Chironomus ramosus Larval Microbiome Composition Provides Evidence for the Presence of Detoxifying Enzymes

Chironomids (Diptera; Chironomidae) are aquatic insects that are abundant in freshwater. We aimed to study the endogenous microbiota composition of Chironomus ramosus larvae that were sampled from the Mutha River and a laboratory culture in India. Furthermore, we performed a metagenomic analysis of the larval microbiome, sampled from the Mutha River. Significant differences were found between the bacterial community composition of C. ramosus larvae that were sampled from the Mutha River and the laboratory culture. A total of 54.7% of the amplicon sequence variants (ASVs) that were identified in the larvae from the Mutha River were unique, compared to only 12.9% of unique ASVs that were identified from the laboratory-reared larvae. The four most abundant phyla across all samples were: Proteobacteria, Fusobacteria, Firmicutes, and Bacteroidetes, while the nine most abundant genera were: Aeromonas, Alkanindiges, Breznakia, Cetobacterium, Chryseobacterium, Desulfovibrio, Dysgonomonas, Thiothrix, and Vibrio. Moreover, in the metagenomic analysis, we detected bacterial genes and bacterial pathways that demonstrated the ability to degrade different toxic compounds, detoxify metal, and confer resistance to antibiotics and UV radiation, amongst other functions. The results illuminate the fact that there are detoxifying enzymes in the C. ramosus larval microbiome that possibly play a role in protecting the insect in polluted environments.

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

Marine Drugs ◽

10.3390/md18060298 ◽

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.

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Immune Gene Expression Covaries with Gut Microbiome Composition in Stickleback

mBio ◽

10.1128/mbio.00145-21 ◽

2021 ◽

Vol 12 (3) ◽

Author(s):

Lauren E. Fuess ◽

Stijn den Haan ◽

Fei Ling ◽

Jesse N. Weber ◽

Natalie C. Steinel ◽

...

Keyword(s):

Gene Expression ◽

Microbial Communities ◽

Gut Microbiome ◽

Alpha Diversity ◽

Host Immunity ◽

Host Gene ◽

Microbiota Composition ◽

Host Gene Expression ◽

Microbiome Composition ◽

Immune Genes

ABSTRACT Commensal microbial communities have immense effects on their vertebrate hosts, contributing to a number of physiological functions, as well as host fitness. In particular, host immunity is strongly linked to microbiota composition through poorly understood bi-directional links. Gene expression may be a potential mediator of these links between microbial communities and host function. However, few studies have investigated connections between microbiota composition and expression of host immune genes in complex systems. Here, we leverage a large study of laboratory-raised fish from the species Gasterosteus aculeatus (three-spined stickleback) to document correlations between gene expression and microbiome composition. First, we examined correlations between microbiome alpha diversity and gene expression. Our results demonstrate robust positive associations between microbial alpha diversity and expression of host immune genes. Next, we examined correlations between host gene expression and abundance of microbial taxa. We identified 15 microbial families that were highly correlated with host gene expression. These families were all tightly correlated with host expression of immune genes and processes, falling into one of three categories—those positively correlated, negatively correlated, and neutrally related to immune processes. Furthermore, we highlight several important immune processes that are commonly associated with the abundance of these taxa, including both macrophage and B cell functions. Further functional characterization of microbial taxa will help disentangle the mechanisms of the correlations described here. In sum, our study supports prevailing hypotheses of intimate links between host immunity and gut microbiome composition. IMPORTANCE Here, we document associations between host gene expression and gut microbiome composition in a nonmammalian vertebrate species. We highlight associations between expression of immune genes and both microbiome diversity and abundance of specific microbial taxa. These findings support other findings from model systems which have suggested that gut microbiome composition and host immunity are intimately linked. Furthermore, we demonstrate that these correlations are truly systemic; the gene expression detailed here was collected from an important fish immune organ (the head kidney) that is anatomically distant from the gut. This emphasizes the systemic impact of connections between gut microbiota and host immune function. Our work is a significant advancement in the understanding of immune-microbiome links in nonmodel, natural systems.

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Comparative Microbiota Composition Across Developmental Stages of Natural and Laboratory-Reared Chironomus circumdatus Populations From India

Frontiers in Microbiology ◽

10.3389/fmicb.2021.746830 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sivan Laviad-Shitrit ◽

Rotem Sela ◽

Yehonatan Sharaby ◽

Leena Thorat ◽

Bimalendu B. Nath ◽

...

