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Zhang S, Zhang H, Zhang C, Wang G, Shi C, Li Z, Gao F, Cui Y, Li M, Yang G. Composition and evolutionary characterization of the gut microbiota in pigs. Int Microbiol 2024; 27:993-1008. [PMID: 37982990 PMCID: PMC11300507 DOI: 10.1007/s10123-023-00449-8] [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: 09/10/2022] [Revised: 10/28/2023] [Accepted: 11/10/2023] [Indexed: 11/21/2023]
Abstract
The intestinal microbiota plays significant role in the physiology and functioning of host organisms. However, there is limited knowledge of the composition and evolution of microbiota-host relationships from wild ancestors to modern domesticated species. In this study, the 16S rRNA gene V3-V4 in the intestinal contents of different pig breeds was analyzed and was compared using high-throughput sequencing. This identified 18 323 amplicon sequence variants, of which the Firmicutes and Actinobacteria phyla and Bifidobacterium and Allobaculum genera were most prevalent in wild pigs (WP). In contrast, Proteobacteria and Firmicutes predominated in Chinese Shanxi Black pigs (CSB), while Firmicutes were the most prevalent phylum in Large White pigs (LW) and Iberian pigs (IB), followed by Bacteroidetes in IB and Proteobacteria in LW. At the genus level, Shigella and Lactobacillus were most prevalent in CSB and LW, while Actinobacillus and Sarcina predominated in IB. Differential gene expression together with phylogenetic and functional analyses indicated significant differences in the relative abundance of microbial taxa between different pig breeds. Although many microbial taxa were common to both wild and domestic pigs, significant diversification was observed in bacterial genes that potentially influence host phenotypic traits. Overall, these findings suggested that both the composition and functions of the microbiota were closely associated with domestication and the evolutionary changes in the host. The members of the microbial communities were vertically transmitted in pigs, with evidence of co-evolution of both the hosts and their intestinal microbial communities. These results enhance our understanding and appreciation of the complex interactions between intestinal microbes and hosts and highlight the importance of applying this knowledge in agricultural and microbiological research.
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Affiliation(s)
- Shuhong Zhang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Huan Zhang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Cheng Zhang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guan Wang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Chuanxing Shi
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Zhiqiang Li
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Fengyi Gao
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Yanyan Cui
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Guangli Yang
- College of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China.
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2
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Marbun KT, Sugata M, Purnomo JS, Dikson, Mudana SO, Jan TT, Jo J. Genomic Characterization and Safety Assessment of Bifidobacterium breve BS2-PB3 as Functional Food. J Microbiol Biotechnol 2024; 34:871-879. [PMID: 38494884 DOI: 10.4014/jmb.2311.11031] [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: 11/21/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 03/19/2024]
Abstract
Our group had isolated Bifidobacterium breve strain BS2-PB3 from human breast milk. In this study, we sequenced the whole genome of B. breve BS2-PB3, and with a focus on its safety profile, various probiotic characteristics (presence of antibiotic resistance genes, virulence factors, and mobile elements) were then determined through bioinformatic analyses. The antibiotic resistance profile of B. breve BS2-PB3 was also evaluated. The whole genome of B. breve BS2-PB3 consisted of 2,268,931 base pairs with a G-C content of 58.89% and 2,108 coding regions. The average nucleotide identity and whole-genome phylogenetic analyses supported the classification of B. breve BS2-PB3. According to our in silico assessment, B. breve BS2-PB3 possesses antioxidant and immunomodulation properties in addition to various genes related to the probiotic properties of heat, cold, and acid stress, bile tolerance, and adhesion. Antibiotic susceptibility was evaluated using the Kirby-Bauer disk-diffusion test, in which the minimum inhibitory concentrations for selected antibiotics were subsequently tested using the Epsilometer test. B. breve BS2-PB3 only exhibited selected resistance phenotypes, i.e., to mupirocin (minimum inhibitory concentration/MIC >1,024 μg/ml), sulfamethoxazole (MIC >1,024 μg/ml), and oxacillin (MIC >3 μg/ml). The resistance genes against those antibiotics, i.e., ileS, mupB, sul4, mecC and ramA, were detected within its genome as well. While no virulence factor was detected, four insertion sequences were identified within the genome but were located away from the identified antibiotic resistance genes. In conclusion, B. breve BS2-PB3 demonstrated a sufficient safety profile, making it a promising candidate for further development as a potential functional food.
