scholarly journals Temporal and Spatial Analysis of Forward and Backward Microbial Contamination in a Mars Analog Mission

2021 ◽  
Vol 8 ◽  
Author(s):  
Yael Yair ◽  
Leah Reshef ◽  
Camelia Shopen-Gochev ◽  
Gal Yoffe ◽  
Gil Azulay ◽  
...  
Keyword(s):  
Diversity Index ◽  
Environmental Dna ◽  
Population Diversity ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Mars Analog ◽  
Sequencing Platforms ◽  
Contamination Events

As human exploration missions to Mars are on the horizon, microbial cross-contamination remains a key issue to address. These issues can be approached today using advances in molecular metagenomics methods, which include rapid and sensitive sequencing platforms for characterizing microbial populations. Combined with analog missions, these methods provide powerful tools for assessing the challenges associated with planetary exploration. Here, we designed a protocol to monitor forward and backward contamination events and progression in an 11-days Mars analog mission in the Ramon crater in Israel. Forward contamination soil samples were collected daily from three sites–two sites in close proximity to the habitat and one isolated site. Backward contamination was determined in samples from nitrile gloves of six analog astronauts before and after extravehicular activities Temperature, relative humidity and soil composition data were also collected for all sites. Environmental DNA samples were extracted in the main habitat and 16S (bacterial) and 18S (eukaryotic, fungal) rRNA gene amplicons were sequenced and analyzed to study microbial population diversity and composition. Shannon Diversity index analysis and Principal Coordinates analysis (PCoA) of rRNA genes indicated that differences in the diversity and population composition were significant in sites closer to the habitat when compared to a reference site. These samples also demonstrated the introduction of human-associated taxa to the environment. Backward contamination consisted of bacterial taxa found on gloves upon return from EVA and also detected in soil, altogether 44 genera, indicating backward contamination events. To our knowledge, this is the first protocol to utilize advanced molecular technologies to investigate forward and backward contamination in a Mars analog mission.

scholarly journals Comparative analysis of the tonsillar microbiota in IgA nephropathy and other glomerular diseases

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ji In Park ◽  
Tae-Yoon Kim ◽  
Bumjo Oh ◽  
Hyunjeong Cho ◽  
Ji Eun Kim ◽  
...  
Keyword(s):  
Immunoglobulin A ◽  
Upper Airway ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Healthy Controls ◽  
Principal Coordinates Analysis ◽  
Glomerular Diseases ◽  
Principal Coordinates ◽  
Airway Infections ◽  
Repeated Events

Abstract Immunoglobulin A nephropathy (IgAN) involves repeated events of gross haematuria with concurrent upper airway infections. The mucosal immune system, especially the tonsil, is considered the initial site of inflammation, although the role of the tonsillar microbiota has not been established in IgAN. In this study, we compared the tonsillar microbiota of patients with IgAN (n = 21) and other glomerular diseases (n = 36) as well as, healthy controls (n = 23) from three medical centres in Korea. The microbiota was analysed from tonsil swabs using the Illumina MiSeq system based on 16S rRNA gene. Tonsillar bacterial diversity was higher in IgAN than in other glomerular diseases, although it did not differ from that of healthy controls. Principal coordinates analysis revealed differences between the tonsillar microbiota of IgAN and both healthy and disease controls. The proportions of Rahnella, Ruminococcus_g2, and Clostridium_g21 were significantly higher in patients with IgAN than in healthy controls (corrected p < 0.05). The relative abundances of several taxa were correlated with the estimated glomerular filtration rate, blood urea nitrogen, haemoglobin, and serum albumin levels. Based on our findings, tonsillar microbiota may be associated with clinical features and possible immunologic pathogenesis of IgAN.

scholarly journals Understanding population differentiation using geographical, morphological and genetic characterization in Erodium cicunium

2020 ◽  
Vol 80 (04) ◽  
Author(s):  
Xingxing Si ◽  
Lei GAO ◽  
Yuwei Song ◽  
Majid Khayatnezhad ◽  
Amir Abbas Minaeifar
Keyword(s):  
Genetic Difference ◽  
Morphological Characters ◽  
Molecular Data ◽  
Population Diversity ◽  
Start Codon ◽  
Principal Coordinates Analysis ◽  
Forage Plants ◽  
Principal Coordinates ◽  
Geographical Populations ◽  
Study Population

