scholarly journals Microbiome dynamics during the HI-SEAS IV mission, and implications for future crewed missions beyond Earth

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Alexander Mahnert ◽  
Cyprien Verseux ◽  
Petra Schwendner ◽  
Kaisa Koskinen ◽  
Christina Kumpitsch ◽  
...  
Keyword(s):  
Quantitative Information ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Microbiome Composition ◽  
Microbial Monitoring ◽  
Gene Profiles ◽  
Abiotic Surfaces ◽  
Future Space ◽  
Microbiome Diversity

Abstract Background Human health is closely interconnected with its microbiome. Resilient microbiomes in, on, and around the human body will be key for safe and successful long-term space travel. However, longitudinal dynamics of microbiomes inside confined built environments are still poorly understood. Herein, we used the Hawaii Space Exploration Analog and Simulation IV (HI-SEAS IV) mission, a 1 year-long isolation study, to investigate microbial transfer between crew and habitat, in order to understand adverse developments which may occur in a future outpost on the Moon or Mars. Results Longitudinal 16S rRNA gene profiles, as well as quantitative observations, revealed significant differences in microbial diversity, abundance, and composition between samples of the built environment and its crew. The microbiome composition and diversity associated with abiotic surfaces was found to be rather stable, whereas the microbial skin profiles of individual crew members were highly dynamic, resulting in an increased microbiome diversity at the end of the isolation period. The skin microbiome dynamics were especially pronounced by a regular transfer of the indicator species Methanobrevibacter between crew members within the first 200 days. Quantitative information was used to track the propagation of antimicrobial resistance in the habitat. Together with functional and phenotypic predictions, quantitative and qualitative data supported the observation of a delayed longitudinal microbial homogenization between crew and habitat surfaces which was mainly caused by a malfunctioning sanitary facility. Conclusions This study highlights main routes of microbial transfer, interaction of the crew, and origins of microbial dynamics in an isolated environment. We identify key targets of microbial monitoring, and emphasize the need for defined baselines of microbiome diversity and abundance on surfaces and crew skin. Targeted manipulation to counteract adverse developments of the microbiome could be a highly important strategy to ensure safety during future space endeavors.

scholarly journals Microbiome dynamics during the HI-SEAS IV mission, and implications for future crewed missions beyond Earth

2020 ◽  
Author(s):  
Alexander Mahnert ◽  
Cyprien Verseux ◽  
Petra Schwendner ◽  
Kaisa Koskinen ◽  
Christina Kumpitsch ◽  
...  
Keyword(s):  
Quantitative Information ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Microbiome Composition ◽  
Microbial Monitoring ◽  
Gene Profiles ◽  
Abiotic Surfaces ◽  
Future Space ◽  
Microbiome Diversity ◽  
One Year

Abstract Background Human health is closely interconnected with its microbiome. Resilient microbiomes in, on and around the human body will be key for safe and successful long-term space travel. However, longitudinal dynamics of microbiomes inside confined built environments are still poorly understood. Herein we used the Hawaii Space Exploration Analog and Simulation IV (HI-SEAS IV) mission, a one year-long isolation study, to investigate microbial transfer between crew and habitat, in order to understand adverse developments which may occur in a future outpost on the Moon or Mars. Results Longitudinal 16S rRNA gene profiles, as well as quantitative observations, revealed significant differences in microbial diversity, abundance and composition between samples of the built environment and its crew. The microbiome composition and diversity associated with abiotic surfaces was found to be rather stable, whereas the microbial skin profiles of individual crewmembers were highly dynamic, resulting in an increased microbiome diversity at the end of the isolation period. The skin microbiome dynamics were especially pronounced by a regular transfer of the indicator species Methanobrevibacter between crewmembers within the first 200 days. Quantitative information was used to track the propagation of antimicrobial resistance in the habitat. Together with functional and phenotypic predictions, quantitative and qualitative data supported the observation of a delayed longitudinal microbial homogenization between crew and habitat surfaces which was mainly caused by a malfunctioning sanitary facility. Conclusions This study highlights main routes of microbial transfer, interaction of the crew and origins of microbial dynamics in an isolated environment. We identify key targets of microbial monitoring, and emphasize the need for defined baselines of microbiome diversity and abundance on surfaces and crew skin. Targeted manipulation to counteract adverse developments of the microbiome could be a highly important strategy to ensure safety during future space endeavors.