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Affiliation(s)
- Kristin Talia Marbun
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Marcelia Sugata
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Jonathan Suciono Purnomo
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Dikson
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Samuel Owen Mudana
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Tan Tjie Jan
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Juandy Jo
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
- Mochtar Riady Institute for Nanotechnology, Tangerang 15811, Indonesia
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3
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Suzuki-Hashido N, Tsuchida S, Azumano A, Goossens B, Saldivar DAR, Stark DJ, Tuuga A, Ushida K, Matsuda I. Isolation of Bacteria from Freeze-Dried Samples and the Functional Characterization of Species-Specific Lactic Acid Bacteria with a Comparison of Wild and Captive Proboscis Monkeys. Microorganisms 2023; 11:1458. [PMID: 37374963 DOI: 10.3390/microorganisms11061458] [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: 05/04/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Previously, we isolated a novel lactic acid bacteria species (Lactobacillus nasalidis) from the fresh forestomach contents of a captive proboscis monkey (Nasalis larvatus) in a Japanese zoo. In this study, we isolated two strains of L. nasalidis from the freeze-dried forestomach contents of a wild proboscis monkey inhabiting a riverine forest in Malaysia. The samples had been stored for more than six years. Phenotypic analysis showed that strains isolated from the wild individual had more diverse sugar utilization and lower salt tolerance than strains previously isolated from the captive counterpart. These phenotypic differences are most likely induced by feeding conditions; wild individuals consume a wide variety of natural food, unlike their zoo-raised counterparts that consume formula feed with sodium sufficiency. Since 16s rRNA sequences of L. nasalidis were detected in the previously created 16S rRNA libraries of wild, provisioned, and captive proboscis monkeys in Malaysia and Japan, L. nasalidis may be an essential bacterium of the foregut microbial community of the proboscis monkey. The currently established method for the isolation of gut bacteria from freeze-dried samples under storage will be applicable to many already-stored precious samples.
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Affiliation(s)
- Nami Suzuki-Hashido
- College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Aichi, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku 102-0083, Tokyo, Japan
| | - Sayaka Tsuchida
- College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Aichi, Japan
| | | | - Benoit Goossens
- Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
| | - Diana A Ramirez Saldivar
- Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
| | - Danica J Stark
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
| | - Augustine Tuuga
- Sabah Wildlife Department, Wisma Muis, Kota Kinabalu 88100, Malaysia
| | - Kazunari Ushida
- College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Aichi, Japan
| | - Ikki Matsuda
- Wildlife Research Center, Kyoto University, Sakyo-ku 606-8203, Kyoto, Japan
- Academy of Emerging Sciences, Chubu University, Kasugai 487-8501, Aichi, Japan
- Chubu Institute for Advanced Studies, Chubu University, Kasugai 487-8501, Aichi, Japan
- Institute for Tropical Biology and Conservation, University Malaysia Sabah, Kota Kinabalu 88100, Malaysia
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Moravkova M, Kostovova I, Kavanova K, Pechar R, Stanek S, Brychta A, Zeman M, Kubasova T. Antibiotic Susceptibility, Resistance Gene Determinants and Corresponding Genomic Regions in Lactobacillus amylovorus Isolates Derived from Wild Boars and Domestic Pigs. Microorganisms 2022; 11:103. [PMID: 36677394 PMCID: PMC9863647 DOI: 10.3390/microorganisms11010103] [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: 10/05/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