Erodium cicunium (Geraniaceae) species are distributed in different habitats of Iran. Some species are of medicinal importance while some are well known weeds and used as forage plants. An investigation was carried out to evaluate 124 randomly collected plants of E. cicunium from 15 geographical populations in 5 provinces to study population structure and for morphological and molecular characters. Start Codon Targeted (SCoT) markers were used to analyse molecular diversity. Analysis of molecular variance (AMOVA) revealed significant genetic difference among the studied populations and also revealed that 60% of total genetic variability was due to within population diversity, while 40% genetic differentiation was recorded among populations. Principal Coordinates Analysis (PCoA) of populations based on morphological characters was not in agreement with Metric Multidimensional Scaling (MDS) plot of molecular data.

scholarly journals Comparison of human gut microbial profiles of matched faecal and biopsy samples from healthy individuals using culture dependent and independent methods

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Indrani Mukhopadhya ◽  
Jenny Martin ◽  
Sophie Shaw ◽  
Irini Lazou Ahrén ◽  
Niklas Larsson ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Healthy Volunteers ◽  
Distance Matrix ◽  
Gastrointestinal Diseases ◽  
Rrna Gene ◽  
Sequence Variant ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Faecal Samples ◽  
The Family

Faecal samples have often been used to characterise the gut microbiota in health and disease. There is significant debate whether faecal bacterial communities accurately reflect the mucosa associated bacterial populations, which are considered critical in the aetiopathogenesis of several gastrointestinal diseases. We simultaneously assessed faecal and mucosal microbiota from healthy volunteers to unravel the degree of concordance between the two profiles. Paired fresh rectal biopsies and faecal samples were obtained from ten healthy volunteers and processed under stringent anaerobic conditions. Composition and diversity of the microbiota were studied using next generation sequencing targeting the 16S ribosomal nucleic acid (rRNA) gene and culturomics. Bacterial richness and diversity were comparable between mucosal and faecal samples with no significant statistical differences. The relative abundance of Oxalobacteraceae, Propionibacteriaceae, Campylobacteraceae and Corynebacteriaceae were significantly increased (Corncob analysis; FDR=0.00027, 0.000046, 0.011 and 0.025 respectively) in biopsy compared to faecal samples at the family level. Conversely, there was increased abundance from the family Ruminococcaceae and Clostridiaceae (Corncob analysis; FDR=0.025 and 0.025 respectively) in faecal samples. Principal Coordinates Analysis of a Bray Curtis distance matrix generated from sequence variant tables did not show distinct clustering of biopsy and faecal samples (PERMANOVA; p=0.991). A total of 528 bacteria were isolated from a subset of 6 volunteer samples (biopsy and faeces) out of which there were 97 unique and 39 novel species identified. Our study showed good concordance between faecal and gut mucosal microbial profile, corroborating that faecal samples can act as a convenient surrogate to study gut microbiota.

scholarly journals Changes in the gut bacterial communities in colon cancer surgery patients: an observational study

Gut Pathogens ◽  
2022 ◽  
Vol 14 (1) ◽  
Author(s):  
Mohamed Abbas ◽  
Nadia Gaïa ◽  
Nicolas C. Buchs ◽  
Vaihere Delaune ◽  
Myriam Girard ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Bacterial Communities ◽  
Antimicrobial Prophylaxis ◽  
Colon Surgery ◽  
Cancer Surgery ◽  
Gene Marker ◽  
Rrna Gene ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Colon Cancer Surgery

Abstract Background Colon surgery has been shown to modulate the intestinal microbiota. Our objective was to characterize these changes using state-of-the-art next generation sequencing techniques. Methods We performed a single-centre prospective observational cohort study to evaluate the changes in the gut microbiota, i.e., taxon distribution, before and after elective oncologic colon surgery in adult patients with different antimicrobial prophylaxis regimens (standard prophylaxis with cefuroxime/metronidazole versus carbapenems for extended-spectrum beta-lactamase-producing Enterobacterales [ESBL-E] carriers). We obtained rectal samples on the day of surgery, intraoperative luminal samples, and rectal or stoma samples 3 days after surgery. We performed metataxonomic analysis based on sequencing of the bacterial 16S rRNA gene marker. Similarities and differences between bacterial communities were assessed using Bray–Curtis similarity, visualised using principal coordinates analysis and statistically tested by PERMANOVA. Comparison of taxa relative abundance was performed using ANCOM. Results We included 27 patients between March 27, 2019 and September 17, 2019. The median age was 63.6 years (IQR 56.4–76.3) and 44% were females. Most (81%) patients received standard perioperative prophylaxis as they were not ESBL carriers. There was no significant association between ESBL carriage and differences in gut microbiome. We observed large and significant increases in the genus Enterococcus between the preoperative/intraoperative samples and the postoperative sample, mainly driven by Enterococcus faecalis. There were significant differences in the postoperative microbiome between patients who received standard prophylaxis and carbapenems, specifically in the family Erysipelotrichaceae. Conclusion This hypothesis-generating study showed rapid changes in the rectal microbiota following colon cancer surgery.

