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

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):  
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 Effect of a bioconverted product of Lotus corniculatus seed on the axillary microbiome and body odor

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Min-Ji Kim ◽  
Setu Bazie Tagele ◽  
HyungWoo Jo ◽  
Min-Chul Kim ◽  
YeonGyun Jung ◽  
...  
Keyword(s):  
Volatile Fatty Acids ◽  
Profile Analysis ◽  
16S Rrna Gene Sequencing ◽  
Lotus Corniculatus ◽  
Biologically Active ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Body Odor ◽  
Rrna Gene Sequencing ◽  
Study Participants

AbstractThe skin microbiome, especially the axillary microbiome, consists of odor-causing bacteria that decompose odorless sweat into malodor compounds, which contributes to the formation of body odor. Plant-derived products are a cheap source of bioactive compounds that are common ingredients in cosmetics. Microbial bioconversion of natural products is an ecofriendly and economical method for production of new or improved biologically active compounds. Therefore, in this study, we tested the potential of a Lactobacillus acidophilus KNU-02-mediated bioconverted product (BLC) of Lotus corniculatus seed to reduce axillary malodor and its effect on the associated axillary microbiota. A chemical profile analysis revealed that benzoic acid was the most abundant chemical compound in BLC, which increased following bioconversion. Moreover, BLC treatment was found to reduce the intensity of axillary malodor. We tested the axillary microbiome of 18 study participants, divided equally into BLC and placebo groups, and revealed through 16S rRNA gene sequencing that Staphylococcus, Corynebacterium, and Anaerococcus were the dominant taxa, and some of these taxa were significantly associated with axillary malodor. After one week of BLC treatment, the abundance of Corynebacterium and Anaerococcus, which are associated with well-known odor-related genes that produce volatile fatty acids, had significantly reduced. Likewise, the identified odor-related genes decreased after the application of BLC. BLC treatment enhanced the richness and network density of the axillary microbial community. The placebo group, on the other hand, showed no difference in the microbial richness, odor associated taxa, and predicted functional genes after a week. The results demonstrated that BLC has the potential to reduce the axillary malodor and the associated odor-causing bacteria, which makes BLC a viable deodorant material in cosmetic products.

scholarly journals Skin bacteria of rainbow trout antagonistic to the fish pathogen Flavobacterium psychrophilum

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mio Takeuchi ◽  
Erina Fujiwara-Nagata ◽  
Taiki Katayama ◽  
Hiroaki Suetake
Keyword(s):  
Rainbow Trout ◽  
Culture Media ◽  
Amplicon Sequencing ◽  
Effective Vaccine ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Fish Disease ◽  
Flavobacterium Psychrophilum ◽  
Skin Bacteria ◽  
Coldwater Disease

AbstractRainbow trout fry syndrome (RTFS) and bacterial coldwater disease (BCWD) is a globally distributed freshwater fish disease caused by Flavobacterium psychrophilum. In spite of its importance, an effective vaccine is not still available. Manipulation of the microbiome of skin, which is a primary infection gate for pathogens, could be a novel countermeasure. For example, increasing the abundance of specific antagonistic bacteria against pathogens in fish skin might be effective to prevent fish disease. Here, we combined cultivation with 16S rRNA gene amplicon sequencing to obtain insight into the skin microbiome of the rainbow trout (Oncorhynchus mykiss) and searched for skin bacteria antagonistic to F. psychrophilum. By using multiple culture media, we obtained 174 isolates spanning 18 genera. Among them, Bosea sp. OX14 and Flavobacterium sp. GL7 respectively inhibited the growth of F. psychrophilum KU190628-78 and NCIMB 1947T, and produced antagonistic compounds of < 3 kDa in size. Sequences related to our isolates comprised 4.95% of skin microbial communities, and those related to strains OX14 and GL7 respectively comprised 1.60% and 0.17% of the skin microbiome. Comparisons with previously published microbiome data detected sequences related to strains OX14 and GL7 in skin of other rainbow trout and Atlantic salmon.

scholarly journals Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Yacine Amar ◽  
Ilias Lagkouvardos ◽  
Rafaela L. Silva ◽  
Oluwaseun Ayodeji Ishola ◽  
Bärbel U. Foesel ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Bacterial Load ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Mock Community ◽  
Skin Bacteria ◽  
Α Diversity ◽  
Microbial Turnover ◽  
Microbial Dna

