - Monika Kumari
- School of Biotechnology, University of Jammu, J&K, 180006, India
| | - Jyoti Vakhlu
- School of Biotechnology, University of Jammu, J&K, 180006, India.
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Yang J, Chen R, Peng Y, Chai J, Li Y, Deng F. The role of gut archaea in the pig gut microbiome: a mini-review. Front Microbiol 2023; 14:1284603. [PMID: 37876779 PMCID: PMC10593451 DOI: 10.3389/fmicb.2023.1284603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023] Open
Abstract
The gastrointestinal microbiota of swine harbors an essential but often overlooked component: the gut archaea. These enigmatic microorganisms play pivotal roles in swine growth, health, and yield quality. Recent insights indicate that the diversity of gut archaea is influenced by various factors including breed, age, and diet. Such factors orchestrate the metabolic interactions within the porcine gastrointestinal environment. Through symbiotic relationships with bacteria, these archaea modulate the host's energy metabolism and digestive processes. Contemporary research elucidates a strong association between the abundance of these archaea and economically significant traits in swine. This review elucidates the multifaceted roles of gut archaea in swine and underscores the imperative for strategic interventions to modulate their population and functionality. By exploring the probiotic potential of gut archaea, we envisage novel avenues to enhance swine growth, health, and product excellence. By spotlighting this crucial, yet under-investigated, facet of the swine gut microbiome, we aim to galvanize further scientific exploration into harnessing their myriad benefits.
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Affiliation(s)
- Jianbo Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Routing Chen
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Yunjuan Peng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Jianmin Chai
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Feilong Deng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
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Wei L, Zeng B, Zhang S, Guo W, Li F, Zhao J, Li Y. Hybridization altered the gut microbiota of pigs. Front Microbiol 2023; 14:1177947. [PMID: 37465027 PMCID: PMC10350513 DOI: 10.3389/fmicb.2023.1177947] [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: 03/02/2023] [Accepted: 06/14/2023] [Indexed: 07/20/2023] Open
Abstract
Mammalian gut microbiota plays an important role in the host's nutrient metabolism, growth, and immune regulation. Hybridization can enable a progeny to acquire superior traits of the parents, resulting in the hybridization advantage. However, studies on the effects of hybridization on the pigs' gut microbiota are lacking. Therefore, this study used multi-omics technologies to compare and analyze the gut microbiota of the primary wild boar and its offspring. The 16S rRNA gene sequencing results revealed that the gut microbiota of F4 exhibited a host-like dominance phenomenon with a significant increase in the abundance of Lactobacillus and Bifidobacterium. The beta diversity of Duroc was significantly different from those of F0, F2, and F4; after the host hybridization, the similarity of the beta diversity in the progeny decreased with the decrease in the similarity of the F0 lineage. The metagenomic sequencing results showed that the significantly enriched metabolic pathways in F4, such as environmental, circulatory system, fatty acid degradation adaptation, and fatty acid biosynthesis, were similar to those in F0. Moreover, it also exhibited similar significantly enriched metabolic pathways as those in Duroc, such as carbohydrate metabolism, starch and sucrose metabolism, starch-degrading CAZymes, lactose-degrading CAZymes, and various amino acid metabolism pathways. However, the alpha-amylase-related KOs, lipid metabolism, and galactose metabolism in F4 were significantly higher than those in Duroc and F0. Non-targeted metabolome technology analysis found that several metabolites, such as docosahexaenoic acid, arachidonic acid, and citric acid were significantly enriched in the F4 pigs as compared to those in F0. Based on Spearman correlation analysis, Lactobacillus and Bifidobacterium were significantly positively correlated with these metabolites. Finally, the combined metagenomic and metabolomic analysis suggested that the metabolic pathways, such as valine, leucine, and isoleucine biosynthesis and alanine aspartate and glutamate metabolism were significantly enriched in F4 pigs. In conclusion, the gut microbiota of F4 showed a similar host "dominance" phenomenon, which provided reference data for the genetics and evolution of microbiota and the theory of microbial-assisted breeding.
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Affiliation(s)
- Limin Wei
- Chongqing Key Laboratory of High Active Traditional Chinese Drug Delivery System, Chongqing Medical and Pharmaceutical College, Chongqing, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Siyuan Zhang
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-Origin Food, Chengdu Medical College, Chengdu, China
| | - Wei Guo
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-Origin Food, Chengdu Medical College, Chengdu, China
| | - Feng Li
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Jiangchao Zhao
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
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Sun Y, Yu Y, Guo J, Zhong L, Zhang M. Alterations in Fecal Microbiota Linked to Environment and Sex in Red Deer ( Cervus elaphus). Animals (Basel) 2023; 13:929. [PMID: 36899786 PMCID: PMC10000040 DOI: 10.3390/ani13050929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Gut microbiota play an important role in impacting the host's metabolism, immunity, speciation, and many other functions. How sex and environment affect the structure and function of fecal microbiota in red deer (Cervus elaphus) is still unclear, particularly with regard to the intake of different diets. In this study, non-invasive molecular sexing techniques were used to determine the sex of fecal samples from both wild and captive red deer during the overwintering period. Fecal microbiota composition and diversity analyses were performed using amplicons from the V4-V5 region of the 16S rRNA gene sequenced on the Illumina HiSeq platform. Based on Picrust2 prediction software, potential function distribution information was evaluated by comparing the Kyoto Encyclopedia of Genes and Genome (KEGG). The results showed that the fecal microbiota of the wild deer (WF, n = 10; WM, n = 12) was significantly enriched in Firmicutes and decreased in Bacteroidetes, while the captive deer (CF, n = 8; CM, n = 3) had a significantly higher number of Bacteroidetes. The dominant species of fecal microbiota in the wild and captive red deer were similar at the genus level. The alpha diversity index shows significant difference in fecal microbiota diversity between the males and females in wild deer (p < 0.05). Beta diversity shows significant inter-group differences between wild and captive deer (p < 0.05) but no significant differences between female and male in wild or captive deer. The metabolism was the most important pathway at the first level of KEGG pathway analysis. In the secondary pathway of metabolism, glycan biosynthesis and metabolism, energy metabolism, and the metabolism of other amino acids were significantly different. In summary, these compositional and functional variations in the fecal microbiota of red deer may be helpful for guiding conservation management and policy decision-making, providing important information for future applications of population management and conservation.
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Affiliation(s)
- Yue Sun
- School of Biological Sciences, Guizhou Education University, Guiyang 550018, China
| | - Yanze Yu
- Wildlife Institute of Heilongjiang Province, Harbin 150081, China
| | - Jinhao Guo
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Linqiang Zhong
- College of Life Sciences and Technology, Xinjiang University, Urumqi 830046, China
| | - Minghai Zhang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
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