scholarly journals Microbiome dynamics during the HI-SEAS IV mission, and implications for future crewed missions beyond Earth

2020 ◽  
Author(s):  
Alexander Mahnert ◽  
Cyprien Verseux ◽  
Petra Schwendner ◽  
Kaisa Koskinen ◽  
Christina Kumpitsch ◽  
...  
Keyword(s):  
Built Environment ◽  
Microbial Diversity ◽  
Rrna Gene ◽  
Built Environments ◽  
Microbial Monitoring ◽  
Future Space ◽  
Microbiome Diversity ◽  
Set Up ◽  
One Year

Abstract BackgroundHuman health is closely interconnected with its microbiome. Stable microbiomes in, on and around the human body will be key for safe and successful long-term space travel. However, longitudinal dynamics of microbiomes inside confined built environments are still poorly understood. Herein we used the Hawaii Space Exploration Analog and Simulation IV (HI-SEAS IV) mission, a one year-long isolation study, to investigate microbial transfer between crew and habitat, in order to understand adverse developments which might occur in an outpost on the Moon or Mars in the future.ResultsLongitudinal profiles of the 16S rRNA gene revealed significant differences in microbial diversity and composition between samples of the built environment and its crew. While microbial profiles from individual crew members were highly dynamic, the microbiome on built environment surfaces remained more stable. Especially within the first 200 days, archaeal signatures of Methanobrevibacter were regularly transferred between crew members, but did not impact the microbiome on habitat surfaces. In contrast to a rather stable microbial diversity recovered from surfaces of the habitat, microbial diversity from the crew’s skin increased over time. Quantitative observations based on qPCR supported observations of dissimilarity between the built environment and its crew and was also used to track the propagation of antimicrobial resistances in the habitat. Together with functional and phenotypic predictions, quantitative and qualitative data both supported the observation of a delayed longitudinal homogenization between the crew and their habitat, that was mainly caused by the hygiene infrastructure.ConclusionsThe study highlights main routes of microbial transfer, interaction of its crew and origins of microbial dynamics in an isolated set-up. We identified key targets of microbial monitoring, and emphasize the need for defined baselines of microbiome diversity and abundance on surfaces and skin. Targeted manipulation to counteract adverse developments of the microbiome will be a highly important strategy to ensure safety during future space endeavors.

scholarly journals Surveying the sweetpotato rhizosphere, endophyte, and surrounding soil microbiomes at two North Carolina farms reveals underpinnings of sweetpotato microbiome community assembly

2019 ◽  
Author(s):  
C Pepe-Ranney ◽  
C Keyser ◽  
J Trimble ◽  
B Bissinger
Keyword(s):  
North Carolina ◽  
Community Assembly ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Sequence Variant ◽  
Skin Microbiome ◽  
Microbiome Composition ◽  
Pests And Diseases ◽  
Sub Saharan ◽  
Surrounding Soil

AbstractFarmers grow sweetpotatoes worldwide and some sub-Saharan African and Asian diets include sweetpotato as a staple, yet the sweetpotato microbiome is conspicuously less studied relative to crops such as maize, soybean, and wheat. Studying sweetpotato microbiome ecology may reveal paths to engineer the microbiome to improve sweetpotato yield, and/or combat sweetpotato pests and diseases. We sampled sweetpotatoes and surrounding soil from two North Carolina farms. We took samples from sweetpotato fields under two different land management regimes, conventional and organic, and collected two sweetpotato cultivars, ‘Beauregard’ and ‘Covington’. By comparing SSU rRNA gene amplicon sequence profiles from sweetpotato storage root skin, rhizosphere, and surrounding soil we found the skin microbiome possessed the least composition heterogeneity among samples and lowest alpha-diversity and was significantly nested by the rhizosphere in amplicon sequence variant (ASV) membership. Many ASVs were specific to a single field and/or only found in either the skin, rhizosphere, or surrounding soil. Notably, sweetpotato skin enriched for Planctomycetaceae in relative abundance at both farms. This study elucidates underpinnings of sweetpotato microbiome community assembly, quantifies microbiome composition variance within a single farm, and reveals microorganisms associated with sweetpotato skin that belong to common but uncultured soil phylotypes.

