FEMS microbiology ecology最新文献

Commensal microbes play important roles in modulating host health through varied mechanisms. Enterococcus faecalis, a Gram-positive commensal bacterium found across a wide range of hosts, has the potential to benefit its host through probiotic, antimicrobial and detoxification properties. However, it can also cause adverse effects, disrupting the host's healthy microbial communities and responses to co-stressors. Its context-dependent impact on the health of the agriculturally important pollinator - Apis mellifera - has been sparsely explored. Here, we examined the effects on honey bee brood survivorship and development when exposed at different concentrations and when co-exposed with chemical stressors (acetamiprid, thymol, glyphosate, and a mixture of the three). We found high doses of E. faecalis significantly reduced larval survivorship and size of brood at multiple developmental stages. Conversely, we found that low doses of E. faecalis increased larval size when individuals were co-exposed to the pesticide mixture. We also found that glyphosate alone and the pesticide mixture reduced the mass of brown-eyed pupae. These results are the first to show the dual role of E. faecalis in honey bee health is dependent on the concentration of the microbe and the co-stressors that brood are exposed to.

Plastics in the world's oceans are exposed to diverse environmental stressors that accelerate fragmentation and the leaching of associated additives. The impact of potentially toxic plastic degradation products and additives on marine microorganisms remains poorly understood. We assessed the impact of plastic leachate on marine microbial communities in vitro by exposure to one of four plastic leachates [from linear low-density polyethylene (LLPDE), polyamide-6 (or polycaprolactam; PA6), polyethylene terephthalate (PET), and polylactic acid (PLA)], prepared by immersing plastics in artificial seawater salts broth for three months at 80°C. Microbial communities were then exposed to different leachates. PLA-leachate-exposed communities differed significantly in composition from other plastic-leachate-exposed communities (PERMANOVA, P=0.001) as assessed by 16S rRNA gene and ITS region amplicon sequencing. Communities exposed to PLA leachate contained a higher proportion of Proteobacteria, specifically Halomonas spp. Greater relative abundances of Psathyrellaceae fungi also distinguished PLA-leachate communities. Despite significant differences in the structure of communities exposed to PLA leachate, we found no difference in the relative abundances of differentially expressed gene transcripts associated with known plastic degradation genes. While biodegradable plastics persist for shorter times in the environment than traditional plastics, our study indicates the potential for these plastic types to impact marine microbial communities.

Tick microbiota influences Borrelia colonization, but changes in the microbiota-derived metabolite and how this affects tick physiology and vector competence is unclear. We investigated whether microbiota-induced metabolite modifications influence tick physiology and pathogen transmission. Using an antimicrobiota vaccine (live Escherichia coli) to immunize mice, we generated host antibodies that modulated the tick microbiome, decreasing bacterial abundance and increasing lysine levels in ticks. Elevated lysine correlated with increased tick weight. Lysine supplementation experiments enhanced defensin expression with DefMT6 exhibiting anti-Borrelia activity, reducing pathogen load in ticks. Our findings demonstrate that antimicrobiota vaccines induce metabolite changes, affecting tick physiology, immunity, and vector competence. These insights open new avenues for developing microbiota-targeted strategies to control tick-borne diseases.

Ticks, particularly Ixodes ricinus, and the associated Lyme borreliosis risk, represent key concerns within the One Health framework, prompting extensive research in this field. However, comprehensive studies that jointly consider landscape characteristics, local forest structure and management, climate, and host community composition-alongside direct measures of tick density and infection status with Borrelia spp., the bacterial agents causing Lyme borreliosis, are scarce. In this study, we test the hypothesis that habitat diversity exerts a dilution effect, primarily by supporting greater diversity of mammal hosts. Therefore, we examined I. ricinus tick density and Borrelia spp. prevalence in relation to a comprehensive set of habitat and host-related variables. Ticks were collected using the flagging method and mammal hosts were monitored using an innovative camera-trapping approach across 25 forest plots along a land-use gradient within the Schwäbische Alb exploratory in Germany. Both tick density and Borrelia spp. prevalence are influenced by a complex combination of habitat factors across different spatial scales, as well as the mammal host community composition. Overall, our results provide novel support to the dilution effect hypothesis, suggesting that greater habitat and host diversity contribute to a reduced Lyme borreliosis risk in this region.