Restrictions on the use of antibiotics in pigs lead to the continuous search for new probiotics serving as an alternative to antibiotics. One of the key parameters for probiotic bacteria selection is the absence of horizontally transmissible resistance genes. The aim of our study was to determine antibiotic susceptibility profiles in 28 Lactobacillus amylovorus isolates derived from the digestive tract of wild boars and farm pigs by means of the broth microdilution method and whole genome sequencing (WGS). We revealed genetic resistance determinants and examined sequences flanking resistance genes in these strains. Our findings indicate that L. amylovorus strains from domestic pigs are predominantly resistant to tetracycline, erythromycin and ampicillin. WGS analysis of horizontally transmissible genes revealed only three genetic determinants (tetW, ermB and aadE) of which all tetW and ermB genes were present only in strains derived from domestic pigs. Sequence analysis of coding sequences (CDS) in the neighborhood of the tetW gene revealed the presence of site-specific recombinase (xerC/D), site-specific DNA recombinase (spoIVCA) or DNA-binding transcriptional regulator (xre), usually directly downstream of the tetW gene. In the case of ermB, CDS for omega transcriptional repressor or mobilization protein were detected upstream of the ermB gene.
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Affiliation(s)
- Monika Moravkova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic
| | - Iveta Kostovova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Hudcova 296/70, 621 00 Brno, Czech Republic
| | - 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
| | - Radko Pechar
- Food Research Institute Prague, Radiová 1285/7, 102 00 Prague, Czech Republic
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | | | - Ales Brychta
- MIKROP ČEBÍN a.s., Čebín 416, 664 23 Čebín, Czech Republic
| | - Michal Zeman
- 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
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5
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Mansilla FI, Ficoseco CA, Miranda MH, Puglisi E, Nader-Macías MEF, Vignolo GM, Fontana CA. Administration of probiotic lactic acid bacteria to modulate fecal microbiome in feedlot cattle. Sci Rep 2022; 12:12957. [PMID: 35902668 PMCID: PMC9334624 DOI: 10.1038/s41598-022-16786-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 07/15/2022] [Indexed: 11/20/2022] Open
Abstract
Modulation of animal gut microbiota is a prominent function of probiotics to improve the health and performance of livestock. In this study, a large-scale survey to evaluate the effect of lactic acid bacteria probiotics on shaping the fecal bacterial community structure of feedlot cattle during three experimental periods of the fattening cycle (163 days) was performed. A commercial feedlot located in northwestern Argentina was enrolled with cattle fed mixed rations (forage and increasing grain diet) and a convenience-experimental design was conducted. A pen (n = 21 animals) was assigned to each experimental group that received probiotics during three different periods. Groups of n = 7 animals were sampled at 40, 104 and 163 days and these samples were then pooled to one, thus giving a total of 34 samples that were subjected to high-throughput sequencing. The microbial diversity of fecal samples was significantly affected (p < 0.05) by the administration period compared with probiotic group supplementation. Even though, the three experimental periods of probiotic administration induced changes in the relative abundance of the most representative bacterial communities, the fecal microbiome of samples was dominated by the Firmicutes (72-98%) and Actinobacteria (0.8-27%) phyla, while a lower abundance of Bacteroidetes (0.08-4.2%) was present. Probiotics were able to modulate the fecal microbiota with a convergence of Clostridiaceae, Lachnospiraceae, Ruminococcaceae and Bifidobacteriaceae associated with health and growth benefits as core microbiome members. Metabolic functional prediction comparing three experimental administration periods (40, 104 and 163 days) showed an enrichment of metabolic pathways related to complex plant-derived polysaccharide digestion as well as amino acids and derivatives during the first 40 days of probiotic supplementation. Genomic-based knowledge on the benefits of autochthonous probiotics on cattle gastrointestinal tract (GIT) microbiota composition and functions will contribute to their selection as antibiotic alternatives for commercial feedlot.
