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1. Clean room microbiome complexity impacts planetary protection bioburden

   https://doi.org/10.1186/s40168-021-01159-x  

   Hendrickson, Ryan; Urbaniak, Camilla; Minich, Jeremiah J.; Aronson, Heidi S.; Martino, Cameron; Stepanauskas, Ramunas; Knight, Rob; Venkateswaran, Kasthuri (December 2021, Microbiome)

   Abstract BackgroundThe Spacecraft Assembly Facility (SAF) at the NASA’s Jet Propulsion Laboratory is the primary cleanroom facility used in the construction of some of the planetary protection (PP)-sensitive missions developed by NASA, including the Mars 2020 Perseverance Rover that launched in July 2020. SAF floor samples (n=98) were collected, over a 6-month period in 2016 prior to the construction of the Mars rover subsystems, to better understand the temporal and spatial distribution of bacterial populations (total, viable, cultivable, and spore) in this unique cleanroom. ResultsCleanroom samples were examined for total (living and dead) and viable (living only) microbial populations using molecular approaches and cultured isolates employing the traditional NASA standard spore assay (NSA), which predominantly isolated spores. The 130 NSA isolates were represented by 16 bacterial genera, of which 97% were identified as spore-formers via Sanger sequencing. The most spatially abundant isolate wasBacillus subtilis, and the most temporally abundant spore-former wasVirgibacillus panthothenticus. The 16S rRNA gene-targeted amplicon sequencing detected 51 additional genera not found in the NSA method. The amplicon sequencing of the samples treated with propidium monoazide (PMA), which would differentiate between viable and dead organisms, revealed a total of 54 genera: 46 viable non-spore forming genera and 8 viable spore forming genera in these samples. The microbial diversity generated by the amplicon sequencing corresponded to ~86% non-spore-formers and ~14% spore-formers. The most common spatially distributed genera wereSphinigobium,Geobacillus, andBacilluswhereas temporally distributed common genera wereAcinetobacter,Geobacilllus, andBacillus. Single-cell genomics detected 6 genera in the sample analyzed, with the most prominent beingAcinetobacter. ConclusionThis study clearly established that detecting spores via NSA does not provide a complete assessment for the cleanliness of spacecraft-associated environments since it failed to detect several PP-relevant genera that were only recovered via molecular methods. This highlights the importance of a methodological paradigm shift to appropriately monitor bioburden in cleanrooms for not only the aeronautical industry but also for pharmaceutical, medical industries, etc., and the need to employ molecular sequencing to complement traditional culture-based assays. 

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2. 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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3. New perspectives on picocyanobacteria and understudied cyanobacterial diversity in the Albemarle Pamlico sound system, North Carolina, USA

   https://doi.org/10.3389/fmicb.2025.1539050  

   Sánchez-Gallego, Joel; Curtis, Nathaniel P; Paerl, Hans W; Paerl, Ryan W (May 2025, Frontiers in Microbiology)

   Cyanobacteria are important primary producers, sources of secondary metabolites, and sentinels of environmental change in aquatic ecosystems – including large estuaries. Here, we newly investigated cyanobacterial diversity within the Albemarle Pamlico Sound System (APES) using (16S rRNA) gene amplicon sequencing analyses. Substantial cyanobacterial diversity including lineages lacking current isolates were recovered (46 genera, 17 potentially cyanotoxic), with oligohaline waters of the Albemarle Sound and its tributaries being notable regional hotspot for diversity. Salinity and temperature were influential drivers of cyanobacterial community composition. Picocyanobacteria (cells <3 µm in diameter) were abundant in amplicon sequence libraries (72% of cyanobacterial sequences) – especially populations withinSynechococcusSubClade 5.2. Picocyanobacteria along with picoeukaryotes were large contributors to total phytoplankton biomass comprising ~47% of chlorophyll a. Further, the picocyanobacterial generaSynechococcus,Cyanobium, andSynechocystis(55.4%, 14.8%, and 12.9% of cyanobacterial sequences, respectively) formed a core community spanning from freshwater regions (eastern AST, D949) to polyhaline environments (NRE100 downstream stations to PS5), suggesting resilience to significant salinity fluctuations and associated environmental changes. Amplicon sequence variant (ASV) and environmental data indicate the presence of several putative ecotypes, as well as distinct abundance patterns among closely related populations, highlighting substantial fitness variability among subspecies. Notably, potentially cyanotoxic genera,Synechocystis,Planktothrix,Plectonema, andDolichospermumwere the four more abundant detected in polyhaline APES regions, far beyond conspicuous freshwater sources. These findings reveal previously unrecognized potential sources of cyanotoxics in estuarine food webs and habitats, underscoring the ecological significance of cyanobacterial community dynamics across salinity gradients. 

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4. Cadaver Microbial Signatures of the Submandibular Glands and Thyroid for Forensic Investigations

   Sheree Finley, PhD*; Matteo Moretti, MD; Silvia Visonà, PhD; Gulnaz Javan, PhD* (January 2023, Cadaver Microbial Signatures of the Submandibular Glands and Thyroid for Forensic Investigations)

   The study of the thyroid is an emerging topic, particularly in postmortem microbiome studies, due to the organ’s ability to affect the endocrine system. Also, the submandibular gland is a promising, emerging gland of study due to its position relative to the oral cavity. Previous thanatomicrobiome studies have demonstrated that bacteria belonging to the phyla Firmicutes, Proteobacteria, Bacteroides, and Pseudomonadota predominate internal organs and have been considered an important biomarker for postmortem interval. Further, Clostridium species that dominate in internal organs are linked to the hypoxic change that occurs after death, which leads to the switch of bacteria to become obligate anaerobes. Therefore, obligate anaerobes dominate the body after death due to their ability to thrive off fermentation products. 16S rRNA gene sequencing has been critical in thanatomicrobiome studies, which refers to the human microbiome (microorganisms within the body) after death. Currently, it has not been elucidated regarding the microorganisms that are associated with the decay of submandibular and thyroid glands. We hypothesized that through sequencing of the 16S rRNA gene of the submandibular and thyroid glands, the presence of Firmicutes and Proteobacteria will indicate potential biomarkers for postmortem interval. The present study revealed the postmortem microbial signatures of the submandibular and thyroid glands using the 16S rRNA gene, specifically the V3-V4 hypervariable regions, using universal primers 341F and 805R. We investigated a total of 37 cadavers obtained from ongoing criminal casework, 17 submandibular samples and 20 thyroid samples, and found that there is a correlation between microbial abundance in these postmortem glands. The predominating phyla of interest found in both glands were Firmicutes and Proteobacteria. The predominating genera were Paeniclostridium and Streptococcus in both glands, respectively. Further experimentation of the submandibular and thyroid glands will help to link oral thanatomicrobiome communities to “microbial clock” determinations, thus enhancing postmortem interval estimation. 

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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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