Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments

Microbial communities on microplastics from seawater and mussels: Insights from the northern Adriatic Sea

Microplastics, synthetic solid particles of different sizes (< 5 mm), pose a major challenge to marine ecosystems. Introducing microplastics into the marine environment leads to the formation of complex microbial communities, a topic of growing interest in environmental research. For this study, we selected an area in the northern Adriatic Sea, less affected by human activities, to understand how pristine environmental conditions influence microbial colonization of microplastics. Samples of coastal seawater and Mediterranean mussels (Mytilus galloprovincialis) were collected in a mussel farm near Debeli rtič of the Slovenian coast. Microplastics were isolated, visually and chemically analyzed and DNA was extracted for metagenomics. In the marine water column, 12.7 microplastics per m3 water column and 0.58 microplastics per individual mussel were found. Sufficient DNA was available to analyze six particles, five originating from seawater, and one from a mussel. This was the first-ever sequenced microplastic particle from a mussel. Genera of Pseudomonas and Serratia were identified in all samples. In one of the samples, the most abundant was a marine genus Pseudoalteromonas, while in another sample Campylobacter was present with >30 % abundance. The microbiomes of the mussel- and seawater-isolated particles were similar, suggesting a common microbial colonization pattern, which may have implications for the transfer of microplastic-associated microbes, including potential pathogens, through the food web to the consumers. Microplastic pollution is a complex issue requiring further research, especially regarding microbial biofilms, pathogen colonization and the potential of pathogen transmission via microplastic particles. Our findings enhance the understanding of microplastic pollution in the Adriatic Sea and stress the necessity for comprehensive strategies to mitigate the impact on marine ecosystems.

Preventive effects of a nutraceutical mixture of berberine, citrus and apple extracts on metabolic disturbances in Zucker fatty rats

BACKGROUND

The prevention of obesity represents a major health and socio-economic challenge. Nutraceuticals are regularly highlighted for their beneficial effects in preventing the metabolic disturbances associated with obesity. However, few studies have described the combined action of nutraceutical mixtures combining polyphenols with alkaloids.

OBJECTIVE

The aim of this study was to evaluate the effects of long-term dietary supplementation with a mixture of Berberine, Citrus and Apple extracts (BCA) in the primary prevention of obesity and its metabolic and vascular complications in the obese Zucker rat, a spontaneous model of genetic obesity and insulin resistance.

METHODS

Sixteen 8-week-old obese Zucker male rats were randomly divided into two groups: all rats received oral gavage daily either with water, untreated obese (U-ObZ) or BCA (BCA-ObZ) mixture for thirteen weeks. Morphological and metabolic parameters were measured along the study. Cumulative concentration-response curves to insulin, acetylcholine and phenylephrine were determined on isolated thoracic aorta. Colon permeability measurements were performed using the Ussing chamber technique. Fecal samples collected at the beginning and the end of the protocol were used as a template for amplification of the V3-V4 region of the 16S rDNA genes.

RESULTS

BCA supplementation reduced weight gain (p<0.05) and food intake (p<0.05) in the BCA-ObZ group rats compared to the U-ObZ group rats. It also improved glucose tolerance (p<0.001) and decreased fasting insulin and Homeostasis model assessment index (p<0.05). Through ex vivo experiments, the BCA mixture enhanced significantly aortic insulin relaxation (p<0.01), reduced α1-adrenoceptor-mediated vasoconstriction (p<0.01), and decreased distal colon permeability. Moreover, short-chain fatty acid producers such as Bacteroides, Blautia, and Akkermansia were found to be increased by the BCA mixture supplementation.

CONCLUSION

The results showed that a 13-week-supplementation with BCA mixture prevented weight gain and improved glucose metabolism in obese Zucker rats. We also demonstrated that BCA supplementation improved vascular function, colonic barrier permeability and gut microbiota profile.

A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one among the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems and particular attributes of thirty-two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.

