High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems

Meaden, Sean; Biswas, Ambarish; Arkhipova, Ksenia; Morales, Sergio E.; Dutilh, Bas E.; Westra, Edze R.; Fineran, Peter C.

doi:10.1101/2021.06.24.449667

Cited by 10 publications

(13 citation statements)

References 48 publications

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“…3B). This is in line with previous studies, which had shown that high CRISPR-Cas diversity is associated with anaerobic growth, high temperatures and non-host environments (13–15), all of which are characteristics of cheese environments.…”

Section: Resultssupporting

confidence: 93%

“…12/13). This is in line with previous results obtained for the Earth Microbiome Project (15) and supports the idea that spacers targeting highly abundant phages are under positive selection and thus dominant in the community (38). Notably, in our previous study focusing on a single cheese starter culture we had found the opposite pattern.…”

Section: Crispr Spacer Abundances Correlates With Target Abundancesupporting

confidence: 93%

“…Previous studies have used shotgun metagenomics to characterize CRISPR diversity in bacteria found on the human body, in the ocean or the soil (15, 24). Cheese-associated communities are much simpler than these previously analyzed communities (47, 48).…”

Section: Discussionmentioning

confidence: 99%

“…Various factors have been discussed to influence the distribution of defense systems across bacteria (12). Notably, the presence of CRISPR-Cas has been associated with environmental factors such as temperature, oxygen levels or phage abundance (13)(14)(15). Also, genetic incompatibilities of defense systems with other cellular functions, including other defense systems, have been reported (16,17).…”

Section: Introductionmentioning

confidence: 99%

“…Comparative genomics of closely related isolates combined with shotgun metagenomics provide excellent opportunities to assess the diversity of phage defense systems in natural bacterial communities and can help to advance our understanding of their evolutionary ecology (23). Two recent shotgun metagenomic studies have looked at CRISPR spacer diversity in microbial communities, one focusing on environmental samples from the Earth Microbiome Project (15) and another one focusing on diverse samples from the human microbiome (24). Meaden et al identified a positive association between CRISPR spacer and the abundance of the corresponding phage target sequences (protospacer), suggesting that there is a direct link between phage pressure and the maintenance of corresponding spacer sequences.…”

Section: Introductionmentioning

confidence: 99%

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Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities

Somerville

Schowing

Chabas

et al. 2022

Preprint

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Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2'778 bacterial genomes and 158 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments. We find that nearly identical strains of cheese-associated bacteria contain diverse and highly variable arsenals of innate and adaptive (i.e CRISPR-Cas) immunity suggesting rapid turnover of defense mechanisms in these communities. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, suggesting that CRISPR does not provide complete immunity against all phages, and that the innate immune mechanisms may have complementary roles. Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships.

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Section: Resultssupporting

confidence: 93%

Section: Crispr Spacer Abundances Correlates With Target Abundancesupporting

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities

Somerville

Schowing

Chabas

et al. 2022

Preprint

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Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam

et al. 2022

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Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin and epidemiology of these outbreaks, 20 N . seriolae strains collected from farms in four provinces in the South Central Coast region of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. PFGE identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and SNP genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no diversity within clades (0–5 SNPs). There was no association between geographical origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. The Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 220 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55 to 7.96 Mbp in size, have an average G+C content of 68.2 % and encode 7 602–7958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into the epidemiology and pathogenicity of N. seriolae and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.

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Long-term CRISPR array dynamics and stable host-virus co-existence in subsurface fractured shales

Amundson

Roux

Shelton

et al. 2023

Preprint

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Viruses are the most ubiquitous biological entities on earth. Even so, elucidating the impact of viruses on microbial communities and associated ecosystem processes often requires identification of strong host-virus linkages - an undeniable challenge in many ecosystems. Subsurface fractured shales present a unique opportunity to first make these strong linkages and subsequently reveal complex long-term host-virus dynamics and trends in CRISPR array size and frequency. Here, we sampled two replicated sets of fractured shale wells for nearly 800 days (Denver-Julesburg Basin, Colorado, USA). We identified a relatively diverse microbial community with widely encoded CRISPR viral defense systems, which facilitated 2,110 CRISPR-based viral linkages across 90 host MAGs representing 25 phyla. Leveraging these linkages with timeseries data across differing well ages, we observed how patterns of host-virus co-existence develop and converge in this closed ecosystem through time. We observed a transition to smaller CRISPR arrays in older, more established wells, potentially reflecting a natural progression where CRISPR arrays harbor fewer, yet more effective spacers that target viral genes with fewer mutations. Together, our findings shed light on the complexities of host-virus temporal dynamics as well as possible drivers of spacer loss and acquisition within CRISPR arrays of diverse microbial populations through time.

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High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems

Cited by 10 publications

References 48 publications

Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities

Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities

Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam

Long-term CRISPR array dynamics and stable host-virus co-existence in subsurface fractured shales

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