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Affiliation(s)
| | | | | | - Edoardo Puglisi
- Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Cremona-Piacenza, Italy
| | | | | | - Cecilia Alejandra Fontana
- Instituto Nacional de Tecnología Agropecuaria INTA EEA-Famaillá, Tucumán, Argentina.
- Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Cremona-Piacenza, Italy.
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6
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Liu M, Zhang W, Yao J, Niu J. Production, purification, characterization, and biological properties of Rhodosporidium paludigenum polysaccharide. PLoS One 2021; 16:e0246148. [PMID: 33513164 PMCID: PMC7845956 DOI: 10.1371/journal.pone.0246148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 01/14/2021] [Indexed: 11/18/2022] Open
Abstract
The yield of marine red yeast polysaccharide (MRYP) obtained from Rhodosporidium paludigenum was increased by optimizing fermentation conditions, and the pure polysaccharide was extracted by column chromatography. The molecular weight of pure MRYP and the ratio of mannose to glucose in components of MRYP were determined. Antioxidant and antibacterial abilities of MRYP were investigated in vitro and in vivo. The optimal fermentation parameters were as follows: Medium 4, pH = 6.72, temperature = 30.18°C, blades speed = 461.36 r/min; the optimized yield reached 4323.90 mg/L, which was 1.31 times the original yield. The sequence of factors that affected the MRYP yield was the blades speed>pH>temperature. The main components of MRYP were MYH-1 and MYH-2. The molecular weights of MYH-1 and MYH-2 were 246.92 kDa and 21.88 kDa, respectively; they accounted for 53.60% and 28.75% of total polysaccharide. In MYH-1 and MYH-2, the proportion of glucose and mannose accounted for 46.94%, 38.46%, and 67.10%, 7.17%, respectively. In vitro, the ability of scavenging DPPH•, •OH, and •O2− radical was 32.26%, 24.34%, and 22.09%; the minimum inhibitory concentration (MIC) of MRYP was 480 μg/mg. In vivo, MRYP improved the lambs’ body weight, antioxidant enzyme activity, and the number of probiotics, but it reduced the feed/gain (F/G) ratio and the number of pathogenic bacteria in 60-days-old lambs.
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Affiliation(s)
- Mengjian Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - WenJu Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
- * E-mail:
| | - Jun Yao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Junli Niu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
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7
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A critical review of antibiotic resistance in probiotic bacteria. Food Res Int 2020; 136:109571. [PMID: 32846610 DOI: 10.1016/j.foodres.2020.109571] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022]
Abstract
Probiotics are defined as live microorganisms that, when administered in adequate amounts, confer a health benefit upon the host. At present, probiotics are gaining popularity worldwide and are widely used in food and medicine. Consumption of probiotics is increasing with further in-depth research on the relationship between intestinal flora and host health. Most people pay more attention to the function of probiotics but ignore their potential risks, such as infection and antibiotic resistance transfer to pathogenic microbes. Physiological functions, effects and mechanisms of action of probiotics were covered in this review, as well as the antibiotic resistance phenotypes, mechanisms and genes found in probiotics. Typical cases of antibiotic resistance of probiotics were also highlighted, as well as the potential risks (including pathogenicity, infectivity and excessive immune response) and corresponding strategies (dosage, formulation, and administration route). This timely study provides an avenue for further research, development and application of probiotics.