scholarly journals The Root Nodule Microbiome of Cultivated and Wild Halophytic Legumes Showed Similar Diversity but Distinct Community Structure in Yellow River Delta Saline Soils

2020 ◽  
Vol 8 (2) ◽  
pp. 207 ◽  
Author(s):  
Yanfen Zheng ◽  
Jing Liang ◽  
Dong-Lin Zhao ◽  
Chen Meng ◽  
Zong-Chang Xu ◽  
...  
Keyword(s):  
Root Nodule ◽  
Yellow River ◽  
Glycine Soja ◽  
Bacterial Species ◽  
Yellow River Delta ◽  
River Delta ◽  
Saline Soils ◽  
Rrna Gene ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates

Symbiotic associations between leguminous plants and their nodule microbiome play a key role in sustainable agriculture by facilitating the fixation of atmospheric nitrogen and enhancing plant stress resistance. This study aimed to decipher the root nodule microbiome of two halophytic legumes, Sesbania cannabina and Glycine soja, which grow in saline soils of the Yellow River Delta, China, using PacBio’s circular consensus sequencing for full-length bacterial 16S rRNA gene to obtain finer taxonomic information. The cultivated legume Glycine max was used for comparison. We identified 18 bacterial genera and 55 species in nodule samples, which mainly classified to Proteobacteria, and rhizobial genus Ensifer was the predominant group. The three legumes showed similarity in operational taxonomic unit (OTU) diversity but distinction in OTU richness, indicating that they harbor similar bacterial species with different relative contents. The results of principal coordinates analysis and ANOSIM tests indicated that G. soja and G. max have similar nodule bacterial communities, and these communities differ from that of S. cannabina. Wild legumes S. cannabina and G. soja both harbored a higher number of rhizobia, while G. max possessed more non-rhizobial bacteria. These differences could be associated with their adaptability to saline–alkali stress and revealed clues on the nodule endophytes with relative importance of culturable rhizobial symbionts.

scholarly journals Gut microbial characteristics of adult patients with allergy rhinitis

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Libing Zhu ◽  
Feng Xu ◽  
Wenrong Wan ◽  
Bin Yu ◽  
Lin Tang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacterial Diversity ◽  
Bacterial Invasion ◽  
Rrna Gene ◽  
Life Questionnaire ◽  
Healthy Individuals ◽  
Alpha Linolenic Acid ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Significant Difference

Abstract Background Although recent studies have indicated that intestinal microbiota dweller are involved in the pathogenesis of allergy rhinitis (AR), the influence of gut microbiota on AR adult has not been fully elucidated yet. Hence, we carried out this study to uncover the distinctive bacterial taxa that differentiate allergy rhinitis patients from healthy individuals. Feces samples from thirty three AR patients and thirty one healthy individuals were analyzed by 16S rRNA gene sequencing. Results Results showed that the bacterial diversity in AR group was significantly higher than that of the non-AR group. Bacterial communities between AR and non-AR group were significantly differentiated as revealed by Principal coordinates analysis (PCoA) and the variation within non-AR were higher than that of the counterpart. Firmicutes, Fusobacteria, Actinobacteria, Cyanobacteria and Chloroflexi were the significantly differed phyla taxa and the top significantly distinguished bacterial genus included Prevotella_9, Phascolarctobacterium, Roseburia, Megamonas, Alistipes, Lachnoclostridium and Fusobacterium. The higher network complexity in AR group were dominated by taxa belonging to Firmicutes. The predicted function, alpha linolenic acid metabolism and bacterial invasion of epithelial cells pathway were higher in non-AR group while gonadotropin-releasing hormone (GnRH) signaling pathway, Fc γ-R mediated phagocytosis and endocytosis were higher in AR patients. Although the bacterial diversity between moderate and severe AR patients showed no significant difference, the significant correlation between featured genus and total nasal symptom score or rhinoconjunctivitis quality of life questionnaire, such as Butyricicoccus and Eisenbergiella, revealed the potential to intervene the AR status by means of gut microbiota. Conclusions In conclusion, patients with allergy rhinitis had distinguished gut microbiota characteritics in comparison with healthy controls. The results suggest that gut microbiota might play crucial roles in influencing the course and different symptoms of AR. Trial registration ChiCTR, ChiCTR1900028613. Registered 29 December 2019, https://www.chictr.org.cn/showproj.aspx?proj=47650.

