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1. The Effects of Social Experience on Host Gut Microbiome in Male Zebrafish ( Danio rerio )

   https://doi.org/10.1086/729377  

   Scott, Emily; Brewer, Michael S; Peralta, Ariane L; Issa, Fadi A (February 2024, The Biological Bulletin)

   Derby, C (Ed.)

   Although the gut and the brain vastly differ in physiological function, they have been interlinked in a variety of different neurological and behavioral disorders. The bacteria that comprise the gut microbiome communicate and influence the function of various physiological processes within the body, including nervous system function. However, the effects of social experience in the context of dominance and social stress on gut microbiome remain poorly understood. Here, we examined whether social experience impacts the host zebrafish (Danio rerio) gut microbiome. We studied how social dominance during the first 2 weeks of social interactions changed the composition of zebrafish gut microbiome by comparing gut bacterial composition, diversity, and relative abundance between socially dominant, submissive, social isolates and control group–housed communal fish. Using amplicon sequencing of the 16S rRNA gene, we report that social dominance significantly affects host gut bacterial community composition but not bacterial diversity. At the genus level, Aeromonas and unclassified Enterobacteriaceae relative abundance decreased in dominant individuals while commensal bacteria (e.g., Exiguobacterium and Cetobacterium) increased in relative abundance. Conversely, the relative abundance of Psychrobacter and Acinetobacter was increased in subordinates, isolates, and communal fish compared to dominant fish. The shift in commensal and pathogenic bacteria highlights the impact of social experience and the accompanying stress on gut microbiome, with potentially similar effects in other social organisms. 

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2. Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection

   https://doi.org/10.1073/pnas.1908600116  

   Morella, Norma M.; Weng, Francis Cheng-Hsuan; Joubert, Pierre M.; Metcalf, C. Jessica; Lindow, Steven; Koskella, Britt (January 2020, Proceedings of the National Academy of Sciences)

   There is increasing interest in the plant microbiome as it relates to both plant health and agricultural sustainability. One key unanswered question is whether we can select for a plant microbiome that is robust after colonization of target hosts. We used a successive passaging experiment to address this question by selecting upon the tomato phyllosphere microbiome. Beginning with a diverse microbial community generated from field-grown tomato plants, we inoculated replicate plants across 5 plant genotypes for 4 45-d passages, sequencing the microbial community at each passage. We observed consistent shifts in both the bacterial (16S amplicon sequencing) and fungal (internal transcribed spacer region amplicon sequencing) communities across replicate lines over time, as well as a general loss of diversity over the course of the experiment, suggesting that much of the naturally observed microbial community in the phyllosphere is likely transient or poorly adapted within the experimental setting. We found that both host genotype and environment shape microbial composition, but the relative importance of genotype declines through time. Furthermore, using a community coalescence experiment, we found that the bacterial community from the end of the experiment was robust to invasion by the starting bacterial community. These results highlight that selecting for a stable microbiome that is well adapted to a particular host environment is indeed possible, emphasizing the great potential of this approach in agriculture and beyond. In light of the consistent response of the microbiome to selection in the absence of reciprocal host evolution (coevolution) described here, future studies should address how such adaptation influences host health. 

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3. Orientia, Rickettsia, and the microbiome in rodent attached chiggers in North Carolina, USA

   https://doi.org/10.1371/journal.pone.0311698  

   Richardson, Elise A; Garshong, Reuben; Chen, Kaiying; Crossley, Dac; Mclean, Bryan S; Wasserberg, Gideon; Apperson, Charles S; Roe, R Michael; Ponnusamy, Loganathan (December 2024, PLOS ONE)

   Ganta, Roman R (Ed.)