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8
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Yang G, Shi C, Zhang S, Liu Y, Li Z, Gao F, Cui Y, Yan Y, Li M. Characterization of the bacterial microbiota composition and evolution at different intestinal tract in wild pigs ( Sus scrofa ussuricus). PeerJ 2020; 8:e9124. [PMID: 32518722 PMCID: PMC7258971 DOI: 10.7717/peerj.9124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 04/14/2020] [Indexed: 12/29/2022] Open
Abstract
Commensal microorganisms are essential to the normal development and function of many aspects of animal biology, including digestion, nutrient absorption, immunological development, behaviors, and evolution. The specific microbial composition and evolution of the intestinal tracts of wild pigs remain poorly characterized. This study therefore sought to assess the composition, distribution, and evolution of the intestinal microbiome of wild pigs. For these analyses, 16S rRNA V3-V4 regions from five gut sections prepared from each of three wild sows were sequenced to detect the microbiome composition. These analyses revealed the presence of 6,513 operational taxonomic units (OTUs) mostly distributed across 17 phyla and 163 genera in these samples, with Firmicutes and Actinobacteria being the most prevalent phyla of microbes present in cecum and jejunum samples, respectively. Moreover, the abundance of Actinobacteria in wild pigs was higher than that in domestic pigs. At the genus level the Bifidobacterium and Allobaculum species of microbes were most abundant in all tested gut sections, with higher relative abundance in wild pigs relative to domestic pigs, indicating that in the process of pig evolution, the intestinal microbes also evolved, and changes in the intestinal microbial diversity could have been one of the evolutionary forces of pigs. Intestinal microbial functional analyses also revealed the microbes present in the small intestine (duodenum, jejunum, and ileum) and large intestine (cecum and colon) of wild pigs to engage distinct metabolic spatial structures and pathways relative to one another. Overall, these results offer unique insights that would help to advance the current understanding of how the intestinal microbes interact with the host and affect the evolution of pigs.
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Affiliation(s)
- Guangli Yang
- Department of Biology and Food Sciences, Shangqiu Normal University, Shangqiu City, Henan Province, China
| | - Chuanxin Shi
- Department of Biology and Food Sciences, Shangqiu Normal University, Shangqiu City, Henan Province, China
| | - Shuhong Zhang
- Department of Biology and Food Sciences, Shangqiu Normal University, Shangqiu City, Henan Province, China
| | - Yan Liu
- College of Animal Husbandry Engineering, Henan Vocational College of Agricultural, Zhengzhou City, Henan Province, China
| | - Zhiqiang Li
- Department of Biology and Food Sciences, Shangqiu Normal University, Shangqiu City, Henan Province, China
| | - Fengyi Gao
- Department of Biology and Food Sciences, Shangqiu Normal University, Shangqiu City, Henan Province, China
| | - Yanyan Cui
- Department of Biology and Food Sciences, Shangqiu Normal University, Shangqiu City, Henan Province, China
| | - Yongfeng Yan
- Department of Biology and Food Sciences, Shangqiu Normal University, Shangqiu City, Henan Province, China
| | - Ming Li
- Engineering College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou City, Henan Province, China
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Segawa T, Fukuchi S, Bodington D, Tsuchida S, Mbehang Nguema PP, Mori H, Ushida K. Genomic Analyses of Bifidobacterium moukalabense Reveal Adaptations to Frugivore/Folivore Feeding Behavior. Microorganisms 2019; 7:microorganisms7040099. [PMID: 30987363 PMCID: PMC6518056 DOI: 10.3390/microorganisms7040099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 01/18/2023] Open
Abstract
Despite the essential role of Bifidobacterium in health-promoting gut bacteria in humans, little is known about their functions in wild animals, especially non-human primates. It is difficult to determine in vivo the function of Bifidobacterium in wild animals due to the limited accessibility of studying target animals in natural conditions. However, the genomic characteristics of Bifidobacterium obtained from the feces of wild animals can provide insight into their functionality in the gut. Here, we analyzed the whole genomes of 12 B. moukalabense strains isolated from seven feces samples of wild western lowland gorillas (Gorilla gorilla gorilla), three samples of wild central chimpanzees (Pan troglodytes troglodytes) and two samples of wild forest elephants (Loxodonta cyclotis) in Moukalaba-Doudou National Park, Gabon. In addition, we analyzed the fecal bacterial communities of six wild western lowland gorillas by meta 16S rRNA gene analyses with next generation sequencing. Although the abundance of the genus Bifidobacterium was as low as 0.2% in the total reads, a whole genome analysis of B. moukalabense suggested its contribution digestion of food and nutrition of frugivore/folivore animals. Specifically, the whole genome analysis indicated the involvement of B. moukalabense in hemicellulose degradation for short chain fatty acid production and nucleic acid utilization as nitrogen resources. In comparison with human-associated Bifidobacterium spp., genes for carbohydrate transport and metabolism are not conserved in these wild species. In particular the glycosidases, which are found in all 12 strains of B. moukalabense, were variably detected, or not detected, in human-associated species.