Abstract Background The identification of microbiota based on next-generation sequencing (NGS) of extracted DNA has drastically improved our understanding of the role of microbial communities in health and disease. However, DNA-based microbiome analysis cannot per se differentiate between living and dead microorganisms. In environments such as the skin, host defense mechanisms including antimicrobial peptides and low cutaneous pH result in a high microbial turnover, likely resulting in high numbers of dead cells present and releasing substantial amounts of microbial DNA. NGS analyses may thus lead to inaccurate estimations of microbiome structures and consequently functional capacities. Results We investigated in this study the feasibility of a Benzonase-based approach (BDA) to pre-digest unprotected DNA, i.e., of dead microbial cells, as a method to overcome these limitations, thus offering a more accurate assessment of the living microbiome. A skin mock community as well as skin microbiome samples were analyzed using 16S rRNA gene sequencing and metagenomics sequencing after DNA extraction with and without a Benzonase digest to assess bacterial diversity patterns. The BDA method resulted in less reads from dead bacteria both in the skin mock community and skin swabs spiked with either heat-inactivated bacteria or bacterial-free DNA. This approach also efficiently depleted host DNA reads in samples with high human-to-microbial DNA ratios, with no obvious impact on the microbiome profile. We further observed that low biomass samples generate an α-diversity bias when the bacterial load is lower than 105 CFU and that Benzonase digest is not sufficient to overcome this bias. Conclusions The BDA approach enables both a better assessment of the living microbiota and depletion of host DNA reads. Graphical abstract

scholarly journals Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Marine Drugs ◽  
2020 ◽  
Vol 18 (6) ◽  
pp. 298
Author(s):  
Alison E. Murray ◽  
Nicole E. Avalon ◽  
Lucas Bishop ◽  
Karen W. Davenport ◽  
Erwan Delage ◽  
...  
Keyword(s):  
Marine Invertebrate ◽  
Bioactive Compound ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Specific Sequence ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
The Core ◽  
Synoicum Adareanum ◽  
Palmerolide A

Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64°46′ S, 64°03′ W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.

PSIX-3 Comparison of 16S rRNA gene profiles of rumen microbiome from Raramuri Criollo, European and Criollo x European lineages

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 441-442
Author(s):  
Adrian Maynez-Perez ◽  
Francisco Jahuey-Martinez ◽  
Jose A Martinez-Quintana ◽  
Michael E Hume ◽  
Robin C Anderson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Beta Diversity ◽  
Chihuahuan Desert ◽  
Reference Database ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Microbiome Composition ◽  
Northern Mexico ◽  
Rumen Microbiome

Abstract Raramuri Criollo cattle from the Chihuahuan desert in northern Mexico have been described as an ecological ecotype due to their enormous advantage in land grass utilization and their capacity to diversify their diet with cacti, forbs and woody plants. This diversification in diet utilization, could reflect upon their microbiome composition. The aim of this study was to characterize the rumen microbiome of Raramuri criollo cattle and to compare it to other lineages that graze in the same area. A total of 28 cows representing three linages [Criollo (n = 13), European (n = 9) and Criollo x European Crossbred (n = 6)] were grazed without supplementation for 45 days. DNA was extracted from ruminal samples and the V4 region of the 16S rRNA gene was sequenced on an Illumina platform. Data were analyzed with the QIIME2 software package and DADA2 plugin and the amplicon sequence variants were taxonomically classified with naïve Bayesian using the SILVA 16S rRNA gene reference database (version 132). Statistical analysis was performed by ANOVA and PERMANOVA for alpha and beta diversity indexes, respectively, and the non-strict version of linear discriminant analysis effect size (LEfSe) was used to determine significantly different taxa among lineages. Differences in beta diversity indexes (P &lt; 0.05) were found in ruminal microbiome composition between Criollo and European groups, whereas the Crossbred showed intermediate values when compared to the pure breeds (Table 1). LEfSe analysis identified a total of 20 bacterial groups that explained differences between lineages, including one for Crossbreed, ten for European and nine for Criollo. These results show ruminal microbiome differences between Raramuri criollo cattle and the mainstream European breeds used in the northern Mexico Chihuahuan desert and reflect that those differences could be a consequence of dissimilar grazing behavior.

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