Decoding the intestinal microbiota repertoire of sow and weaned pigs using culturomic and metagenomic approaches
1
조회
0
다운로드
2
인용
0
참고문헌
키워드
초록
To elucidate the role and mechanism of microbes, we combined culture-dependent and culture- independent approaches to investigate differences in gut bacterial composition between sows and weaned pigs. Under anaerobic conditions, several nonselective and selective media were used for isolation from fecal samples. All isolated bacteria were identified and classified through 16S rRNA sequencing, and the microbiota composition of the fecal samples was analyzed by metagenomics using next generation sequencing (NGS) technology. A total of 278 and 149 colonies were acquired from the sow and weaned pig fecal samples, respectively. Culturomics analysis revealed that diverse bacterial genus and species belonged to Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were isolated from sow and weaned pigs. When comparing culture-dependent and culture-independent analyses, 191 bacterial species and 2 archaeal bacterial species were detected through culture-independent analysis, and a total of 23 bacteria were isolated through a culture-dependent approach, of which 65% were not detected by metagenomics. In conclusion, culturomics and metagenomics should be properly combined to fully understand the intestinal microbiota, and livestock-derived microbial resources should be informed by culturomic approaches to understand and utilize the mechanism of host-microbe interactions.
Abstract
To elucidate the role and mechanism of microbes, we combined culture-dependent and culture- independent approaches to investigate differences in gut bacterial composition between sows and weaned pigs. Under anaerobic conditions, several nonselective and selective media were used for isolation from fecal samples. All isolated bacteria were identified and classified through 16S rRNA sequencing, and the microbiota composition of the fecal samples was analyzed by metagenomics using next generation sequencing (NGS) technology. A total of 278 and 149 colonies were acquired from the sow and weaned pig fecal samples, respectively. Culturomics analysis revealed that diverse bacterial genus and species belonged to Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were isolated from sow and weaned pigs. When comparing culture-dependent and culture-independent analyses, 191 bacterial species and 2 archaeal bacterial species were detected through culture-independent analysis, and a total of 23 bacteria were isolated through a culture-dependent approach, of which 65% were not detected by metagenomics. In conclusion, culturomics and metagenomics should be properly combined to fully understand the intestinal microbiota, and livestock-derived microbial resources should be informed by culturomic approaches to understand and utilize the mechanism of host-microbe interactions.
참고문헌 (36)
- Junjie Qin, "A human gut microbial gene catalogue established by metagenomic sequencing", Nature, 464(7285), pp.59~65 (2010), Springer Science and Business Media LLC[DOI]
- Valentina Tremaroli, "Functional interactions between the gut microbiota and host metabolism", Nature, 489(7415), pp.242~249 (2012), Springer Science and Business Media LLC[DOI]
- Inna Sekirov, "Gut Microbiota in Health and Disease", Physiological Reviews, 90(3), pp.859~904 (2010), American Physiological Society[DOI]
- June L. Round, "The gut microbiota shapes intestinal immune responses during health and disease", Nature Reviews Immunology, 9(5), pp.313~323 (2009), Springer Science and Business Media LLC[DOI]
- Lora V. Hooper, "Interactions Between the Microbiota and the Immune System", Science, 336(6086), pp.1268~1273 (2012), American Association for the Advancement of Science (AAAS)[DOI]
- Jeremy K. Nicholson, "Host-Gut Microbiota Metabolic Interactions", Science, 336(6086), pp.1262~1267 (2012), American Association for the Advancement of Science (AAAS)[DOI]
- Chenhong Zhang, "Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice", The ISME Journal, 4(2), pp.232~241 (2010), Springer Science and Business Media LLC[DOI]
- Miriam Popkes, "Microbiota–host interactions shape ageing dynamics", Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1808), pp.20190596~ (2020), The Royal Society[DOI]
- Morgane Mailhe, "Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing", BMC Microbiology, 18(1), pp.157~ (2018), Springer Science and Business Media LLC[DOI]
- Jean-Christophe Lagier, "Culturing the human microbiota and culturomics", Nature Reviews Microbiology, 16(9), pp.540~550 (2018), Springer Science and Business Media LLC[DOI]
