scholarly journals Highly Variable and Non-complex Diazotroph Communities in Corals From Ambient and High CO2 Environments

2021 ◽  
Vol 8 ◽  
Author(s):  
Laura Geissler ◽  
Valentine Meunier ◽  
Nils Rädecker ◽  
Gabriela Perna ◽  
Riccardo Rodolfo-Metalpa ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Coral Species ◽  
Amplicon Sequencing ◽  
Pocillopora Damicornis ◽  
Bacterial Assemblage ◽  
Galaxea Fascicularis ◽  
Coral Holobiont ◽  
Community Assemblages ◽  
Community Variability ◽  
Family Rhodobacteraceae

The ecological success of corals depends on their association with microalgae and a diverse bacterial assemblage. Ocean acidification (OA), among other stressors, threatens to impair host-microbial metabolic interactions that underlie coral holobiont functioning. Volcanic CO2 seeps offer a unique opportunity to study the effects of OA in natural reef settings and provide insight into the long-term adaptations under a low pH environment. Here we compared nitrogen-fixing bacteria (diazotrophs) associated with four coral species (Pocillopora damicornis, Galaxea fascicularis, Acropora secale, and Porites rus) collected from CO2 seeps at Tutum Bay (Papua New Guinea) with those from a nearby ambient CO2 site using nifH amplicon sequencing to characterize the effects of seawater pH on bacterial communities and nitrogen cycling. Diazotroph communities were of generally low diversity across all coral species and for both sampling sites. Out of a total of 25 identified diazotroph taxa, 14 were associated with P. damicornis, of which 9 were shared across coral species. None of the diazotroph taxa, however, were consistently found across all coral species or across all samples within a species pointing to a high degree of diazotroph community variability. Rather, the majority of sampled colonies were dominated by one or two diazotroph taxa of high relative abundance. Pocillopora damicornis and Galaxea fascicularis that were sampled in both environments showed contrasting community assemblages between sites. In P. damicornis, Gammaproteobacteria and Cyanobacteria were prevalent under ambient pCO2, while a single member of the family Rhodobacteraceae was present at high relative abundance at the high pCO2 site. Conversely, in G. fascicularis diazotroph communities were indifferent between both sites. Diazotroph community changes in response to OA seem thus variable within as well as between host species, potentially arguing for haphazard diazotroph community assembly. This warrants further research into the underlying factors structuring diazotroph community assemblages and their functional role in the coral holobiont.

scholarly journals Conventional myelosuppressive chemotherapy for non-haematological malignancy disrupts the intestinal microbiome

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lito E. Papanicolas ◽  
Sarah K. Sims ◽  
Steven L. Taylor ◽  
Sophie J. Miller ◽  
Christos S. Karapetis ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Haematological Malignancy ◽  
Amplicon Sequencing ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Conventional Chemotherapy ◽  
Myelosuppressive Chemotherapy ◽  
Gram Positive Bacteria ◽  
Faecal Samples

Abstract Background The gut microbiota influences many aspects of host physiology, including immune regulation, and is predictive of outcomes in cancer patients. However, whether conventional myelosuppressive chemotherapy affects the gut microbiota in humans with non-haematological malignancy, independent of antibiotic exposure, is unknown. Methods Faecal samples from 19 participants with non-haematological malignancy, who were receiving conventional chemotherapy regimens but not antibiotics, were examined prior to chemotherapy, 7–12 days after chemotherapy, and at the end of the first cycle of treatment. Gut microbiota diversity and composition was determined by 16S rRNA gene amplicon sequencing. Results Compared to pre-chemotherapy samples, samples collected 7–12 days following chemotherapy exhibited increased richness (mean 120 observed species ± SD 38 vs 134 ± 40; p = 0.007) and diversity (Shannon diversity: mean 6.4 ± 0.43 vs 6.6 ± 0.41; p = 0.02). Composition was significantly altered, with a significant decrease in the relative abundance of gram-positive bacteria in the phylum Firmicutes (pre-chemotherapy median relative abundance [IQR] 0.78 [0.11] vs 0.75 [0.11]; p = 0.003), and an increase in the relative abundance of gram-negative bacteria (Bacteroidetes: median [IQR] 0.16 [0.13] vs 0.21 [0.13]; p = 0.01 and Proteobacteria: 0.015 [0.018] vs 0.03 [0.03]; p = 0.02). Differences in microbiota characteristics from baseline were no longer significant at the end of the chemotherapy cycle. Conclusions Conventional chemotherapy results in significant changes in gut microbiota characteristics during the period of predicted myelosuppression post-chemotherapy. Further study is indicated to link microbiome changes during chemotherapy to clinical outcomes.

