Bdellovibrio and Like Organisms Are Predictors of Microbiome Diversity in Distinct Host Groups
Biodiversity is generally believed to be a main determinant of ecosystem functioning. This principle also applies to the microbiome and could consequently contribute to host health. According to ecological theory, communities are shaped by top predators whose direct and indirect interactions with community members cause stability and diversity. Bdellovibrio and like organisms (BALOs) are a neglected group of predatory bacteria that feed on Gram-negative bacteria and can thereby influence microbiome composition. We asked whether BALOs can predict biodiversity levels in microbiomes from distinct host groups and environments. We demonstrate that genetic signatures of BALOs are commonly found within the 16S rRNA reads from diverse host taxa. In many cases, their presence, abundance, and especially richness are positively correlated with overall microbiome diversity. Our findings suggest that BALOs can act as drivers of microbial alpha-diversity and should therefore be considered candidates for the restoration of microbiomes and the prevention of dysbiosis.
KeywordsBiodiversity Predator Prey Microbiome Bdellovibrio
We are grateful for advice from members of the Schulenburg group and the Collaborative Research Center CRC1182 on Origin and Function of Metaorganisms.
This work was funded by the CRC1182, projects A4 and B2.
Compliance with Ethical Standards
Conflict of Interest
The authors declare that they have no conflict of interest.
The nucleotide sequence data reported are available in the EMBL databases under the accession number PRJEB30476.
- 7.Holling CS (1973) Resilience and stability of ecological systems. Annu Rev Ecol Syst 4:1–23. https://doi.org/10.1146/annurev.es.04.110173.000245 CrossRefGoogle Scholar
- 13.Sockett RE (2009) Predatory lifestyle of Bdellovibrio bacteriovorus. Annu Rev Microbiol 63:523–539. https://doi.org/10.1146/annurev.micro.091208.073346 CrossRefGoogle Scholar
- 15.Iebba V, Santangelo F, Totino V, Nicoletti M, Gagliardi A, de Biase RV, Cucchiara S, Nencioni L, Conte MP, Schippa S (2013) Higher prevalence and abundance of Bdellovibrio bacteriovorus in the human gut of healthy subjects. PLoS One 8:e61608. https://doi.org/10.1371/journal.pone.0061608 CrossRefGoogle Scholar
- 16.Negus D, Moore C, Baker M, Raghunathan D, Tyson J, Sockett RE (2017) Predator versus pathogen: how does predatory Bdellovibrio bacteriovorus interface with the challenges of killing Gram-negative pathogens in a host setting? Annu Rev Microbiol 71:441–457. https://doi.org/10.1146/annurev-micro-090816-093618 CrossRefGoogle Scholar
- 19.Thomas T, Moitinho-Silva L, Lurgi M, Björk JR, Easson C, Astudillo-García C, Olson JB, Erwin PM, López-Legentil S, Luter H, Chaves-Fonnegra A, Costa R, Schupp PJ, Steindler L, Erpenbeck D, Gilbert J, Knight R, Ackermann G, Victor Lopez J, Taylor MW, Thacker RW, Montoya JM, Hentschel U, Webster NS (2016) Diversity, structure and convergent evolution of the global sponge microbiome. Nat Commun 7:11870. https://doi.org/10.1038/ncomms11870 CrossRefGoogle Scholar
- 22.Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R (2013) Cohabiting family members share microbiota with one another and with their dogs. eLife 2:e00458. https://doi.org/10.7554/eLife.00458 CrossRefGoogle Scholar
- 23.Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vazquez-Baeza Y, van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA (2014) Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 345:1048–1052. https://doi.org/10.1126/science.1254529 CrossRefGoogle Scholar
- 25.Zhang H, John R, Peng Z, Yuan J, Chu C, du G, Zhou S (2012) The relationship between species richness and evenness in plant communities along a successional gradient: a study from sub-alpine meadows of the eastern Qinghai-Tibetan plateau, China. PLoS One 7:e49024. https://doi.org/10.1371/journal.pone.0049024 CrossRefGoogle Scholar