1887

Abstract

Two novel members of the bacterial phylum ‘’, strains CAG34 and CV41, were isolated from the guts of and ants, respectively. Strains CAG34 and CV41 were coccoid, Gram-stain-negative, non-motile, and formed cream-coloured colonies on trypticase soy agar. Optimum growth occurred under an atmosphere of 12–20 % O and 1 % CO for both strains, although strain CV41 could not grow without supplemental CO. Growth was possible under NaCl concentrations of 0.5–1.5 % (w/v) and temperatures of 23–37 °C for both strains, and pH values of 6.9–7.7 for strain CAG34 and 6.9–7.3 for strain CV41. The G+C content of the genomic DNA was 60.7 mol% for strain CAG34 and 60.5 mol% for strain CV41. The major fatty acids for both strains were anteiso-C, iso-C, C, and C 5. Based on the phylogenetic analysis of 16S rRNA gene sequences, the closest cultivated relative for both strains was the type strain of (91.8 % similarity). Hence, strains CAG34 and CV41 are considered to represent a new genus within the ‘ family , for which we propose the name gen. nov. Given that strains CAG34 and CV41 share 97.7 % 16S rRNA gene sequence similarity with each other and are physiologically distinct, we propose to classify the isolates as representing two novel species, sp. nov. for strain CAG34 (=NCIMB 15004 =ATCC TSD-38) and sp. nov. for strain CV41 (=NCIMB 15005 =ATCC TSD-39 =DSM 100879).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001141
2016-08-01
2021-10-27
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/8/3034.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001141&mimeType=html&fmt=ahah