scholarly journals Gut Microbiome and Metabolome Profiles Associated with High-Fat Diet in Mice

Metabolites ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 482
Author(s):  
Jae-Kwon Jo ◽  
Seung-Ho Seo ◽  
Seong-Eun Park ◽  
Hyun-Woo Kim ◽  
Eun-Ju Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
High Fat Diet ◽  
Amplicon Sequencing ◽  
Gas Chromatography Mass Spectrometry ◽  
Control Group ◽  
Rrna Gene ◽  
High Fat ◽  
Underlying Mechanisms ◽  
Insight Into

Obesity can be caused by microbes producing metabolites; it is thus important to determine the correlation between gut microbes and metabolites. This study aimed to identify gut microbiota-metabolomic signatures that change with a high-fat diet and understand the underlying mechanisms. To investigate the profiles of the gut microbiota and metabolites that changed after a 60% fat diet for 8 weeks, 16S rRNA gene amplicon sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomic analyses were performed. Mice belonging to the HFD group showed a significant decrease in the relative abundance of Bacteroidetes but an increase in the relative abundance of Firmicutes compared to the control group. The relative abundance of Firmicutes, such as Lactococcus, Blautia, Lachnoclostridium, Oscillibacter, Ruminiclostridium, Harryflintia, Lactobacillus, Oscillospira, and Erysipelatoclostridium, was significantly higher in the HFD group than in the control group. The increased relative abundance of Firmicutes in the HFD group was positively correlated with fecal ribose, hypoxanthine, fructose, glycolic acid, ornithine, serum inositol, tyrosine, and glycine. Metabolic pathways affected by a high fat diet on serum were involved in aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, cysteine and methionine metabolism, glyoxylate and dicarboxylate metabolism, and phenylalanine, tyrosine, and trypto-phan biosynthesis. This study provides insight into the dysbiosis of gut microbiota and metabolites altered by HFD and may help to understand the mechanisms underlying obesity mediated by gut microbiota.

scholarly journals Relative and quantitative rhizosphere microbiome profiling result in distinct abundance patterns

2021 ◽  
Author(s):  
Hamed Azarbad ◽  
Julien Tremblay ◽  
Luke D. Bainard ◽  
Etienne Yergeau
Keyword(s):  
Water Stress ◽  
Relative Abundance ◽  
Its Region ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Real Time Quantitative Pcr ◽  
Rhizosphere Microbiome ◽  
History Of ◽  
Almost All

AbstractNext-generation sequencing is recognized as one of the most popular and cost-effective way of characterizing microbiome in multiple samples. However, most of the currently available amplicon sequencing approaches are inherently limited, as they are often presented based on the relative abundance of microbial taxa, which may not fully represent actual microbiome profiles. Here, we combined amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) with real-time quantitative PCR (qPCR) to characterize the rhizosphere microbiome of wheat. We show that the increase in relative abundance of major microbial phyla does not necessarily result in an increase in abundance. One striking observation when comparing relative and quantitative abundances was a substantial increase in the abundance of almost all phyla associated with the rhizosphere of plants grown in soil with no history of water stress as compared with the rhizosphere of plants growing in soil with a history of water stress, which was in contradiction with the trends observed in the relative abundance data. Our results suggest that the estimated absolute abundance approach gives a different perspective than the relative abundance approach, providing complementary information that helps to better understand the rhizosphere microbiome.

scholarly journals Transgenerational inheritance of shuffled symbiont communities in the coral Montipora digitata

2018 ◽  
Author(s):  
Kate M. Quigley ◽  
Bette L. Willis ◽  
Carly D. Kenkel
Keyword(s):  
Thermal Tolerance ◽  
Coral Species ◽  
Early Life History ◽  
Amplicon Sequencing ◽  
Life History Stages ◽  
Genetic Mechanisms ◽  
Symbiont Transmission ◽  
Plastic Changes ◽  
Cell Densities ◽  
Symbiont Shuffling