scholarly journals The Impact of NOD2 Genetic Variants on the Gut Mycobiota in Crohn’s Disease Patients in Remission and in Individuals Without Gastrointestinal Inflammation

2020 ◽  
Author(s):  
Andrew Nelson ◽  
Christopher J Stewart ◽  
Nicholas A Kennedy ◽  
John K Lodge ◽  
Mark Tremelling ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Relative Abundance ◽  
Mucosal Inflammation ◽  
Rrna Gene ◽  
Wild Type ◽  
Candida Spp ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
The Impact

Abstract Background and Aims Historical and emerging data implicate fungi in Crohn’s disease [CD] pathogenesis. However, a causal link between mycobiota, dysregulated immunity, and any impact of NOD2 variants remains elusive. This study aims to evaluate associations between NOD2 variants and faecal mycobiota in CD patients and non-CD subjects. Methods Faecal samples were obtained from 34 CD patients [18 NOD2 mutant, 16 NOD2 wild-type] identified from the UK IBD Genetics Consortium. To avoid confounding influence of mucosal inflammation, CD patients were in clinical remission and had a faecal calprotectin &lt;250 μg/g; 47 non-CD subjects were included as comparator groups, including 22 matched household [four NOD2 mutant] and 25 non-household subjects with known NOD2 genotype [14 NOD2 mutant] identified by the NIHR BioResource Cambridge. Faecal mycobiota composition was determined using internal transcribed spacer 1 [ITS1] sequencing and was compared with 16S rRNA gene sequences and volatile organic compounds. Results CD was associated with higher numbers of fungal observed taxonomic units [OTUs] [p = 0.033]. Principal coordinates analysis using Jaccard index [p = 0.018] and weighted Bray-Curtis dissimilarities [p = 0.01] showed Candida spp. clustered closer to CD patients whereas Cryptococcus spp. clustered closer to non-CD. In CD, we found higher relative abundance of Ascomycota [p = 0.001] and lower relative abundance Basidiomycota [p = 0.019] phyla. An inverse relationship was found between bacterial and fungal Shannon diversity in NOD2 wild-type which was independent of CD [r = -0.349; p = 0.029]. Conclusions This study confirms compositional changes in the gut mycobiota in CD and provides evidence that fungi may play a role in CD pathogenesis. No NOD2 genotype-specific differences were observed in the faecal mycobiota.

scholarly journals Comparative Analysis of Gut Microbiota in Captive and Wild Oriental White Storks: Implications for Conservation Biology

2021 ◽  
Vol 12 ◽  
Author(s):  
Hong Wu ◽  
Fang-Ting Wu ◽  
Qi-Hai Zhou ◽  
Da-Peng Zhao
Keyword(s):  
Community Structure ◽  
Comparative Analysis ◽  
Gut Microbiota ◽  
Species Composition ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Α Diversity ◽  
White Storks

The oriental white stork (Ciconia boyciana) is considered an endangered species based on the International Union for Conservation of Nature (IUCN) Red List. This study presents the first evidence on comparative analysis of gut microbial diversity of C. boyciana from various breeding conditions. To determine the species composition and community structure of the gut microbiota, 24 fecal samples from Tianjin Zoo and Tianjin Qilihai Wetland were characterized by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Firmicutes was found to be the predominant phylum. Analysis of community structure revealed significant differences in the species diversity and richness between the populations of the two breeding conditions. The greatest α-diversity was found in wild C. boyciana, while artificial breeding storks from Tianjin Zoo had the least α-diversity. Principal coordinates analysis showed that the microbial communities were different between the two studied groups. In conclusion, this study reveals the species composition and structure of the gut microbiota of oriental white storks under two breeding conditions, and our findings could contribute to the integrative conservation of this endangered bird.