scholarly journals Effect of temperature and time on the thanatomicrobiome of the cecum, ileum, kidney, and lung of domestic rabbits

2019 ◽  
Vol 31 (2) ◽  
pp. 155-163 ◽  
Author(s):  
Kelsey E. Lawrence ◽  
Khiem C. Lam ◽  
Andrey Morgun ◽  
Natalia Shulzhenko ◽  
Christiane V. Löhr
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Effect Of Temperature ◽  
Postmortem Changes ◽  
Rrna Gene ◽  
Limited Information ◽  
Microbiome Composition ◽  
Microbiome Diversity ◽  
Domestic Rabbits ◽  
High Concentrations ◽  
Rrna Gene Sequencing

Knowledge of changes in the composition of microbial communities (microbiota) in tissues after death, over time, is critical to correctly interpret results of microbiologic testing from postmortem examinations. Limited information is available about postmortem changes of the microbiota and the associated microbial genes (microbiome) of internal organs in any species. We examined the effect of time and ambient temperature on the postmortem microbiome (thanatomicrobiome) of tissues typically sampled for microbiologic testing during autopsies. Twenty rabbits were euthanized and their bodies stored at 4°C or 20°C for 6 or 48 h. Ileum, cecum, kidney, and lung tissue were sampled. Bacterial DNA abundance was determined by RT-qPCR. Microbiome diversity was determined by 16S rRNA gene sequencing. By relative abundance of the microbiome composition, intestinal tissues were clearly separated from lungs and kidneys, which were similar to each other, over all times and temperatures. Only cecal thanatomicrobiomes had consistently high concentrations and consistent composition in all conditions. In lungs and kidneys, but not intestine, proteobacteria were highly abundant at specific times and temperatures. Thanatomicrobiome variation was not explained by minor subclinical lesions identified upon microscopic examination of tissues. Bacterial communities typically found in the intestine were not identified at extra-intestinal sites in the first 48 h at 4°C and only in small amounts at 20°C. However, changes in tissue-specific microbiomes during the postmortem interval should be considered when interpreting results of microbiologic testing.

scholarly journals Long-term gut microbiome dynamics in Drosophila melanogaster reveal environment-specific associations between bacterial taxa at the family level

2021 ◽  
Vol 288 (1965) ◽  
Author(s):  
Rupert Mazzucco ◽  
Christian Schlötterer
Keyword(s):  
Drosophila Melanogaster ◽  
Longitudinal Studies ◽  
Microbiome Composition ◽  
Temperature Regimes ◽  
Microbiome Diversity ◽  
The Family ◽  
Single Host ◽  
Post Hoc ◽  
Genome Dataset

The influence of the microbiome on its host is well-documented, but the interplay of its members is not yet well-understood. Even for simple microbiomes, the interaction among members of the microbiome is difficult to study. Longitudinal studies provide a promising approach to studying such interactions through the temporal covariation of different taxonomic units. By contrast to most longitudinal studies, which span only a single host generation, we here present a post hoc analysis of a whole-genome dataset of 81 samples that follows microbiome composition for up to 180 host generations, which cover nearly 10 years. The microbiome diversity remained rather stable in replicated Drosophila melanogaster populations exposed to two different temperature regimes. The composition changed, however, systematically across replicates of the two temperature regimes. Significant associations between families, mostly specific to one temperature regime, indicate functional interdependence of different microbiome components. These associations also involve moderately abundant families, which emphasizes their functional importance, and highlights the importance of looking beyond the common constituents of the Drosophila microbiome.

scholarly journals Microbiome structure of a wild Drosophila community along tropical elevational gradients and comparison to laboratory lines

2021 ◽  
Author(s):  
Joel J Brown ◽  
Anna Jandova ◽  
Christopher T Jeffs ◽  
Megan Higgie ◽  
Eva Nováková ◽  
...  
Keyword(s):  
Environmental Gradients ◽  
Bacterial Species ◽  
Tropical Rainforests ◽  
Elevational Gradients ◽  
Free Living ◽  
Microbiome Composition ◽  
Community Turnover ◽  
Microbiome Diversity ◽  
Warming World

