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Volume 74, Issue 1

Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken Open Access

Abstract

Eight anaerobic strains obtained from crop, jejunum and ileum of chicken were isolated, characterized and genome analysed to observe their metabolic profiles, adaptive strategies and to serve as novel future references. The novel species sp. nov. (DSM 113870=LMG 32876), sp. nov. (DSM 113833=LMG 32623), sp. nov. (DSM 113849=LMG 32671), sp. nov. (DSM 115077=LMG 32877), sp. nov. (DSM 113835=LMG 32625), sp. nov. (DSM 114195=LMG 32875) and (DSM 115076=LMG 32878) are found in the upper gastrointestinal tract and present consistent adaptations that enable us to predict their ecological role. Molecular characterization using 16S rRNA gene analysis and long-read whole genome sequencing, confirmed the description of the novel genus gen. nov. with gen. nov. sp. nov. (DSM 113860=LMG 32675) as genus type species. After phylogenetic and taxonomic analysis, we recommend the reclassification of the species and to the genus . Exploration of the microbiome from crop and small intestine of chicken expands our knowledge on the taxonomic diversity and adaptive functions of the inhabiting bacteria. The novel species identified in this project are part of a wider cultivation effort that represents the first repository of bacteria obtained from the crop and small intestine of chicken using culturomics, improving the potential handling of chicken microorganisms with biotechnological applications.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): chicken , crop , culture collection , ileum , jejunum , Lactobacillaceae , microbiome and novel taxa
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2024-01-17
2024-05-11
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References