Structure of Benthic Microbial Communities in the Northeastern Part of the Barents Sea

The Barents Sea shelf is one of the most economically promising regions in the Arctic in terms of its resources and geographic location. However, benthic microbial communities of the northeastern Barents Sea are still barely studied. Here, we present a detailed systematic description of the structures of microbial communities located in the sediments and bottom water of the northeastern Barents Sea based on 16S rRNA profiling and a qPCR assessment of the total prokaryotic abundance in 177 samples. Beta- and alpha-diversity analyses revealed a clear difference between the microbial communities of diverse sediment layers and bottom-water fractions. We identified 101 microbial taxa whose representatives had statistically reliable distribution patterns between these ecotopes. Analysis of the correlation between microbial community structure and geological data yielded a number of important results-correlations were found between the abundance of individual microbial taxa and bottom relief, thickness of marine sediments, presence of hydrotrolite interlayers, and the values of pH and Eh. We also demonstrated that a relatively high abundance of prokaryotes in sediments can be caused by the proliferation of Deltaproteobacteria representatives, in particular, sulfate and iron reducers.

Role of mucin glycosylation in the gut microbiota-brain axis of core 3 O-glycan deficient mice

Alterations in intestinal mucin glycosylation have been associated with increased intestinal permeability and sensitivity to inflammation and infection. Here, we used mice lacking core 3-derived O-glycans (C3GnT-/-) to investigate the effect of impaired mucin glycosylation in the gut-brain axis. C3GnT-/- mice showed altered microbial metabolites in the caecum associated with brain function such as dimethylglycine and N-acetyl-L-tyrosine profiles as compared to C3GnT+/+ littermates. In the brain, polysialylated-neural cell adhesion molecule (PSA-NCAM)-positive granule cells showed an aberrant phenotype in the dentate gyrus of C3GnT-/- mice. This was accompanied by a trend towards decreased expression levels of PSA as well as ZO-1 and occludin as compared to C3GnT+/+. Behavioural studies showed a decrease in the recognition memory of C3GnT-/- mice as compared to C3GnT+/+ mice. Combined, these results support the role of mucin O-glycosylation in the gut in potentially influencing brain function which may be facilitated by the passage of microbial metabolites through an impaired gut barrier.

The Cynomolgus Macaque Intestinal Mycobiome Is Dominated by the Kazachstania Genus and K. pintolopesii Species

The cynomolgus macaque, Macaca fascicularis, is a non-human primate (NHP) widely used in biomedical research as its genetics, immunology and physiology are similar to those of humans. They may also be a useful model of the intestinal microbiome as their prokaryome resembles that of humans. However, beyond the prokaryome relatively little is known about other constituents of the macaque intestinal microbiome including the mycobiome. Here, we conducted a region-by-region taxonomic survey of the cynomolgus intestinal mycobiota, from duodenum to distal colon, of sixteen captive animals of differing age (from young to old). Using a high-throughput ITS1 amplicon sequencing-based approach, the cynomolgus gut mycobiome was dominated by fungi from the Ascomycota phylum. The budding yeast genus Kazachstania was most abundant, with the thermotolerant species K. pintolopesii highly prevalent, and the predominant species in both the small and large intestines. This is in marked contrast to humans, in which the intestinal mycobiota is characterised by other fungal genera including Candida and Saccharomyces, and Candida albicans. This study provides a comprehensive insight into the fungal communities present within the captive cynomolgus gut, and for the first time identifies K. pintolopesii as a candidate primate gut commensal.

Absence of Bacteria Permits Fungal Gut-To-Brain Translocation and Invasion in Germfree Mice but Ageing Alone Does Not Drive Pathobiont Expansion in Conventionally Raised Mice

Age-associated changes in the structure of the intestinal microbiome and in its interaction with the brain via the gut-brain axis are increasingly being implicated in neurological and neurodegenerative diseases. Intestinal microbial dysbiosis and translocation of microbes and microbial products including fungal species into the brain have been implicated in the development of dementias such as Alzheimer's disease. Using germ-free mice, we investigated if the fungal gut commensal, Candida albicans, an opportunistic pathogen in humans, can traverse the gastrointestinal barrier and disseminate to brain tissue and whether ageing impacts on the gut mycobiome as a pre-disposing factor in fungal brain infection. C. albicans was detected in different regions of the brain of colonised germ-free mice in both yeast and hyphal cell forms, often in close association with activated (Iba-1+) microglial cells. Using high-throughput ITS1 amplicon sequencing to characterise the faecal gut fungal composition of aged and young SPF mice, we identified several putative gut commensal fungal species with pathobiont potential although their abundance was not significantly different between young and aged mice. Collectively, these results suggest that although some fungal species can travel from the gut to brain where they can induce an inflammatory response, ageing alone is not correlated with significant changes in gut mycobiota composition which could predispose to these events. These results are consistent with a scenario in which significant disruptions to the gut microbiota or intestinal barrier, beyond those which occur with natural ageing, are required to allow fungal escape and brain infection.