AbstractAdult organisms may “prime” their offspring for environmental change through a number of genetic and non-genetic mechanisms, termed parental effects. Some coral species can alter their thermal tolerance by shuffling the proportions of Symbiodinium types within their endosymbiotic communities, but it is unclear if this plasticity can be transferred to offspring in corals that have maternal symbiont transmission. We evaluated symbiont community composition in tagged colonies of Montipora digitata from Orpheus Island, Australia, over two successive annual spawning seasons, the second of which overlapped with the 2016 mass coral bleaching event on the Great Barrier Reef. We applied amplicon sequencing of the ITS2 locus to samples of four families (parent colonies and 10-12 eggs per family) to characterize their potential for symbiont shuffling and to determine if shuffled abundances were preserved in gametes. Symbiont cell densities and photochemical efficiencies of the symbionts’ photosystem II differed significantly among adults in 2016, suggesting differential responses to increased temperatures. Although abundances of the dominant symbiont haplotype, a representative of clade C15, did not differ among families or over time, low-abundance (“background”) ITS2 types differed more among years (2015 vs. 2016) than between life stages (parent vs. offspring). Results indicate that background symbiont shuffling can occur in a canonically ‘stable’ symbiosis, and that such plastic changes to the symbiont community are heritable. To our knowledge, this is the first evidence that shuffled Symbiodinium communities can be inherited by early life-history stages and supports the hypothesis that plastic changes in microbial communities may serve as a mechanism of rapid coral acclimation to changing environmental conditions.

scholarly journals Experimental evidence pointing to rain as a reservoir of tomato phyllosphere microbiota

2021 ◽  
Author(s):  
Marco Enrique Mechan Llontop ◽  
Long Tian ◽  
Parul Sharma ◽  
Logan Heflin ◽  
Vivian Angelica Bernal Galeano ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Microbial Population ◽  
Amplicon Sequencing ◽  
Crop Productivity ◽  
Sterile Water ◽  
Tomato Plants ◽  
Operational Taxonomic Units ◽  
16S Rrna Amplicon Sequencing ◽  
Plant Microbiota

Plant microbiota play essential roles in plant health and crop productivity. Comparisons of community composition have suggested seeds, soil, and the atmosphere as reservoirs of phyllosphere microbiota. After finding that leaves of tomato (Solanum lycopersicum) plants exposed to rain carried a higher microbial population size than leaves of tomato plants not exposed to rain, we experimentally tested the hypothesis that rain is a so far neglected reservoir of phyllosphere microbiota. Rain microbiota were thus compared with phyllosphere microbiota of tomato plants either treated with concentrated rain microbiota, filter-sterilized rain, or sterile water. Based on 16S rRNA amplicon sequencing, one-hundred and four operational taxonomic units (OTUs) significantly increased in relative abundance after inoculation with concentrated rain microbiota but no OTU significantly increased after treatment with either sterile water or filter-sterilized rain. Some of the genera to which these 104 OTUs belonged were also found at higher relative abundance on tomatoes exposed to rain outdoors than on tomatoes grown protected from rain in a commercial greenhouse. Taken together, these results point to precipitation as a reservoir of phyllosphere microbiota and show the potential of controlled experiments to investigate the role of different reservoirs in the assembly of phyllosphere microbiota.

scholarly journals Taxonomic diversity of bacterial assemblage in technosol of the revegetating fly ash dump

2019 ◽  
Vol 2 (3) ◽  
Author(s):  
Natalia B. Naumova ◽  
Ivan P. Belanov ◽  
Tatiana Yu. Alikina
Keyword(s):  
Fly Ash ◽  
16S Rrna ◽  
Thermoelectric Power ◽  
Relative Abundance ◽  
Rrna Genes ◽  
Gene Sequences ◽  
Power Station ◽  
Bacterial Assemblage ◽  
Early Stages ◽  
Bacterial Assemblages