  1. Rios-Galicia B, Sáenz JS, Yergaliyev T, Roth C, Camarinha-Silva A et al.Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken Figshare 2024 [View Article]
     [Google Scholar]
  2. Witzig M, Camarinha-Silva A, Green-Engert R, Hoelzle K, Zeller E et al. Spatial variation of the gut microbiota in broiler chickens as affected by dietary available phosphorus and assessed by T-RFLP analysis and 454 pyrosequencing. PLoS One 2015; 10:e0143442 [View Article] [PubMed]
     [Google Scholar]
  3. Xiao Y, Xiang Y, Zhou W, Chen J, Li K et al. Microbial community mapping in intestinal tract of broiler chicken. Poult Sci 2017; 96:1387–1393 [View Article] [PubMed]
     [Google Scholar]
  4. Borda-Molina D, Seifert J, Camarinha-Silva A. Current perspectives of the chicken gastrointestinal tract and its microbiome. Comput Struct Biotechnol J 2018; 16:131–139 [View Article] [PubMed]
     [Google Scholar]
  5. Glendinning L, Stewart RD, Pallen MJ, Watson KA, Watson M. Assembly of hundreds of novel bacterial genomes from the chicken caecum. Genome Biol 2020; 21:34 [View Article] [PubMed]
     [Google Scholar]
  6. Gong J, Si W, Forster RJ, Huang R, Yu H et al. 16S rRNA gene-based analysis of mucosa-associated bacterial community and phylogeny in the chicken gastrointestinal tracts: from crops to ceca. FEMS Microbiol Ecol 2007; 59:147–157 [View Article] [PubMed]
     [Google Scholar]
  7. Kers JG, Velkers FC, Fischer EAJ, Hermes GDA, Lamot DM et al. Take care of the environment: housing conditions affect the interplay of nutritional interventions and intestinal microbiota in broiler chickens. Anim Microbiome 2019; 1:10 [View Article] [PubMed]
     [Google Scholar]
  8. Videnska P, Sedlar K, Lukac M, Faldynova M, Gerzova L et al. Succession and replacement of bacterial populations in the caecum of egg laying hens over their whole life. PLoS One 2014; 9:e115142 [View Article] [PubMed]
     [Google Scholar]
  9. Feng Y, Wang Y, Zhu B, Gao GF, Guo Y et al. Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes. Commun Biol 2021; 4:1305 [View Article] [PubMed]
     [Google Scholar]
  10. Künzel S, Borda-Molina D, Zuber T, Hartung J, Siegert W et al. Relative phytase efficacy values as affected by response traits, including ileal microbiota composition. Poult Sci 2021; 100:101133 [View Article] [PubMed]
     [Google Scholar]
  11. Classen HL, Apajalahti J, Svihus B, Choct M. The role of the crop in poultry production. Worlds Poult Sci J 2016; 72:459–472 [View Article]
     [Google Scholar]
  12. Glendinning L, Watson KA, Watson M. Development of the duodenal, ileal, jejunal and caecal microbiota in chickens. Anim Microbiome 2019; 1:17 [View Article] [PubMed]
     [Google Scholar]
  13. Gilroy R, Ravi A, Getino M, Pursley I, Horton DL et al. Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ 2021; 9: [View Article] [PubMed]
     [Google Scholar]
  14. Medvecky M, Cejkova D, Polansky O, Karasova D, Kubasova T et al. Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures. BMC Genomics 2018; 19:561 [View Article] [PubMed]
     [Google Scholar]
  15. Crhanova M, Karasova D, Juricova H, Matiasovicova J, Jahodarova E et al. Systematic culturomics shows that half of chicken caecal microbiota members can be grown in vitro except for two lineages of Clostridiales and a single lineage of Bacteroidetes. Microorganisms 2019; 7:11 [View Article] [PubMed]
     [Google Scholar]
  16. Zenner C, Hitch TCA, Riedel T, Wortmann E, Tiede S et al. Early-life immune system maturation in chickens using a synthetic community of cultured gut bacteria. mSystems 2021; 6:e01300-20 [View Article] [PubMed]
     [Google Scholar]
  17. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK et al. Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A 2003; 100:4678–4683 [View Article] [PubMed]
     [Google Scholar]
  18. Tanaka T, Kawasaki K, Daimon S, Kitagawa W, Yamamoto K et al. A hidden pitfall in the preparation of agar media undermines microorganism cultivability. Appl Environ Microbiol 2014; 80:7659–7666 [View Article] [PubMed]
     [Google Scholar]
  19. Einarsson H, Snygg BG, Eriksson C. Inhibition of bacterial growth by Maillard reaction products. J Agric Food Chem 1983; 31:1043–1047 [View Article]
     [Google Scholar]
  20. Ulrich RL, Hughes TA. A rapid procedure for isolating chromosomal DNA from Lactobacillus species and other gram-positive bacteria. Lett Appl Microbiol 2008; 32:52–56 [View Article]
     [Google Scholar]
  21. Relman DA. Universal bacterial 16S rRNA amplification and sequencing. Diag Mol Microbiol 1993489–495
     [Google Scholar]
  22. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article] [PubMed]
     [Google Scholar]
  23. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article] [PubMed]
     [Google Scholar]
  24. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 2019; 47:W256–W259 [View Article] [PubMed]
     [Google Scholar]
  25. Bushnell B, Rood J, Singer E. BBMerge - accurate paired shotgun read merging via overlap. PLoS One 2017; 12:e0185056 [View Article] [PubMed]
     [Google Scholar]
  26. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  27. Wick RR, Judd LM, Cerdeira LT, Hawkey J, Méric G et al. Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biol 2021; 22:266 [View Article] [PubMed]
     [Google Scholar]
  28. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  29. Zhou Z, Tran PQ, Breister AM, Liu Y, Kieft K et al. METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome 2022; 10:33 [View Article] [PubMed]
     [Google Scholar]
  30. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH, Hancock J. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
     [Google Scholar]
  31. Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE et al. Community-led, integrated, reproducible multi-omics with anvi’o. Nat Microbiol 2021; 6:3–6 [View Article] [PubMed]
     [Google Scholar]
  32. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  33. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
     [Google Scholar]
  34. Ludwig W, Viver T, Westram R, Francisco Gago J, Bustos-Caparros E et al. Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains. Syst Appl Microbiol 2021; 44:126218 [View Article] [PubMed]
     [Google Scholar]
  35. Soriano S, Soriano A. Nueva bacteria anaerobia productora de una alteracion en sordinas envasadas. Rev Asoc Argent Dietol 1948; 6:36–41
     [Google Scholar]
  36. Afanzar O, Di Paolo D, Eisenstein M, Levi K, Plochowietz A et al. The switching mechanism of the bacterial rotary motor combines tight regulation with inherent flexibility. EMBO J 2021; 40:e104683 [View Article] [PubMed]
     [Google Scholar]
  37. Lagier J-C, Bibi F, Ramasamy D, Azhar EI, Robert C et al. Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov. Stand Genomic Sci 2014; 9:1003–1019 [View Article] [PubMed]
     [Google Scholar]
  38. Borda-Molina D, Vital M, Sommerfeld V, Rodehutscord M, Camarinha-Silva A. Insights into broilers’ gut microbiota fed with phosphorus, calcium, and phytase supplemented diets. Front Microbiol 2016; 7:2033 [View Article] [PubMed]
     [Google Scholar]
  39. Rehman HU, Vahjen W, Awad WA, Zentek J. Indigenous bacteria and bacterial metabolic products in the gastrointestinal tract of broiler chickens. Arch Anim Nutr 2007; 61:319–335 [View Article] [PubMed]
     [Google Scholar]
  40. Stanley D, Geier MS, Hughes RJ, Denman SE, Moore RJ. Highly variable microbiota development in the chicken gastrointestinal tract. PLoS One 2013; 8:e84290 [View Article] [PubMed]
     [Google Scholar]
  41. Denoncourt A, Downey M. Model systems for studying polyphosphate biology: a focus on microorganisms. Curr Genet 2021; 67:331–346 [View Article] [PubMed]
     [Google Scholar]
  42. Riesenfeld G, Sklan D, Bar A, Eisner U, Hurwitz S. Glucose absorption and starch digestion in the intestine of the chicken. J Nutr 1980; 110:117–121 [View Article] [PubMed]
     [Google Scholar]
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Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken
Int J Syst Evol Microbiol 74, 006210 (2024); https://doi.org/10.1099/ijsem.0.006210
/content/journal/ijsem/10.1099/ijsem.0.006210
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