Most equipment used in aquaculture farms is made of plastic. Plastics-associated biofilms may contain potential human pathogenic bacteria (PHPB) and antibiotic-resistant bacteria (ARB). Understanding the influence of farming practices on the biofouling development and composition is thus essential to control associated microbiological risks. We combined results from metabarcoding analyses, bacterial cultures, and antibiotic susceptibility testing to compare the bacterial pathobiome and resistome associated with plastic aquaculture equipment, including two polyamide nets and a polyester liner, with those associated to a hemp net and a glass control. Over the 3 months of incubation in an aquaculture farm, plastics exhibited neither higher levels of PHPB nor more multiple antibiotic resistance compared to other solid substrates, but they did present specific PHPB and ARB profiles. Bacterial members of the Vibrionaceae and Staphylococcaceae families were more abundant in plastic PHPB communities (respectively 47% and 22% of PHPB reads) than in other substrate ones (4% and 0.22% of PHPB reads). The plastic-associated antibiotic resistance profiles showed higher resistance against quinolones. These results suggest that aquaculture equipment could act as a reservoir for some PHPB and ARB, and that equipment composition and immersion time could be levers to control associated sanitary risks.

Depuration, or the process of clearing impurities from the gut, is commonly applied to marine food products due to its efficacy in removing human pathogens from shellfish and edible ascidians. Recent studies also reported that depuration of filter-feeding animals helped reduce transient bacteria and identify resident symbionts in gut microbiome studies. Here, we examined the impact of depuration on bacteria in the branchial sac, gut, and hepatic gland of the solitary ascidian Pyura vittata. Replicates were kept in filtered seawater for 4 days prior to dissection (aquaria-depuration) and compared to samples that were immediately processed following collection (wild-no depuration) and replicates kept in unfiltered seawater for 4 days (aquaria-control). 16S rRNA gene sequence analysis revealed no significant differences among ascidian sources for microbial alpha-diversity but significant shifts in beta-diversity. Depuration reduced the number of core bacteria markedly (66%-84%) across all body regions, and bacteria that remained postdepuration consisted of genera associated with enhanced host health and resilience within other marine symbioses. Our results suggest that microbial profiles obtained following depuration do not substantially differ from those of nondepurated animals, but depuration can help differentiate transient from core and resident taxa in complex host-microbiome symbioses.

Glycans are crucial for infant gut microbiota development. Human milk contains prebiotic human milk oligosaccharides (HMOs) that stimulate gut microbes. Simultaneously, the glycan-rich mucus layer develops and attracts mucin glycan-degrading bacteria. As HMOs and mucin are degraded by homologous enzymes, bacterial glycan-degrading abilities overlap. However, less is known about how infant gut microbial communities form when both types of glycans are available. To study this, we created a synthetic community with specialist glycan degraders and cross-feeders from the infant gut (BabyBac). We evaluated it in different in vitro conditions including combinations of diet-derived [HMOs, galactooligosaccharides (GOS), and fructooligosaccharides (FOS)] and mucus glycans. Glycan combinations significantly affected the community composition and metabolic output. The glycan type affected the overall community, with mucin and HMOs being the top drivers of variation. HMOs favoured glycan degraders and cross-feeders, whereas mucin glycan degrader Akkermansia muciniphila was outcompeted. Conversely, when mucin was present, A. muciniphila thrived. Addition of mucin monomers and 2'-FL to GOS/FOS did not reinstate A. muciniphila abundance. This suggests that A. muciniphila cannot compete with infant-related bacteria without the complete mucin structure. Overall, our findings suggest that the interplay between dietary and mucus glycans creates niche differentiation in the infant gut microbiota.