Keyword(s):

Developmental Stages ◽

Laboratory Culture ◽

Sampling Location ◽

Scaling Analysis ◽

Life Stages ◽

Microbiota Composition ◽

Aquatic Life ◽

Egg Masses ◽

Microbial Profile ◽

Field Environment

Chironomids are aquatic insects that undergo a complete metamorphosis of four life stages. Here we studied, for the first time, the microbiota composition of Chironomus circumdatus, a tropical midge species, both from the Mula and Mutha Rivers in Pune, India and as a laboratory-reared culture. We generated a comparative microbial profile of the eggs, larvae and pupae, the three aquatic life stages of C. circumdatus. Non-metric multidimensional scaling analysis (NMDS) demonstrated that the developmental stage had a more prominent effect on the microbiota composition compared to the sampling location. Notably, the microbiota composition of the egg masses from the different sampling points clustered together and differed from laboratory culture larvae. Proteobacteria was the dominant phylum in all the environmental and laboratory-reared egg masses and pupal samples, and in the laboratory-reared larvae, while Fusobacteria was the dominant phylum in the larvae collected from the field environment. The most abundant genera were Cetobacterium, Aeromonas, Dysgonomonas, Vibrio, and Flavobacterium. The ten amplicon sequence variants (ASVs) that most significantly contributed to differences in microbiota composition between the three sampled locations were: Burkholderiaceae (ASVs 04 and 37), C39 (Rhodocyclaceae, ASV 14), Vibrio (ASV 07), Arcobacter (ASV 21), Sphaerotilus (ASV 22), Bacteroidia (ASVs 12 and 28), Flavobacterium (ASV 29), and Gottschalkia (ASV 10). No significant differences were found in the microbial richness (Chao1) or diversity (Shannon H’) of the three sampled locations. In contrast, significant differences were found between the microbial richness of the three life stages. Studying the microbiota of this Chironomus species may contribute to a better understanding of the association of C. circumdatus and its microbial inhabitants.

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Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis

Gene ◽

10.1016/j.gene.2018.04.072 ◽

2018 ◽

Vol 665 ◽

pp. 174-184 ◽

Cited By ~ 5

Author(s):

Toshiaki Kudo ◽

Atsushi Kobiyama ◽

Jonaira Rashid ◽

Md. Shaheed Reza ◽

Yuichiro Yamada ◽

...

Keyword(s):

Seasonal Changes ◽

Metagenomic Analysis ◽

Bacterial Genes

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820 – Prospective Longitudinal Gut Metagenomic Analysis Suggests Altered Microbiome Composition and Function in Infants Prior to Celiac Disease Onset

Gastroenterology ◽

10.1016/s0016-5085(19)37228-2 ◽

2019 ◽

Vol 156 (6) ◽

pp. S-175

Author(s):

Maureen M. Leonard ◽

Poorani Subramanian ◽

Francesco Valitutti ◽

Gloria Serena ◽

Victoria Kenyon ◽

...

Keyword(s):

Celiac Disease ◽

Disease Onset ◽

Metagenomic Analysis ◽

Microbiome Composition ◽

And Function ◽

Prospective Longitudinal

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Cow responses and evolution of the rumen bacterial and methanogen community following a complete rumen content transfer

The Journal of Agricultural Science ◽

10.1017/s0021859618001053 ◽

2018 ◽

Vol 156 (8) ◽

pp. 1047-1058

Author(s):

T. De Mulder ◽

L. Vandaele ◽

N. Peiren ◽

A. Haegeman ◽

T. Ruttink ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Community Composition ◽

Rumen Content ◽

Short Term ◽

Microbiome Composition ◽

Nutritional Conditions ◽

Microbiome Diversity ◽

Methanogen Community ◽

New Community

AbstractUnderstanding the rumen microbial ecosystem requires the identification of factors that influence the community structure, such as nutrition, physiological condition of the host and host–microbiome interactions. The objective of the current study was to describe the rumen microbial communities before, during and after a complete rumen content transfer. The rumen contents of one donor cow were removed completely and used as inoculum for the emptied rumen of the donor itself and three acceptor cows under identical physiological and nutritional conditions. Temporal changes in microbiome composition and rumen function were analysed for each of four cows over a period of 6 weeks. Shortly after transfer, the cows showed different responses to perturbation of their rumen content. Feed intake depression in the first 2 weeks after transfer resulted in short-term changes in milk production, methane emission, fatty acid composition and rumen bacterial community composition. These effects were more pronounced in two cows, whose microbiome composition showed reduced diversity. The fermentation metrics and microbiome diversity of the other two cows were not affected. Their rumen bacterial community initially resembled the composition of the donor but evolved to a new community profile that resembled neither the donor nor their original composition. Descriptive data presented in the current paper show that the rumen bacterial community composition can quickly recover from a reduction in microbiome diversity after a severe perturbation. In contrast to the bacteria, methanogenic communities were more stable over time and unaffected by stress or host effects.