   Chiggers are larval mites that pose a significant health risk globally via the spread of scrub typhus. However, fundamental studies into the bacterial microbiome in North America have never been considered. In this investigation, chiggers were collected in the wild from two locally common rodent host species (i.e.,Sigmodon hispidusandPeromyscus leucopus) in three different ecoregions of North Carolina (NC), United States to investigate the composition of their bacterial communities, including potential pathogens. DNA was extracted from the chiggers, and the V3-V4 regions of the bacterial 16S rRNA gene were sequenced using next-generation sequencing (NGS). Alpha diversity metrics revealed significant differences in bacterial diversity among different collection counties. Beta diversity metrics also revealed that bacterial communities across counties were significantly different, suggesting changes in the microbiome as the environment changed. Specifically, we saw that the two western NC collection counties had similar bacterial composition as did the two eastern collection counties. In addition, we found that the chigger microbiome bacterial diversity and composition differed between rodent host species. The 16S rRNA sequence reads were assigned to 64 phyla, 106 orders, 199 families, and 359 genera. The major bacterial phylum was Actinobacteria. The most abundant species were in the generaCorynebacterium,Propionibacterium, class ZB2, andMethylobacterium. Sequences derived from potential pathogens within the generaOrientiaandRickettsiawere also detected. Our findings provide the first insights into the ecology of chigger microbiomes in the US. Further research is required to determine if the potential pathogens found detected in chiggers are a threat to humans and wildlife. 

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4. Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations

   https://doi.org/10.1038/s41467-023-39876-6  

   McCauley, M.; Goulet, T. L.; Jackson, C. R.; Loesgen, S. (August 2023, Nature Communications)

   Abstract Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. We unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pipeline. We reprocess 12,010 cnidarian microbiome samples from 186 studies, alongside 3,388 poriferan, 370 seawater samples, and 245 cultured Symbiodiniaceae, unifying ~6.5 billion sequence reads. Samples are partitioned by hypervariable region and sequencing platform to reduce sequencing variability. This systematic review uncovers an incredible diversity of 86 archaeal and bacterial phyla associated with Cnidaria, and highlights key bacteria hosted across host sub-phylum, depth, and microhabitat. Shallow (< 30 m) water Alcyonacea and Actinaria are characterized by highly shared and relatively abundant microbial communities, unlike Scleractinia and most deeper cnidarians. Utilizing the V4 region, we find that cnidarian microbial composition, richness, diversity, and structure are primarily influenced by host phylogeny, sampling depth, and ocean body, followed by microhabitat and sampling date. We identify host and geographical generalist and specificEndozoicomonasclades within Cnidaria and Porifera. This systematic review forms a framework for understanding factors governing cnidarian microbiomes and creates a baseline for assessing stress associated dysbiosis. 

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5. No apparent correlation between honey bee forager gut microbiota and honey production

   https://doi.org/10.7717/peerj.1329  

   Horton, Melissa A.; Oliver, Randy; Newton, Irene L. (January 2015, PeerJ)

   null (Ed.)

   One of the best indicators of colony health for the European honey bee ( Apis mellifera ) is its performance in the production of honey. Recent research into the microbial communities naturally populating the bee gut raise the question as to whether there is a correlation between microbial community structure and colony productivity. In this work, we used 16S rRNA amplicon sequencing to explore the microbial composition associated with forager bees from honey bee colonies producing large amounts of surplus honey (productive) and compared them to colonies producing less (unproductive). As supported by previous work, the honey bee microbiome was found to be dominated by three major phyla: the Proteobacteria, Bacilli and Actinobacteria, within which we found a total of 23 different bacterial genera, including known “core” honey bee microbiome members. Using discriminant function analysis and correlation-based network analysis, we identified highly abundant members (such as Frischella and Gilliamella ) as important in shaping the bacterial community; libraries from colonies with high quantities of these Orbaceae members were also likely to contain fewer Bifidobacteria and Lactobacillus species (such as Firm-4). However, co-culture assays, using isolates from these major clades, were unable to confirm any antagonistic interaction between Gilliamella and honey bee gut bacteria. Our results suggest that honey bee colony productivity is associated with increased bacterial diversity, although this mechanism behind this correlation has yet to be determined. Our results also suggest researchers should not base inferences of bacterial interactions solely on correlations found using sequencing. Instead, we suggest that depth of sequencing and library size can dramatically influence statistically significant results from sequence analysis of amplicons and should be cautiously interpreted. 

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