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1. Microbial rewilding in the gut microbiomes of captive ring-tailed lemurs (Lemur catta) in Madagascar

   https://doi.org/10.1038/s41598-022-26861-0  

   Bornbusch, Sally_L; Clarke, Tara_A; Hobilalaina, Sylvia; Reseva, Honore_Soatata; LaFleur, Marni; Drea, Christine_M (December 2022, Scientific Reports)

   Abstract Microbial rewilding, whereby exposure to naturalistic environments can modulate or augment gut microbiomes and improve host-microbe symbiosis, is being harnessed as an innovative approach to human health, one that may also have significant value to animal care and conservation. To test for microbial rewilding in animal microbiomes, we used a unique population of wild-born ring-tailed lemurs (Lemur catta) that were initially held as illegal pets in unnatural settings and, subsequently, relocated to a rescue center in Madagascar where they live in naturalistic environments. Using amplicon and shotgun metagenomic sequencing of lemur and environmental microbiomes, we found multiple lines of evidence for microbial rewilding in lemurs that were transitioned from unnatural to naturalistic environments: A lemur’s duration of exposure to naturalistic settings significantly correlated with (a) increased compositional similarly to the gut communities of wild lemurs, (b) decreased proportions of antibiotic resistance genes that were likely acquired via human contact during pethood, and (c) greater covariation with soil microbiomes from natural habitats. Beyond the inherent psychosocial value of naturalistic environments, we find that actions, such as providing appropriate diets, minimizing contact with humans, and increasing exposure to natural environmental consortia, may assist in maximizing host-microbe symbiosis in animals under human care. 

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2. Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally occurring isolates of a model plant symbiont

   https://doi.org/10.1098/rspb.2022.0477  

   Batstone, Rebecca T.; Burghardt, Liana T.; Heath, Katy D. (July 2022, Proceedings of the Royal Society B: Biological Sciences)

   Given the need to predict the outcomes of (co)evolution in host-associated microbiomes, whether microbial and host fitnesses tend to trade-off, generating conflict, remains a pressing question. Examining the relationships between host and microbe fitness proxies at both the phenotypic and genomic levels can illuminate the mechanisms underlying interspecies cooperation and conflict. We examined naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti , paired with each of two host Medicago truncatula genotypes in single- or multi-strain experiments to determine how multiple proxies of microbial and host fitness were related to one another and test key predictions about mutualism evolution at the genomic scale, while also addressing the challenge of measuring microbial fitness. We found little evidence for interspecies fitness conflict; loci tended to have concordant effects on both microbe and host fitnesses, even in environments with multiple co-occurring strains. Our results emphasize the importance of quantifying microbial relative fitness for understanding microbiome evolution and thus harnessing microbiomes to improve host fitness. Additionally, we find that mutualistic coevolution between hosts and microbes acts to maintain, rather than erode, genetic diversity, potentially explaining why variation in mutualism traits persists in nature. 

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3. Microbiome research: Application of “omics” technology

   https://doi.org/10.26717/BJSTR.2022.46.007300  

   Flowers, L. (September 2022, Biomedical journal of scientific technical research)

   Microbiome research is a thriving field focused on characterizing the composition and functionality of microbial populations or microbiomes from a wide array of ecological niches. Microbiomes occupy living organisms, soil, the atmosphere, and bodies of water and exist in moderate and extreme climates. Understanding the intractable microbial universes in various environments is challenging and potentially rewarding to humankind. Historically, elucidating pathogenic microbes and their impact on host species has dominated microbiome-based studies. Moreover, a tiny percentage of microbes can be cultured using classical culturing methods. With advancements in high throughput experimentation and computational tools derived from microbial ecology, there is a driving force to gain insight into the entire microbial consortium from various environmental and biological locations. Metagenomics, the study of all the microbial genomes in a sample using sequencing techniques (e.g., 16s rRNA amplicon sequencing and shotgun sequencing), has so far dominated the types of investigations conducted in the field of microbiome research. More recently, however, researchers are becoming increasingly interested in better understanding the complex microbe-associated molecular network and specific protein and metabolite functions associated with microbial genetic potential. Metaproteomic, meta transcriptomics, and metabolomics are three potent methods to accumulate information about microbial proteins, messenger RNA, and metabolites in a microbial community. These methods are currently being applied in laboratory settings to address our general lack of understanding of microbe-microbe interactions and microbe-environment interactions. 

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4. A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes

   https://doi.org/10.1073/pnas.2204146119  

   Amend, Anthony S.; Swift, Sean O.; Darcy, John L.; Belcaid, Mahdi; Nelson, Craig E.; Buchanan, Joshua; Cetraro, Nicolas; Fraiola, Kauaoa M.; Frank, Kiana; Kajihara, Kacie; et al (August 2022, Proceedings of the National Academy of Sciences)

   Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts’ microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition. 

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5. Manipulation of the seagrass‐associated microbiome reduces disease severity

   https://doi.org/10.1111/1462-2920.16582  

   Graham, Olivia_J; Adamczyk, Emily_M; Schenk, Siobhan; Dawkins, Phoebe; Burke, Samantha; Chei, Emily; Cisz, Kaitlyn; Dayal, Sukanya; Elstner, Jack; Hausner, Arjun_Lev_Pillai; et al (January 2024, Environmental Microbiology)

   Abstract Host‐associated microbes influence host health and function and can be a first line of defence against infections. While research increasingly shows that terrestrial plant microbiomes contribute to bacterial, fungal, and oomycete disease resistance, no comparable experimental work has investigated marine plant microbiomes or more diverse disease agents. We test the hypothesis that the eelgrass (Zostera marina) leaf microbiome increases resistance to seagrass wasting disease. From field eelgrass with paired diseased and asymptomatic tissue,16S rRNAgene amplicon sequencing revealed that bacterial composition and richness varied markedly between diseased and asymptomatic tissue in one of the two years. This suggests that the influence of disease on eelgrass microbial communities may vary with environmental conditions. We next experimentally reduced the eelgrass microbiome with antibiotics and bleach, then inoculated plants withLabyrinthula zosterae, the causative agent of wasting disease. We detected significantly higher disease severity in eelgrass with a native microbiome than an experimentally reduced microbiome. Our results over multiple experiments do not support a protective role of the eelgrass microbiome againstL. zosterae. Further studies of these marine host–microbe–pathogen relationships may continue to show new relationships between plant microbiomes and diseases. 

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