While the biogeography of free-living microbial communities is well-studied, community turnover along environmental gradients in host-associated communities is not well understood. In particular, patterns of host-microbiome diversity along elevational gradients remain largely uncharacterized. Because elevational gradients may serve as natural proxies for climate change, understanding these temperature-influenced patterns can inform our understanding of the threats facing hosts and their microbes in a warming world. In this study, we analysed microbiomes from pupae & adults of four Drosophila species native to Australian tropical rainforests. We sampled wild individuals at high and low elevation along two mountain gradients, to determine natural diversity patterns, and sampled laboratory-reared individuals from isofemale lines established from the same localities, to see if any natural patterns would be retained in the lab. In both environments, we controlled for diet to help elucidate other deterministic patterns of microbiome composition. Microbiome community composition differed radically between laboratory-reared and field-caught flies but did not significantly differ across elevation. We found some notable taxonomic differences in Drosophila microbiomes between different species and elevations. We also found similar microbiome composition from both types of provided food, and we therefore suggest the significant differences in richness are the products of environments with different bacterial species pools. We conclude that elevational differences in temperature are not a major factor in determining Drosophila microbiome composition and we caution against determining microbiome composition from lab-only specimens, particularly long-term cultures.

Alterations of gut microbiome in patients with type 2 diabetes mellitus who had undergone cholecystectomy

2021 ◽  
Vol 320 (1) ◽  
pp. E113-E121
Author(s):  
Bin Wei ◽  
Yakun Wang ◽  
Shoukui Xiang ◽  
Yan Jiang ◽  
Rong Chen ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Stool Samples ◽  
Rrna Gene Sequencing ◽  
And Function ◽  
New Onset

The gut microbiome of long-term T2DM patients who had undergone cholecystectomy and age- and/or sex-matched subjects of new-onset and long-term T2DM without cholecystectomy was assessed using 16S rRNA gene sequencing in stool samples. The findings suggest that, cholecystectomy could partially alleviate long-term diabetes-induced dysbiosis of gut microbiome composition and function.

scholarly journals Skin microbiome dysbiosis in leprosy cases

2021 ◽  
Vol 7 (5) ◽  
pp. 741
Author(s):  
Vannia C. Teng ◽  
Prima K. Esti
Keyword(s):  
Microbial Community ◽  
Microvascular Dysfunction ◽  
Skin Lesions ◽  
Skin Microbiome ◽  
Capillary Structure ◽  
Skin Microbiota ◽  
Microbiome Composition ◽  
Cutaneous Immunity ◽  
Leprosy Patients

<p>The human skin possesses a microenvironment conducive to the growth of the skin microbiome, which plays in many physiological functions in cutaneous immunity homeostasis and maturation. The microbiome composition depends on many variables, such as endogenous (host condition) or exogenous (environmental) factors and topographic location. Host-skin microbes’ interaction can be mutualism or pathogenicity. Dysbiosis or alteration in skin microbiota is associated with various dermatological diseases, including leprosy. Dysbiosis is driven by the alteration of the microbial communities themselves or due to the intrinsic features of the host. Leprosy is a chronic granulomatous disease caused by <em>Mycobacterium leprae</em> targeting the nerves and skin, leading to loss of sensation on the skin, with or without dermatologic lesions, and correlated with long term consequences, such as deformities or disability. Microvascular dysfunction and significant alterations in capillary structure due to invasion of <em>M. leprae</em> lead to altered hydration levels of the skin caused by disruption of blood flow; which changes the resident microbial community structure. The skin microbiome composition differences in leprosy patient’s skin lesions were observed; skin microbial diversity in the leprosy patients was lower than in healthy individuals. The diversity reduction was observed in freshly diagnosis leprosy patients, those at various stages of MDT, and post-MDT; indicated that both the interaction between skin microbial community and<strong> </strong><em>M. leprae</em> or the ongoing therapeutic regimen impacted the skin microbiome variation. </p><p> </p>

scholarly journals Starvation causes changes in the intestinal transcriptome and microbiome that are reversed upon refeeding