Background. The aim of the study was to assess the composition and structure of bacterial assemblages by estimating 16S rRNA gene sequences diversity in a young Technosol, developing on a revegetating fly ash dump. Location and place of the study. Two soils were chosen for the study in the environs of the thermoelectric power station No.5 in Novosibirsk region: 1) nine years old Technosol (54°59' NL, 83°03' EL), developing on the spontaneously revegetating fly ash dump, and 2) Phaeozem under undisturbed white birch forest (55°00' NL, 83°04' EL). Soils were sampled from the 0-5 cm layer as three individual replicates each. Materials and methods. The total DNA extracted from soil samples was used as a matrix for PCR amplification using V-3-V4 primers for 16S rRNA genes. The obtained amplicons were sequenced on Illumina MiSeq platform in the Genomics Core Facility of the Institute of Chemical Biology and Fundamental Medicine SB RAS (Novosibirsk, Russia). Descriptive statistics and principal components analysis were used to analyze and present the data. Results. Overall 4887 different operational taxonomic units (OTUs) were found at the 97% similarity level; the OTUs were ascribed to 306 genera, 212 families, 123 orders, 84 classes and 32 phyla of bacteria domain. At the phylum level bacterial assemblages in both soils were dominated by Proteobacteria, Acidobacteria and Actinobacteria, showing rather similar outline of the phyla relative abundance, confirming the direction of pedogenesis towards Phaeozem. Higher abundance of Chloroflexi a physiologically diverse phyla with aerobic and anaerobic thermophiles, anoxigenic phototrophs and anaerobes, able to respire organic halides, in the young Technosol complies with harsh edaphic conditions there. Although the relative abundance of Rhizobiales, Actinomycetales and unclassified Acidobacteria_Gp6 and Acidobacteria_Gp3 was found to be 1.5–2.4 times higher in the undisturbed Phaeozem, they also were predominating in the Technosol samples. The α-biodiversity indices, pertaining mostly to species/OTUs richness, i.e. Chao-1, OTUs number, Margalef, Fisher’s alpha, were higher in Phaeozem, whereas evenness and equitability were higher in Technosol. Both soils demonstrated similar Shanno indices, which were rather high (6.3). Conclusions. Nine years of spontaneous revegetation on the terminated fly ash dump of the thermoelectric power station resulted in the development of the Technosol, containing quite rich and diverse bacterial assemblage, which was rather close in structure at the phylum taxonomic level to the adjacent undisturbed Phaeozem. Overall the early stages of pedogenesis were dominated by specific bacterial assemblage (Chloroflexi, Xanthomonadales, Geobacter, Aciditerrimonas, Iamiaceae and some others), performing weathering of the pedogenic substrate, i.e. fly ash. The present of nitrificators (Nitrospira), denitrificators денитрификаторов (Reyranella) together with diazotrophs (Bradyrhizobium, Rhizobiales) dominance evidences the establishment of the entire network of nitrogen transformation process already at the early stages of revegetation of the fly ash dump. Large percentage (17%) of Bacteria, the information about which ribosomal gene sequences is most likely absent in the respective data bases necessitates more detailed research into the soil microbiome on fly ash dumps.

scholarly journals Composition and Diversity of the Ocular Surface Microbiota in Patients With Blepharitis in Northwestern China

2021 ◽  
Vol 8 ◽  
Author(s):  
Changhao Wang ◽  
Xiuhong Dou ◽  
Jian Li ◽  
Jie Wu ◽  
Yan Cheng ◽  
...  
Keyword(s):  
16S Rdna ◽  
Relative Abundance ◽  
Ocular Surface ◽  
Amplicon Sequencing ◽  
Northwestern China ◽  
Healthy Control Group ◽  
Control Group ◽  
Eyelid Margin ◽  
16S Rdna Amplicon Sequencing ◽  
Healthy Control

Purpose: To investigate the composition and diversity of the microbiota on the ocular surface of patients with blepharitis in northwestern China via 16S rDNA amplicon sequencing.Methods: Thirty-seven patients with blepharitis divided into groups of anterior, posterior and mixed blepharitis and twenty healthy controls from northwestern China were enrolled in the study. Samples were collected from the eyelid margin and conjunctival sac of each participant. The V3–V4 region of bacterial 16S rDNA in each sample was amplified and sequenced on the Illumina HiSeq 2500 sequencing platform, and the differences in taxonomy and diversity among different groups were compared.Results: The composition of the ocular surface microbiota of patients with blepharitis was similar to that of healthy subjects, but there were differences in the relative abundance of each bacterium. At the phylum level, the abundances of Actinobacteria, Cyanobacteria, Verrucomicrobia, Acidobacteria, Chloroflexi, and Atribacteria were significantly higher in the blepharitis group than in the healthy control group, while the relative abundance of Firmicutes was significantly lower (p < 0.05, Mann-Whitney U). At the genus level, the abundances of Lactobacillus, Ralstonia, Bacteroides, Akkermansia, Bifidobacterium, Escherichia-Shigella, Faecalibacterium, and Brevibacterium were significantly higher in the blepharitis group than in the healthy control group, while the relative abundances of Bacillus, Staphylococcus, Streptococcus, and Acinetobacter were significantly lower in the blepharitis group (p < 0.05, Mann-Whitney U). The microbiota of anterior blepharitis was similar to that of mixed blepharitis but different from that of posterior blepharitis. Lactobacillus and Bifidobacterium are biomarkers of posterior blepharitis, and Ralstonia is a biomarker of mixed blepharitis. There was no significant difference in the ocular surface microbiota between the eyelid margin and conjunctival sac with or without blepharitis.Conclusion: The ocular surface microbiota of patients with blepharitis varied among different study groups, according to 16S rDNA amplicon sequencing analysis. The reason might be due to the participants being from different environments and having different lifestyles. Lactobacillus, Bifidobacterium, Akkermansia, Ralstonia, and Bacteroides may play important roles in the pathogenesis of blepharitis.