- Melhem Bilen, "The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species", Microbiome, 6(1), pp.94~ (2018), Springer Science and Business Media LLC[DOI]
- Hilary P. Browne, "Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation", Nature, 533(7604), pp.543~546 (2016), Springer Science and Business Media LLC[DOI]
- Ibrahim Hamad, "Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota", Scientific Reports, 7(1), pp.16788~ (2017), Springer Science and Business Media LLC[DOI]
- Ami Diakite, "Extensive culturomics of 8 healthy samples enhances metagenomics efficiency", PLOS ONE, 14(10), pp.e0223543~ (2019), Public Library of Science (PLoS)[DOI]
- Pamela Afouda, "Alcohol pretreatment of stools effect on culturomics", Scientific Reports, 10(1), pp.5190~ (2020), Springer Science and Business Media LLC[DOI]
- Paul E. Moote, "Application of culturomics to characterize diverse anaerobic bacteria from the gastrointestinal tract of broiler chickens in relation to environmental reservoirs", Canadian Journal of Microbiology, 66(4), pp.288~302 (2020), Canadian Science Publishing[DOI]
- Fenske GJ, "Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome", FEMS Microbiol Ecol, 96, pp.fiaa022~ (2020)[DOI]
- Joan K. Lunney, "Advances in Swine Biomedical Model Genomics", International Journal of Biological Sciences, 3, pp.179~184 (2007), Ivyspring International Publisher[DOI]
- Liang Xiao, "A reference gene catalogue of the pig gut microbiome", Nature Microbiology, 1(12), pp.1616~ (2016), Springer Science and Business Media LLC[DOI]
- Narjis Kraimi, "Influence of the microbiota-gut-brain axis on behavior and welfare in farm animals: A review", Physiology & Behavior, 210, pp.112658~ (2019), Elsevier BV[DOI]
- Nassima Rabhi, "Association Between Tail-Biting and Intestinal Microbiota Composition in Pigs", Frontiers in Veterinary Science, 7, pp.563762~ (2020), Frontiers Media SA[DOI]
- Congying Chen, "Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome", Nature Communications, 12(1), pp.1106~ (2021), Springer Science and Business Media LLC[DOI]
- Paul E. Moote, "Comparison of Strategies for Isolating Anaerobic Bacteria from the Porcine Intestine", Applied and Environmental Microbiology, 87(9), pp.e00088~21 (2021), American Society for Microbiology[DOI]
- Mincheol Kim, "Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes", International Journal of Systematic and Evolutionary Microbiology, 64(Pt_2), pp.346~351 (2014), Microbiology Society[DOI]
- V.D.V. Valeriano, "Probiotic roles ofLactobacillussp. in swine: insights from gut microbiota", Journal of Applied Microbiology, 122(3), pp.554~567 (2017), Wiley[DOI]
- Jianping Quan, "Metagenomic Characterization of Intestinal Regions in Pigs With Contrasting Feed Efficiency", Frontiers in Microbiology, 11, pp.32~ (2020), Frontiers Media SA[DOI]
- Sophie Amrane, "Metagenomic and culturomic analysis of gut microbiota dysbiosis during Clostridium difficile infection", Scientific Reports, 9(1), pp.12807~ (2019), Springer Science and Business Media LLC[DOI]
- Qing Niu, "Characteristics of Gut Microbiota in Sows and Their Relationship with Apparent Nutrient Digestibility", International Journal of Molecular Sciences, 20(4), pp.870~ (2019), MDPI AG[DOI]
- Y.J. Ji, "Stages of pregnancy and weaning influence the gut microbiota diversity and function in sows", Journal of Applied Microbiology, 127(3), pp.867~879 (2019), Wiley[DOI]
- G. E. Felis, "Reclassification of Pediococcus urinaeequi (ex Mees 1934) Garvie 1988 as Aerococcus urinaeequi comb. nov.", INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 55(3), pp.1325~1327 (2005), Microbiology Society[DOI]
- 성호선, "Purification and Characterization of an Antibacterial Substance from Aerococcus urinaeequi Strain HS36", Journal of Microbiology and Biotechnology, 30(1), pp.93~100 (2020), 한국미생물·생명공학회
- Nadeem O. Kaakoush, "Insights into the Role of Erysipelotrichaceae in the Human Host", Frontiers in Cellular and Infection Microbiology, 5, pp.84~ (2015), Frontiers Media SA[DOI]
- Tereza Kubasova, "Effects of host genetics and environmental conditions on fecal microbiota composition of pigs", PLOS ONE, 13(8), pp.e0201901~ (2018), Public Library of Science (PLoS)[DOI]
- Jinyuan Wu, "Isolation and genomic characterization of five novel strains of Erysipelotrichaceae from commercial pigs", BMC Microbiology, 21(1), pp.125~ (2021), Springer Science and Business Media LLC[DOI]
- Jean-Christophe Lagier, "Culture of previously uncultured members of the human gut microbiota by culturomics", Nature Microbiology, 1(12), pp.16203~ (2016), Springer Science and Business Media LLC[DOI]
- Ito T, "Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria", Gut Microbes, 10, pp.77~91 (2019)[DOI]