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Host species, pathogens and disease associated with divergent nasal microbial communities in tortoises

Royal Society Open Science ◽

10.1098/rsos.181068 ◽

2018 ◽

Vol 5 (10) ◽

pp. 181068

Author(s):

Chava L. Weitzman ◽

Franziska C. Sandmeier ◽

C. Richard Tracy

Keyword(s):

Host Species ◽

Bacterial Communities ◽

Sonoran Desert ◽

Bacterial Community Composition ◽

Operational Taxonomic Unit ◽

Nasal Discharge ◽

Microbiome Composition ◽

Technological Advances ◽

Repeated Sampling ◽

Pathogen Colonization

Diverse bacterial communities are found on every surface of macro-organisms, and they play important roles in maintaining normal physiological functions in their hosts. While the study of microbiomes has expanded with the influx of data enabled by recent technological advances, microbiome research in reptiles lags behind other organisms. We sequenced the nasal microbiomes in a sample of four North American tortoise species, and we found differing community compositions among tortoise species and sampling sites, with higher richness and diversity in Texas and Sonoran desert tortoises. Using these data, we investigated the prevalence and operational taxonomic unit (OTU) diversity of the potential pathogen Pasteurella testudinis and found it to be common, abundant and highly diverse. However, the presence of this bacterium was not associated with differences in bacterial community composition within host species. We also found that the presence of nasal discharge from tortoises at the time of sampling was associated with a decline in diversity and a change in microbiome composition, which we posit is due to the harsh epithelial environment associated with immune responses. Repeated sampling across seasons, and at different points of pathogen colonization, should contribute to our understanding of the causes and consequences of different bacterial communities in these long-lived hosts.

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Gut microbiome composition and response to sunitinib in metastatic renal cell carcinoma (mRCC).

Journal of Clinical Oncology ◽

10.1200/jco.2018.36.6_suppl.657 ◽

2018 ◽

Vol 36 (6_suppl) ◽

pp. 657-657 ◽

Cited By ~ 1

Author(s):

Jun Gong ◽

Nazli Dizman ◽

Valeriy Poroyko ◽

Haejung Won ◽

Cristiane Decat Bergerot ◽

...

Keyword(s):

Human Study ◽

Pcr Amplification ◽

Standard Of Care ◽

Microbiota Composition ◽

Dissimilarity Matrix ◽

Significant Discrepancy ◽

Microbiome Composition ◽

Genus Level ◽

16S Rna ◽

The Difference

657 Background: Recent evidence supports a link between stool microbiome composition and immunotherapy response. However, it is unclear how the microbiome may influence clinical outcome in mRCC where vascular endothelial growth factor-targeted therapies remains a standard of care. Methods: Five consecutive stool samples were collected at baseline and at weeks 2, 3, 4 and 12 of treatment with sunitinib in patients (pts) with mRCC. In responders (R: complete/partial response and stable disease) and non-responders (P: primary progression), gut microbiota composition was assessed through extraction of microbial DNA where 16s RNA gene tags (v4) were generated by PCR amplification and sequenced using MiSeq (Illumina). Sequence reads were processed by Mothur software, assembled in Operational Taxonomic Units (OTUs), taxonomically annotated to the genus level, and used to construct Bray-Curtis dissimilarity matrix. The similarity of samples was visualized by principle coordinate (PCo) analysis and further confirmed by k-means clustering and ANOSIM tests. Differentially abundant taxa were determined by METASTATS. Results: Stool bacteriomic profiling identified 25,304 OTUs attributable to 165 genera from 8 phyla in 4 of 6 pts evaluable for response. PCo analysis revealed clear separation of R and P (accounting for 28.9 % of dataset variation) where subsequent k-means clustering confirmed the difference of microbiota in 2 clusters that perfectly align with R and P groups. The significance of this separation was confirmed by ANOSIM analysis (p = 0.005). Analysis of microbiota composition in P and R groups revealed 14 differentially abundant taxonomic units at the genus level. Of those at ≥1% abundance, Bacteroides, Barnesiella and Phascolarctobacterium were elevated in R, while Bifidobacterium and Dorea were elevated in P (p < 0.01 for all). Of those at < 1% abundance, Lactococcus, Sporobacter, Acidaminococcus, Actinomyces, and Asaccharobacter were elevated in P (p < 0.01 for all). Conclusions: Although limited by sample size, we report the first in-human study to suggest a link between microbiota and response to sunitinib as we identified a significant discrepancy in stool bacteriomic distribution between P and R.

