Metagenome to phenome approach enables isolation and genomics characterization of Kalamiella piersonii gen. nov., sp. nov. from the International Space Station

Singh, Nitin Kumar; Wood, Jason M.; Mhatre, Snehit S.; Venkateswaran, Kasthuri

doi:10.1007/s00253-019-09813-z

Cited by 42 publications

(52 citation statements)

References 69 publications

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“…Extensive microbial diversity studies have been conducted in various Earth-based analog environments (e.g. Mars 500, and multiple samplings of ILMAH) as well as aboard the ISS, all of which relied on standard swabs and wipe kits [11,[13][14][15]26]. Even though NASA has used similar cotton, rayon, and polyester swab devices for sampling spacecraft surfaces and associated environments since the 1970s [16,17], the use of these standard swabs and wipe kits may prove insufficient for valid sampling outside of the ISS and other future spacecraft to monitor and prevent forward contamination .…”

Section: Discussionmentioning

confidence: 99%

“…To aid NASA in developing appropriate closed habitats (a built environment that has minimal atmospheric exchange with the surrounding environment), it will be necessary to characterize and compare the microbial ecology across a variety of closed environments. In this regard, the microbial analysis of several closed systems has been performed, including the spacecraft assembly facilities (SAF) [9], Inflated Lunar/Mars Analogous Habitat (ILMAH) [10,11], long haul commercial aircraft cabin air [12], and the International Space Station (ISS) [13][14][15].…”

Section: Introductionmentioning

confidence: 99%

“…These novel microbial sampling tools have allowed for much more comprehensive collection of both cultivable and yet to be cultivated microbial populations [17,23,25]. Furthermore, these sampling devices were also employed to collect samples from Earth-based Analogs (Mars 500 facility/ILMAH/ Antarctic Concordia Station), and the ISS [11,13,14,[26][27][28].…”

Section: Introductionmentioning

confidence: 99%

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Microbiome and Metagenome Analyses of a Closed Habitat During Human Occupation

Mohan

Parker

Urbaniak

et al. 2020

Preprint

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24Background: Microbial contamination during long-term confinements of space exploration 25 present potential risks for both crew members and spacecraft life support systems. As NASA 26 prepares for manned missions beyond low Earth orbit, deeper into the solar system, the 27 monitoring of microbial populations within closed human habitation will be necessary to ensure 28 the safety of both the crew and the spacecraft. NASA's Johnson Space Center recently 29 developed a microbial swab kit, designed specifically to be used during astronaut 30 Extravehicular Activity (EVA). The EVA swab kit was designed in such a way that it could be held 31 easily within an astronaut's bulky glove and or by a robot's manipulator, making it suitable for 32 microbial sample collection in remote and extreme environments. The previously tested (in 33 laboratory and controlled settings) EVA swab kit was used in this study to sample various 34 surfaces from a submerged, closed, analog habitat in order to characterize the microbial 35 populations in this unique human habitat. 36Results: Samples were collected from various locations across the habitat of which were 37 constructed from various surface materials (linoleum, dry wall, particle board, glass, and metal) 38 and microbial populations examined by culture, qPCR, microbiome 16S rRNA gene sequencing 39 and shot gun metagenomics. Propidium monoazide treated samples identified the viable/intact 40 microbial population of the habitat. The cultivable microbial population ranged from below the 41 detection limit (BDL) to 10 6 CFU/sample and their identity was characterized using Sanger 42 sequencing. Next-generation sequencing (NGS; both 16S rRNA amplicon and shotgun) were 43 used to characterize the microbial dynamics, community profiles and functional attributes revealed abundance of viable Actinobacteria (Brevibacterium, Nesternkonia, Mycobacterium, 46 Pseudonocardia and Corynebacterium), Firmicutes (Virgibacillus, Staphylococcus and 47Oceanobacillus) and Proteobacteria (esp. Acinetobacter) on linoleum, dry wall, and particle 48 board (LDP) surfaces, while members of Firmicutes (Leuconostocaceae) and Proteobacteria 49 (Enterobacteriaceae) were high on the glass/metal surfaces. Non-metric multidimensional 50 scaling (NMDS) determined from both 16S rRNA and metagenomic analyses revealed 51 differential microbial speciation between LDP surfaces and glass/metal surfaces. The shotgun 52 metagenomics sequencing showed bacterial predominance of Brevibacterium (53.6%), 53 Brachybacterium (7.8%), Pseudonocardia (9.9%), Mycobacterium (3.7%), and Staphylococcus 54 (2.1%); while fungal analyses revealed Aspergillus and Penicillium dominance. 55 Conclusion:This study provides the first assessment of monitoring cultivable and viable 56 microorganisms on surfaces within a submerged, closed, analog habitat. The analyses 57 presented herein suggests that the surface material plays a role in microbial community 58 structure as the microbial populations differed between LDP and metal/glass surfaces. T...

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Microbiome and Metagenome Analyses of a Closed Habitat During Human Occupation

Mohan

Parker

Urbaniak

et al. 2020

Preprint

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“…Importantly, these bacteria are able to adapt to extreme conditions such as microgravity and radiation and thus persist, necessitating the development of appropriate countermeasures to control them. Members of the order Enterobacteriales that were found on ISS surfaces were Pantoea brenneri , Pantoea agglomerans , Kalamiella piersonii , and Enterobacter bugandensis ( 4 – 6 ). On Earth, P. agglomerans and P. brenneri were reported to have been isolated from human infections ( 4 ).…”

Section: Announcementmentioning

confidence: 99%

Draft Genome Sequences of Enterobacteriales Strains Isolated from the International Space Station

Bharadwaj

Daudu

Singh

et al. 2020

Microbiol Resour Announc

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“…In our original published manuscript entitled "Metagenome to phenome approach enables isolation and genomics characterization of Kalamiella piersonii gen. nov., sp. nov. from the International Space Station" (Singh et al 2019), we found a taxonomic description format error: As per the Rule 27 of the ICNP, protologue of the genus is to be provided separate from the species. This is required for the validation of the novel genus and species.…”

mentioning

confidence: 97%