Dysbiosis of Gastric Mucosal Fungal Microbiota in the Gastric Cancer Microenvironment

Background

Microbes have been shown to contribute to gastric cancer (GC), gastric bacteria and viruses are associated with gastric carcinogenesis. However, the relationship between gastric fungi and GC is still unclear. Our aim was to evaluate the gastric fungal microbiota in the GC microenvironment.

Methods

Gastric fungal microbiome profiling was performed with internal transcribed spacer (ITS) rDNA sequencing in primary tumor and corresponding paired normal mucosal tissues from 61 GC patients. Differences in microbial composition, taxa diversity, and predicted function were further analyzed.

Results

Dysbiosis of gastric mucosal fungal microbiome was observed between the tumor and normal groups in GC. The tumor group had a higher abundance of certain taxa than the normal group. In the taxa classification, the abundances of Pezizomycetes, Sordariales, Chaetomiaceae, and Rozellomycota were lower in the tumor group than in the normal group. At the genus level, Solicoccozyma (P = 0.033) was found in higher abundance and was differentially enriched in the tumor group with Lefse analysis. Additionally, Solicoccozyma accounted for 0.3% of gastric fungi in the GC microenvironment. Twenty-seven of the 61 GC patients showed positive Solicoccozyma expression in tumors. Solicoccozyma-positive expression in tumors was associated with the Bormann classification and nerve invasion. Solicoccozyma was considered a gastric fungal marker to classify stage I and stage II-IV GC patients with an area under the receiver-operating curve (AUC) of 0.7061, as well as to classify the nerve invasive and nonnerve invasive tumors from GC patients with an AUC of 0.6978. Functional prediction indicated that the positive expression of Solicoccozyma in tumors was associated with the amino acid- and carbohydrate-related metabolic pathways in GC.

Conclusions

This study revealed a novel perspective on the role of Solicoccozyma in tumors and a theoretical basis for therapeutic targets against GC.

Streamlined processing and analysis of 16S rRNA amplicon sequencing data with OCMS_16S and OCMSlooksy

16S rRNA gene sequencing is a cost-effective method for profiling the bacterial component of a microbiome. Nevertheless, processing and analysis of the resulting sequencing data is often constrained by the availability of dedicated bioinformaticians - creating a bottleneck for biological interpretation. Multiple visualisation and analysis tools now exist for downstream analysis of 16S rRNA data. These tools are designed with biological scientists in mind and therefore consist of a graphical user interface that interacts with taxonomic counts tables to perform tasks such as alpha- and beta-diversity analysis and differential abundance. However, generating the input to these applications still relies on bioinformatics experience, creating a disconnect between data processing and data analysis. We aimed to bridge the gap between data processing and data analysis. To do this we have created two tools - OCMS_16S and OCMSlooksy - that perform data processing and data visualisation/analysis, respectively. OCMS_16S is a cgat-core based pipeline that wraps DADA2 functionality in order to facilitate processing of raw sequence reads into tables of amplicon sequence variant (ASV) counts using a simple command line interface. OCMSlooksy is an RShiny application that takes an OCMS_16S-generated SQLite database as input to facilitate data exploration and analysis. Combining these tools provides a simple, user-friendly workflow to facilitate 16S rRNA gene amplicon sequencing data analysis from raw reads to results.