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Population- and Individual-Level Dynamics of the Intestinal Microbiota of a Small Primate

Applied and Environmental Microbiology ◽

10.1128/aem.00559-16 ◽

2016 ◽

Vol 82 (12) ◽

pp. 3537-3545 ◽

Cited By ~ 27

Author(s):

Tuomas Aivelo ◽

Juha Laakkonen ◽

Jukka Jernvall

Keyword(s):

Intestinal Microbiota ◽

Large Scale ◽

Small Body ◽

Bacterial Community Composition ◽

Temporal Trends ◽

Population Level ◽

Microbiota Composition ◽

Individual Level ◽

Mouse Lemurs ◽

Free Ranging

ABSTRACTLongitudinal sampling for intestinal microbiota in wild animals is difficult, leading to a lack of information on bacterial dynamics occurring in nature. We studied how the composition of microbiota communities changed temporally in free-ranging small primates, rufous mouse lemurs (Microcebus rufus). We marked and recaptured mouse lemurs during their mating season in Ranomafana National Park in southeastern mountainous rainforests of Madagascar for 2 years and determined the fecal microbiota compositions of these mouse lemurs with MiSeq sequencing. We collected 160 fecal samples from 71 animals and had two or more samples from 39 individuals. We found small, but statistically significant, effects of site and age on microbiota richness and diversity and effects of sex, year, and site on microbiota composition, while the within-year temporal trends were less clear. Within-host microbiota showed pervasive variation in intestinal bacterial community composition, especially during the second study year. We hypothesize that the biological properties of mouse lemurs, including their small body size and fast metabolism, may contribute to the temporal intraindividual-level variation, something that should be testable with more-extensive sampling regimes.IMPORTANCEWhile microbiome research has blossomed in recent years, there is a lack of longitudinal studies on microbiome dynamics on free-ranging hosts. To fill this gap, we followed mouse lemurs, which are small heterothermic primates, for 2 years. Most studied animals have shown microbiota to be stable over the life span of host individuals, but some previous research also found ample within-host variation in microbiota composition. Our study used a larger sample size than previous studies and a study setting well suited to track within-host variation in free-ranging mammals. Despite the overall microbiota stability at the population level, the microbiota of individual mouse lemurs can show large-scale changes in composition in time periods as short as 2 days, suggesting caution in inferring individual-level patterns from population-level data.

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Metformin Affects Gut Microbiome Composition and Function and Circulating Short-Chain Fatty Acids: A Randomized Trial

10.2337/figshare.14340419 ◽

2021 ◽

Author(s):

Noel T. Mueller ◽

Moira K. Differding ◽

Mingyu Zhang ◽

Nisa Maruthar ◽

Stephen P Juraschek ◽

...

Keyword(s):

Weight Loss ◽

Gut Microbiota ◽

Randomized Trial ◽

Short Chain Fatty Acids ◽

Metagenomic Sequencing ◽

Microbiota Composition ◽

Behavioral Weight Loss ◽

Microbiome Composition ◽

Weight Loss Group ◽

And Function

Objective: To determine the longer-term effects of metformin and behavioral weight loss on gut microbiota and SCFAs. Methods: We conducted a parallel-arm, randomized trial. We enrolled overweight/obese adults who had been treated for solid tumors but had no ongoing cancer treatment and randomized them (n=121) to: 1) metformin (up to 2000mg), 2) coach-directed behavioral weight loss, or 3) self-directed care (control) for 12 months. We collected stool and serum at baseline (n=114), 6 months (n=109) and 12 months (n=105). From stool, we extracted microbial DNA and conducted amplicon and metagenomic sequencing. We measured SCFAs and other biochemical parameters from fasting serum. Results: Of the 121 participants, 79% were female, 46% were black, and the mean age was 60y. Only metformin intervention significantly altered microbiota composition. Compared to control, metformin increased E. Coli and Ruminococcus torques and decreased Intestinibacter Bartletti at both 6 and 12 months, and decreased the genus Roseburia (genus), including R. faecis and R. intestinalis, at 12 months. Effects were similar when comparing metformin to the behavioral weight loss group. Metformin also altered 62 metagenomic functional pathways and increased butyrate, acetate, and valerate at 6 months. Behavioral weight loss vs. control did not significantly alter microbiota composition, but did increase acetate at 6 months. Increases in acetate were associated with decreases in fasting insulin. Conclusions: Metformin, but not behavioral weight loss, impacted gut microbiota composition and function at 6 months and 12 months. Both metformin and behavioral weight loss altered 6-month SCFAs, including increasing acetate which correlated with improved insulin sensitivity.

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