scholarly journals Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

2016 ◽  
Author(s):  
Patrick D Schloss ◽  
Matthew L Jenior ◽  
Charles C. Koumpouras ◽  
Sarah L Westcott ◽  
Sarah K Highlander
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Sequencing ◽  
Error Rate ◽  
Full Length ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Mock Community ◽  
Sequencing Platforms ◽  
The 16S Rrna Gene

Over the past 10 years, microbial ecologists have largely abandoned sequencing 16S rRNA genes by the Sanger sequencing method and have instead adopted highly parallelized sequencing platforms. These new platforms, such as 454 and Illumina's MiSeq, have allowed researchers to obtain millions of high quality, but short sequences. The result of the added sequencing depth has been significant improvements in experimental design. The tradeoff has been the decline in the number of full-length reference sequences that are deposited into databases. To overcome this problem, we tested the ability of the PacBio Single Molecule, Real-Time (SMRT) DNA sequencing platform to generate sequence reads from the 16S rRNA gene. We generated sequencing data from the V4, V3-V5, V1-V3, V1-V5, V1-V6, and V1-V9 variable regions from within the 16S rRNA gene using DNA from a synthetic mock community and natural samples collected from human feces, mouse feces, and soil. The mock community allowed us to assess the actual sequencing error rate and how that error rate changed when different curation methods were applied. We developed a simple method based on sequence characteristics and quality scores to reduce the observed error rate for the V1-V9 region from 0.69 to 0.027%. This error rate is comparable to what has been observed for the shorter reads generated by 454 and Illumina's MiSeq sequencing platforms. Although the per base sequencing cost is still significantly more than that of MiSeq, the prospect of supplementing reference databases with full-length sequences from organisms below the limit of detection from the Sanger approach is exciting.

Genetic characteristics of broodstock and offspring of the seven-band grouper (Hyporthodus septemfasciatus) using fluorescent-AFLP markers

2016 ◽  
Vol 98 (2) ◽  
pp. 261-267
Author(s):  
Yongshuang Xiao ◽  
Shuguang Guan ◽  
Qinghua Liu ◽  
Hongjun Liu ◽  
Daode Yu ◽  
...  
Keyword(s):  
Diversity Index ◽  
Rocky Reef ◽  
Negative Effects ◽  
Principal Coordinates Analysis ◽  
Genetic Characteristics ◽  
Principal Coordinates ◽  
Sustainable Culture ◽  
Breeding Programmes ◽  
Commercial Breeding ◽  
Rocky Reef Fish

Seven-band grouper (Hyporthodus septemfasciatus) is a commercial rocky reef fish in East Asia that has been regarded as a promising species for aquaculture. To investigate the broodstock contributions to offspring for the sustainability of fry production, 62 individuals ofH. septemfasciatusfrom two broodstocks and one offspring population were analysed using fluorescent-AFLP. A total of 602 bands were amplified and 70.10% of them were polymorphic. The numbers of polymorphic loci were 308 (Pbroodstock I= 55.50%) and 356 (Pbroodstock II= 63.12%) in the two broodstocks, and 294 (Poffspring= 52.88%) in the offspring, respectively. The average values of Shannon diversity index (I) and expected heterozygosity (H) were higher in the broodstock (Ibroodstock I= 0.281,Ibroodstock II= 0.244,Hbroodstock I= 0.185,Hbroodstock II= 0.161) than those in the offspring (Ioffspring= 0.243,Hoffspring= 0.161). AMOVA and FSTanalyses showed that significant genetic differentiation between broodstock and offspring populations, and limited effective broodstock population size has contributed to the offspring. Both STRUCTURE and Principal Coordinates Analysis (PCoA) also showed the three populations composed of two stocks and most offspring individuals (95.0%) only originated from 44.0% of the individuals of broodstock I, which may have negative effects on sustainable fry production. Therefore, genetic variation between broodstock and offspring should be monitored, and large effective size of broodstock should be employed to ensure the success of commercial breeding programmes. Our data provide a useful genetic basis for future planning of sustainable culture and management ofH. septemfasciatus.

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