References

  1. Anderson K. E., Russell J. A., Moreau C. S., Kautz S., Sullam K. E., Hu Y., Basinger U., Mott B. M., Buck N. et al. 2012; Highly similar microbial communities are shared among related and trophically similar ant species. Mol Ecol 21:2282–2296 [View Article][PubMed]
    [Google Scholar]
  2. Baker G. C., Smith J. J., Cowan D. A. 2003; Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55:541–555[PubMed] [CrossRef]
    [Google Scholar]
  3. Bergmann G. T., Bates S. T., Eilers K. G., Lauber C. L., Caporaso J. G., Walters W. A., Knight R., Fierer N. 2011; The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem 43:1450–1455 [View Article][PubMed]
    [Google Scholar]
  4. Bolger A. M., Lohse M., Usadel B. 2014; Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120 [View Article][PubMed]
    [Google Scholar]
  5. Breznak J. A., Costilow R. N. 2007; Physicochemical factors in growth. In Methods Gen Mol Microbiol, 3rd edn. pp. 309–329 Edited by Marzluf G. A., Reddy C. A., Beveridge T. J., Schmidt T. M., Snyder L. R., Breznak. J. A. American Society of Microbiology;
    [Google Scholar]
  6. Chin K. J., Liesack W., Janssen P. H. 2001; Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division 'Verrucomicrobia' isolated from rice paddy soil. Int J Syst Evol Microbiol 51:1965–1968 [View Article][PubMed]
    [Google Scholar]
  7. Choo Y. J., Lee K., Song J., Cho J. C. 2007; Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ‘Verrucomicrobia'. Int J Syst Evol Microbiol 57:532–537 [View Article][PubMed]
    [Google Scholar]
  8. Dereeper A., Guignon V., Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J. F., Guindon S., Lefort V. et al. 2008; Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36:W465–W469 [View Article][PubMed]
    [Google Scholar]
  9. Derrien M., Vaughan E. E., Plugge C. M., de Vos W. M. 2004; Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol 54:1469–1476 [View Article][PubMed]
    [Google Scholar]
  10. Dillon R. J., Dillon V. M. 2004; The gut bacteria of insects: nonpathogenic interactions. Annu Rev Entomol 49:71–92 [View Article][PubMed]
    [Google Scholar]
  11. Fierer N., Ladau J., Clemente J. C., Leff J. W., Owens S. M., Pollard K. S., Knight R., Gilbert J. A., McCulley R. L. 2013; Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 342:621–624 [View Article][PubMed]
    [Google Scholar]
  12. Freitas S., Hatosy S., Fuhrman J. A., Huse S. M., Welch D. B., Sogin M. L., Martiny A. C., Mark Welch D. B. 2012; Global distribution and diversity of marine Verrucomicrobia . ISME J 6:1499–1505 [View Article][PubMed]
    [Google Scholar]
  13. Guindon S., Lethiec F., Duroux P., Gascuel O. 2005; PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33:W557–W559 [View Article][PubMed]
    [Google Scholar]
  14. Hedlund B. P., Gosink J. J., Staley J. T. 1997; Verrucomicrobia div. nov., a new division of the bacteria containing three new species of Prosthecobacter . Antonie Van Leeuwenhoek 72:29–38[PubMed] [CrossRef]
    [Google Scholar]
  15. Hedlund B. P. 2010; Phylum XXIII. Verrucomicrobia phyl. nov. In Bergey’s Manual Syst Bacteriol pp. 795–841 Edited by Krieg N. R., Staley J. T., Brown D. R., Hedlund B. P., Paster B. J., Ward N. L., Ludwig W., Whitman W. B. New York: Springer;
    [Google Scholar]
  16. Hu Y., Łukasik P., Moreau C. S., Russell J. A. 2014; Correlates of gut community composition across an ant species (Cephalotes varians) elucidate causes and consequences of symbiotic variability. Mol Ecol 23:1284–1300 [View Article][PubMed]
    [Google Scholar]
  17. Hugenholtz P., Goebel B. M., Pace N. R. 1998; Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774[PubMed]
    [Google Scholar]
  18. Kautz S., Rubin B. E., Russell J. A., Moreau C. S. 2013; Surveying the microbiome of ants: comparing 454 pyrosequencing with traditional methods to uncover bacterial diversity. Appl Environ Microbiol 79:525–534 [View Article][PubMed]
    [Google Scholar]
  19. Kim M., Oh H. S., Park S. C., Chun J. 2014; Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351 [View Article][PubMed]
    [Google Scholar]
  20. Lanan M. C., Rodrigues P. A., Agellon A., Jansma P., Wheeler D. E. 2016; A bacterial filter protects and structures the gut microbiome of an insect. ISME J doi:10.1038/ismej.2015.264 [View Article][PubMed]
    [Google Scholar]
  21. Lee S. Y., Bollinger J., Bezdicek D., Ogram A. 1996; Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method. Appl Environ Microbiol 62:3787–3793[PubMed]
    [Google Scholar]
  22. Matson E., Ottesen E., Leadbetter J. 2007; Extracting DNA from the gut microbes of the termite (Zootermopsis nevadensis). J Vis Exp 4:e195
    [Google Scholar]
  23. O'Farrell K. A., Janssen P. H. 1999; Detection of Verrucomicrobia in a pasture soil by PCR-mediated amplification of 16S rRNA genes. Appl Environ Microbiol 65:4280–4284[PubMed]
    [Google Scholar]
  24. Pruesse E., Peplies J., Glöckner F. O. 2012; SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823–1829 [View Article][PubMed]
    [Google Scholar]
  25. Rodrigues J. L. M., Isanapong J. 2014; The family Opitutaceae . In The Prokaryotes pp. 751–756 Edited by Rosenberg E., DeLong E. F., Lory S., Stackebrandt E., Thompson F. Berlin Heidelberg: Springer;
    [Google Scholar]
  26. Russell J. A., Moreau C. S., Goldman-Huertas B., Fujiwara M., Lohman D. J., Pierce N. E. 2009; Bacterial gut symbionts are tightly linked with the evolution of herbivory in ants. Proc Natl Acad Sci USA 106:21236–21241 [View Article][PubMed]
    [Google Scholar]
  27. Sanders J. G., Powell S., Kronauer D. J., Vasconcelos H. L., Frederickson M. E., Pierce N. E. 2014; Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes. Mol Ecol 23:1268–1283 [View Article][PubMed]
    [Google Scholar]
  28. Scheuermayer M., Gulder T. A., Bringmann G., Hentschel U. 2006; Rubritalea marina gen. nov., sp. nov., a marine representative of the phylum ‘Verrucomicrobia', isolated from a sponge (Porifera). Int J Syst Evol Microbiol 56:2119–2124 [View Article][PubMed]
    [Google Scholar]
  29. Tremaroli V., Bäckhed F. 2012; Functional interactions between the gut microbiota and host metabolism. Nature 489:242–249 [View Article][PubMed]
    [Google Scholar]
  30. Van Passel M. W., Kant R., Palva A., Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Pitluck S., Goltsman E. et al. 2011; Genome sequence of the verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems. J Bacteriol 193:2367–2368 [View Article][PubMed]
    [Google Scholar]
  31. Vandekerckhove T. T., Willems A., Gillis M., Coomans A. 2000; Occurrence of novel verrucomicrobial species, endosymbiotic and associated with parthenogenesis in Xiphinema americanum-group species (Nematoda, Longidoridae). Int J Syst Evol Microbiol 50:2197–2205 [View Article][PubMed]
    [Google Scholar]
  32. Wertz J. T., Breznak J. A. 2007; Physiological ecology of Stenoxybacter acetivorans, an obligate microaerophile in termite guts. Appl Environ Microbiol 73:6829–6841 [View Article][PubMed]
    [Google Scholar]
  33. Wertz J. T., Kim E., Breznak J. A., Schmidt T. M., Rodrigues J. L. 2012; Genomic and physiological characterization of the Verrucomicrobia isolate Diplosphaera colitermitum gen. nov., sp. nov., reveals microaerophily and nitrogen fixation genes. Appl Environ Microbiol 78:1544–1555 [View Article][PubMed]
    [Google Scholar]
  34. Yoon J., Yasumoto–Hirose M., Katsuta A., Sekiguchi H., Matsuda S., Kasai H., Yokota A. 2007a; Coraliomargarita akajimensis gen. nov., sp. nov., a novel memberof the phylum ‘Verrucomicrobia’ isolated from seawater in Japan. Int J Syst Evol Microbiol 57:959–963 [CrossRef]
    [Google Scholar]
  35. Yoon J., Yasumoto-Hirose M., Matsuo Y., Nozawa M., Matsuda S., Kasai H., Yokota A. 2007b; Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum 'Verrucomicrobia', isolated from seawater by in situ cultivation. Int J Syst Evol Microbiol 57:1377–1385 [CrossRef]
    [Google Scholar]
  36. Yoon J., Oku N., Matsuda S., Kasai H., Yokota A. 2007c; Pelagicoccus croceus sp. nov., a novel marine member of the family Puniceicoccaceae within the phylum ‘Verrucomicrobia' isolated from seagrass. Int J Syst Evol Microbiol 57:2874–2880 [CrossRef]
    [Google Scholar]
  37. Yoon J. 2011; Phylogenetic studies on the bacterial phylum ‘Verrucomicrobia . Microbiol Cult Coll 27:61–65
    [Google Scholar]
  38. Zerbino D. R., Birney E. 2008; Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001141
Loading
/content/journal/ijsem/10.1099/ijsem.0.001141
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error