Cultivation of a vampire: 'Candidatus Absconditicoccus praedator'

Halorhodospira halophila, one of the most-xerophilic halophiles, inhabits biophysically stressful and energetically expensive, salt-saturated alkaline brines. Here, we report an additional stress factor that is biotic: a diminutive Candidate-Phyla-Radiation bacterium, that we named 'Ca. Absconditicoccus praedator' M39-6, which predates H. halophila M39-5, an obligately photosynthetic, anaerobic purple-sulfur bacterium. We cultivated this association (isolated from the hypersaline alkaline Lake Hotontyn Nur, Mongolia) and characterized their biology. 'Ca. Absconditicoccus praedator' is the first stably cultivated species from the candidate class-level lineage Gracilibacteria (order-level lineage Absconditabacterales). Its closed-and-curated genome lacks genes for the glycolytic, pentose phosphate- and Entner-Doudoroff pathways which would generate energy/reducing equivalents and produce central carbon currencies. Therefore, 'Ca. Absconditicoccus praedator' is dependent on host-derived building blocks for nucleic acid-, protein-, and peptidoglycan synthesis. It shares traits with (the uncultured) 'Ca. Vampirococcus lugosii', which is also of the Gracilibacteria lineage. These are obligate parasitic lifestyle, feeding on photosynthetic anoxygenic Gammaproteobacteria, and absorption of host cytoplasm. Commonalities in their genomic composition and structure suggest that the entire Absconditabacterales lineage consists of predatory species which act to cull the populations of their respective host bacteria. Cultivation of vampire : host associations can shed light on unresolved aspects of their metabolism and ecosystem dynamics at life-limiting extremes.

The Origin of Plasma-Derived Bacterial Extracellular Vesicles in Healthy Individuals and Patients with Inflammatory Bowel Disease: A Pilot Study

The gastrointestinal tract harbors the gut microbiota, structural alterations of which (dysbiosis) are linked with an increase in gut permeability ("leaky gut"), enabling luminal antigens and bacterial products such as nanosized bacterial extracellular vesicles (BEVs) to access the circulatory system. Blood-derived BEVs contain various cargoes and may be useful biomarkers for diagnosis and monitoring of disease status and relapse in conditions such as inflammatory bowel disease (IBD). To progress this concept, we developed a rapid, cost-effective protocol to isolate BEV-associated DNA and used 16S rRNA gene sequencing to identify bacterial origins of the blood microbiome of healthy individuals and patients with Crohn's disease and ulcerative colitis. The 16S rRNA gene sequencing successfully identified the origin of plasma-derived BEV DNA. The analysis showed that the blood microbiota richness, diversity, or composition in IBD, healthy control, and protocol control groups were not significantly distinct, highlighting the issue of 'kit-ome' contamination in low-biomass studies. Our pilot study provides the basis for undertaking larger studies to determine the potential use of blood microbiota profiling as a diagnostic aid in IBD.

Diversity and Activity of Sulfate-Reducing Prokaryotes in Kamchatka Hot Springs

Microbial communities of the Kamchatka Peninsula terrestrial hot springs were studied using radioisotopic and cultural approaches, as well as by the amplification and sequencing of dsrB and 16S rRNA genes fragments. Radioisotopic experiments with 35S-labeled sulfate showed that microbial communities of the Kamchatka hot springs are actively reducing sulfate. Both the cultivation experiments and the results of dsrB and 16S rRNA genes fragments analyses indicated the presence of microorganisms participating in the reductive part of the sulfur cycle. It was found that sulfate-reducing prokaryotes (SRP) belonging to Desulfobacterota, Nitrospirota and Firmicutes phyla inhabited neutral and slightly acidic hot springs, while bacteria of phylum Thermodesulofobiota preferred moderately acidic hot springs. In high-temperature acidic springs sulfate reduction was mediated by archaea of the phylum Crenarchaeota, chemoorganoheterotrophic representatives of genus Vulcanisaeta being the most probable candidates. The 16S rRNA taxonomic profiling showed that in most of the studied communities SRP was present only as a minor component. Only in one microbial community, the representatives of genus Vulcanisaeta comprised a significant group. Thus, in spite of comparatively low sulfate concentrations in terrestrial hot springs of the Kamchatka, phylogenetically and metabolically diverse groups of sulfate-reducing prokaryotes are operating there coupling carbon and sulfur cycles in these habitats.