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Affiliation(s)
- Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan.
| | - Satoshi Fukuchi
- Faculty of Engineering, Maebashi Institute of Technology, Maebashi, Gunma 371-0816, Japan.
| | - Dylan Bodington
- Department of Biological Sciences, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
| | - Sayaka Tsuchida
- Chubu University Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan.
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.
| | | | - Hiroshi Mori
- Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.
| | - Kazunari Ushida
- Chubu University Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan.
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.
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10
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Okubo T, Yossapol M, Maruyama F, Wampande EM, Kakooza S, Ohya K, Tsuchida S, Asai T, Kabasa JD, Ushida K. Phenotypic and genotypic analyses of antimicrobial resistant bacteria in livestock in Uganda. Transbound Emerg Dis 2018; 66:317-326. [PMID: 30260584 DOI: 10.1111/tbed.13024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 09/03/2018] [Accepted: 09/13/2018] [Indexed: 12/11/2022]
Abstract
Antimicrobial resistant bacteria (ARB) in livestock are a global public health concern, not only because they prolong infectious diseases but also they can be transferred from animals to humans via the food chain. Here, we studied ARB in livestock at commercial and subsistence farms (n = 13) in Wakiso and Mpigi districts, Uganda. We enquired from the farmers about the type and the purpose of antimicrobial agents they have used to treat their livestock. After collecting faeces, we isolated antimicrobial resistant Escherichia coli from livestock faeces (n = 134) as an indicator bacterium. These strains showed resistance to ampicillin (44.8%), tetracycline (97.0%), and sulfamethoxazole-trimethoprim (56.7%). The frequency of ampicillin-resistance was significantly correlated with the usage of penicillins to livestock in the farms (p = 0.04). The metagenomics data detected 911 antimicrobial resistant genes that were classified into 16 categories. Genes for multidrug efflux pumps were the most prevalent category in all except in one sample. Interestingly, the genes encoding third-generation cephalosporins (blaCTX-M ), carbapenems (blaACT ), and colistin (arnA) were detected by metagenomics analysis although these phenotypes were not detected in our E. coli strains. Our results suggest that the emergence and transmission of cephalosporin, carbapenem, and/or colistin-resistant bacteria among livestock can occur in future if these antimicrobial agents are used.
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Affiliation(s)
- Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University Graduate School of Health Sciences, Sapporo, Hokkaido, Japan
| | - Montira Yossapol
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.,Office of Academic Affairs, Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham, Thailand
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Eddie M Wampande
- Department of Veterinary Pharmacy, Clinics and Comparative Medicine, School of Veterinary Medicine and Animal Resources, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Steven Kakooza
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Kenji Ohya
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.,Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
| | - Sayaka Tsuchida
- Graduate School of Life and Environmental Science, Kyoto Prefectural University, Kyoto, Japan
| | - Tetsuo Asai
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.,Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
| | - John D Kabasa
- Department of Pharmacy, Clinical and Comparative Medicine, School of Veterinary Medicine and Animal Resources, Makerere University, Kampala, Uganda
| | - Kazunari Ushida
- Graduate School of Life and Environmental Science, Kyoto Prefectural University, Kyoto, Japan.,Chubu University Academy of Emerging Sciences, Kasugai, Aichi, Japan
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