scholarly journals Fungal Signature of Moisture Damage in Buildings: Identification by Targeted and Untargeted Approaches with Mycobiome Data

2020 ◽  
Vol 86 (17) ◽  
Author(s):  
Rachel I. Adams ◽  
Iman Sylvain ◽  
Michal P. Spilak ◽  
John W. Taylor ◽  
Michael S. Waring ◽  
...  
Keyword(s):  
New York ◽  
Health Effects ◽  
Relative Abundance ◽  
A Priori ◽  
Amplicon Sequencing ◽  
Moisture Damage ◽  
Microbiological Analysis ◽  
Indoor Environments ◽  
Adverse Health Effects ◽  
Damage Indicators

ABSTRACT Identifying microbial indicators of damp and moldy buildings remains a challenge at the intersection of microbiology, building science, and public health. Sixty homes in New York City were assessed for moisture-related damage, and three types of dust samples were collected for microbiological analysis. We applied four approaches for detecting fungal signatures of moisture damage in these buildings. Two novel targeted approaches selected specific taxa, identified by a priori hypotheses, from the broad mycobiome as detected with amplicon sequencing. We investigated whether (i) hydrophilic fungi (i.e., requiring high moisture) or (ii) fungi previously reported as indicating damp homes would be more abundant in water-damaged rooms/homes than in nondamaged rooms/homes. Two untargeted approaches compared water-damaged to non-water-damaged homes for (i) differences between indoor and outdoor fungal populations or (ii) differences in the presence or relative abundance of particular fungal taxa. Strong relationships with damage indicators were found for some targeted fungal groups in some sampling types, although not always in the hypothesized direction. For example, for vacuum samples, hydrophilic fungi had significantly higher relative abundance in water-damaged homes, but mesophilic fungi, unexpectedly, had significantly lower relative abundance in homes with visible mold. Untargeted approaches identified no microbial community metrics correlated with water damage variables but did identify specific taxa with at least weak positive links to water-damaged homes. These results, although showing a complex relationship between moisture damage and microbial communities, suggest that targeting particular fungi offers a potential route toward identifying a fungal signature of moisture damage in buildings. IMPORTANCE Living or working in damp or moldy buildings increases the risk of many adverse health effects, including asthma and other respiratory diseases. To date, however, the particular environmental exposure(s) from water-damaged buildings that causes the health effects have not been identified. Likewise, a consistent quantitative measurement that would indicate whether a building is water damaged or poses a health risk to occupants has not been found. In this work, we tried to develop analytical tools that would find a microbial signal of moisture damage amid the noisy background of microorganisms in buildings. The most successful approach taken here focused on particular groups of fungi—those considered likely to grow in damp indoor environments—and their associations with observed moisture damage. With further replication and refinement, this hypothesis-based strategy may be effective in finding still-elusive relationships between building damage and microbiomes.

scholarly journals Physiological traits and relative abundance of species as explanatory variables of co-occurrence pattern of cultivable bacteria associated with chia seeds

2019 ◽  
Vol 65 (9) ◽  
pp. 668-680
Author(s):  
Asma Jaba ◽  
Fadi Dagher ◽  
Amir Mehdi Hamidi Oskouei ◽  
Claude Guertin ◽  
Philippe Constant
Keyword(s):  
Relative Abundance ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Physiological Traits ◽  
Theoretical Frameworks ◽  
Community Assemblage ◽  
Microbial Species ◽  
Cultivable Bacteria ◽  
Occurrence Patterns

Deciphering the rules defining microbial community assemblage is envisioned as a promising strategy to improve predictions of pathogens colonization and proliferation in food. Despite the increasing number of studies reporting microbial co-occurrence patterns, only a few attempts have been made to challenge them in experimental or theoretical frameworks. Here, we tested the hypothesis that observed variations in co-occurrence patterns can be explained by taxonomy, relative abundance, and physiological traits of microbial species. We used PCR amplicon sequencing of taxonomic markers to assess distribution and co-occurrence patterns of bacterial and fungal species found in 25 chia (Salvia hispanica L.) samples originating from eight different sources. The use of nutrient-rich and oligotrophic media enabled isolation of 71 strains encompassing 16 bacterial species, of which five corresponded to phylotypes represented in the molecular survey. Tolerance to different growth inhibitors and antibiotics was tested to assess the physiological traits of these isolates. Divergence of physiological traits and relative abundance of each pair of species explained 69% of the co-occurrence profile displayed by cultivable bacterial phylotypes in chia. Validation of this ecological network conceptualization approach to more food products is required to integrate microbial species co-occurrence patterns in predictive microbiology.

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