Lucinid bivalves harbor environmentally acquired endosymbionts within the class Gammaproteobacteria and genus Candidatus Thiodiazotropha. Despite recent studies focused on lucinid endosymbiont genomic and functional diversity, processes influencing species diversity have been understudied. From the analysis of 333 metagenome-assembled genomes (MAGs) from 40 host species across 8 waterbodies and 77 distinct locations, 272 were high quality MAGs of Ca. Thiodiazotropha endosymbionts that represented 11 genomospecies. Of those, two new genomospecies from lucinids collected from The Bahamas and Florida (USA) were identified, Ca. Thiodiazotropha fisheri and Ca. Thiodiazotropha grosi. Metabolic specialization was evident, such as potential adaptations to diverse carbon sources based on detection of one-carbon (C1) metabolic genes in eight genomospecies. Genes associated with defense, symbiosis/pathogenesis, and horizontal gene transfer (HGT) were also distinct across genomospecies. For instance, Ca. T. taylori exhibited lower abundances of HGT-associated genes compared to other genomospecies, particularly Ca. T. endolucinida, Ca. T. lotti, and Ca. T. weberae. HGT-associated genes were linked to previously unreported retron-type reverse transcriptases, dsDNA phages, and phage resistance. Collectively, the pangenome highlights how lucinid endosymbiont diversity has been shaped by geographic and host-specific interactions linked to gene loss and HGT through time.

The microbial composition of stored food can influence its stability and the microbial species consumed by the organism feeding on it. Many bee species store nectar and pollen in provisions constructed to feed developing offspring. Yet, whether microbial composition is determined by the pollen types within provisions, variation between bee species at the same nesting sites, or geographic distance was unclear. Here, we sampled two species of cooccurring cavity nesting bees in the genus Osmia at 13 sites in California and examined the composition of pollen, fungi, and bacteria in provisions. Pollen composition explained 15% of variation in bacterial composition and ∼30% of variation in fungal composition, whereas spatial distance among sites explained minimal additional variation. Symbiotic microbe genera Ascosphaera, Sodalis, and Wolbachia showed contrasting patterns of association with pollen composition, suggesting distinct acquisition and transmission routes for each. Comparing provisions from both bee species comprised of the same pollens points to environmental acquisition rather than bee species as a key factor shaping the early stages of the bee microbiome in Osmia. The patterns we observed also contrast with Apilactobacillus-dominated provision microbiome in other solitary bee species, suggesting variable mechanisms of microbial assembly in stored food among bee species.

The microbial communities that colonize the human large intestine can influence many aspects of health and Bacillota strains, in particular, have been proposed as next-generation probiotics. Of note are strains including fibre-degraders, butyrate producers, lactate producers and utilizers, and other beneficial metabolic activities that are important for health. To illustrate the potential applications of colonic bacteria to design novel prebiotic formulations, a comparative genomics analysis of 16 bacterial strains isolated from the human gut was performed. This analysis revealed a high number of carbohydrate-active enzymes (CAZymes) in the genome sequences of understudied Lachnospiraceae and Oscillospiraceae members including Roseburia intestinalis L1-82, Roseburia faecis M72/1, Butyrivibrio fibrisolvens 16-4, and Ruminococcus bicirculans 80/3, ranging from 32 to 56 CAZymes across different strains. These strains showed complementary enzymatic profiles covering a wide range of different activities required to degrade prebiotic substrates derived from vegetable sources such as arabino- and xylo-oligosaccharides and pectic-oligosaccharides. These metabolic differences highlight the potential of these strains to cross feed and to allow the design novel probiotic consortia for microbiota-oriented interventions that could target specific disease conditions. These bacterial strains are, however, strict anaerobes and therefore special measures may need to be put in place to overcome these limitations.