2020 ◽  
Author(s):  
Jayanth Jawahar ◽  
Alexander McCumber ◽  
Colin Lickwar ◽  
Caroline Amoroso ◽  
Sol Gomez de la Torre Canny ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ribosome Biogenesis ◽  
16S Rrna Gene Sequencing ◽  
Host Gene ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Host Gene Expression ◽  
Microbiome Composition ◽  
Host Genes

Abstract Background: The ability of animals and their microbiomes to adapt to starvation and then restore homeostasis after refeeding is fundamental to their continued survival and symbiosis. The intestine is the primary site of nutrient absorption and microbiome interaction, however our understanding of intestinal adaptations in host transcriptional programs and microbiome composition remains limited. Additionally, few studies on starvation have investigated intestinal responses to refeeding. The zebrafish presents unique opportunities to study the effects of long-term starvation and refeeding. We used RNA sequencing and 16S rRNA gene sequencing to uncover changes in the intestinal transcriptome and microbiome of zebrafish subjected to long-term starvation and refeeding compared to continuously fed controls. Results: Starvation over 21 days led to increased diversity and altered composition in the intestinal microbiome compared to fed controls, including relative increases in Vibrio and reductions in Plesiomonas bacteria. Starvation also led to significant alterations in host gene expression in the intestine, with distinct pathways affected at early and late stages of starvation. This included increases in the expression of ribosome biogenesis genes early in starvation, followed by decreased expression of genes involved in antiviral immunity and at later stages. These effects of starvation on the host transcriptome and microbiome were within 3 days after refeeding. Comparison with published datasets identified host genes responsive to starvation as well as high-fat feeding or microbiome colonization, and predicted host transcription factors that may be involved in starvation response. Conclusions: Long-term starvation induces progressive changes in microbiome composition and host gene expression in the zebrafish intestine, and these changes are rapidly reversed after refeeding. Our identification of bacterial taxa, host genes and host pathways involved in this response provides a framework for future investigation of the physiological and ecological mechanisms underlying intestinal adaptations to food restriction.

scholarly journals Using supraglottic airways by paramedics for airway management in analogue microgravity increases speed and success of ventilation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jochen Hinkelbein ◽  
Anton Ahlbäck ◽  
Christine Antwerber ◽  
Lisa Dauth ◽  
James DuCanto ◽  
...  
Keyword(s):  
Airway Management ◽  
Success Rate ◽  
Simulated Microgravity ◽  
Laryngeal Tube ◽  
Space Missions ◽  
Airway Device ◽  
Future Space ◽  
Secondary Endpoints ◽  
Present Trial

AbstractIn the next few years, the number of long-term space missions will significantly increase. Providing safe concepts for emergencies including airway management will be a highly challenging task. The aim of the present trial is to compare different airway management devices in simulated microgravity using a free-floating underwater scenario. Five different devices for airway management [laryngeal mask (LM), laryngeal tube (LT), I-GEL, direct laryngoscopy (DL), and video laryngoscopy (VL)] were compared by n = 20 paramedics holding a diving certificate in a randomized cross-over setting both under free-floating conditions in a submerged setting (pool, microgravity) and on ground (normogravity). The primary endpoint was the successful placement of the airway device. The secondary endpoints were the number of attempts and the time to ventilation. A total of 20 paramedics (3 female, 17 male) participated in this study. Success rate was highest for LM and LT and was 100% both during simulated microgravity and normogravity followed by the I-GEL (90% during microgravity and 95% during normogravity). However, the success rate was less for both DL (60% vs. 95%) and VL (20% vs. 60%). Fastest ventilation was performed with the LT both in normogravity (13.7 ± 5.3 s; n = 20) and microgravity (19.5 ± 6.1 s; n = 20). For the comparison of normogravity and microgravity, time to ventilation was shorter for all devices on the ground (normogravity) as compared underwater (microgravity). In the present study, airway management with supraglottic airways and laryngoscopy was shown to be feasible. Concerning the success rate and time to ventilation, the optimum were supraglottic airways (LT, LM, I-GEL) as their placement was faster and associated with a higher success rate. For future space missions, the use of supraglottic airways for airway management seems to be more promising as compared to tracheal intubation by DL or VL.

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