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Bibliography on: Metagenomics

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Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 30 Jun 2022 at 01:31 Created: 

Metagenomics

While genomics is the study of DNA extracted from individuals — individual cells, tissues, or organisms — metagenomics is a more recent refinement that analyzes samples of pooled DNA taken from the environment, not from an individual. Like genomics, metagenomic methods have great potential in many areas of biology, but none so much as in providing access to the hitherto invisible world of unculturable microbes, often estimated to comprise 90% or more of bacterial species and, in some ecosystems, the bulk of the biomass. A recent describes how this new science of metagenomics is beginning to reveal the secrets of our microbial world: The opportunity that stands before microbiologists today is akin to a reinvention of the microscope in the expanse of research questions it opens to investigation. Metagenomics provides a new way of examining the microbial world that not only will transform modern microbiology but has the potential to revolutionize understanding of the entire living world. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual bacterial community members.

Created with PubMed® Query: metagenomic OR metagenomics OR metagenome NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

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RevDate: 2022-06-29

van Heck JIP, Gacesa R, Stienstra R, et al (2022)

The Gut Microbiome Composition Is Altered in Long-Standing Type 1 Diabetes and Associates With Glycemic Control and Disease-Related Complications.

Diabetes care pii:147146 [Epub ahead of print].

OBJECTIVE: People with type 1 diabetes are at risk for developing micro- and macrovascular complications. Little is known about the gut microbiome in long-standing type 1 diabetes. We explored differences in the gut microbiome of participants with type 1 diabetes compared with healthy control subjects and associated the gut microbiome with diabetes-related complications.

RESEARCH DESIGN AND METHODS: Microbiome data of 238 participants with type 1 diabetes with an average disease duration of 28 ± 15 years were compared with 2,937 age-, sex-, and BMI-matched individuals. Clinical characteristics and fecal samples were collected, and metagenomic shotgun sequencing was performed. Microbial taxonomy was associated with type 1 diabetes-related characteristics and vascular complications.

RESULTS: No significant difference in the α-diversity of the gut microbiome was found between participants with type 1 diabetes and healthy control subjects. However, 43 bacterial taxa were significantly depleted in type 1 diabetes, while 37 bacterial taxa were significantly enriched. HbA1c and disease duration explained a significant part of the variation in the gut microbiome (R2 > 0.008, false discovery rate [FDR] <0.05), and HbA1c was significantly associated with the abundance of several microbial species. Additionally, both micro- and macrovascular complications explained a significant part of the variation in the gut microbiome (R2 > 0.0075, FDR < 0.05). Nephropathy was strongly associated with several microbial species. Macrovascular complications displayed similar associations with nephropathy.

CONCLUSIONS: Our data show that the gut microbiome is altered in people with (long-standing) type 1 diabetes and is associated with glycemic control and diabetes-related complications. As a result of the cross-sectional design, the causality of these relationships remains to be determined.

RevDate: 2022-06-29

Ewald JM, Schnoor JL, TE Mattes (2022)

Metagenomes, Metagenome-Assembled Genomes, and Metatranscriptomes from Polychlorinated Biphenyl-Contaminated Sediment Microcosms.

Microbiology resource announcements [Epub ahead of print].

We present a comprehensive data set that describes an anaerobic microbial consortium native to polychlorinated biphenyl (PCB)-contaminated sediments. Obtained from sediment microcosms incubated for 200 days, the data set includes 4 metagenomes, 4 metatranscriptomes (in duplicate), and 62 metagenome-assembled genomes and captures microbial community interactions, structure, and function relevant to anaerobic PCB biodegradation.

RevDate: 2022-06-29

Avuthu N, C Guda (2022)

Meta-Analysis of Altered Gut Microbiota Reveals Microbial and Metabolic Biomarkers for Colorectal Cancer.

Microbiology spectrum [Epub ahead of print].

Colorectal cancer (CRC) is the second leading cause of cancer mortality worldwide. The dysbiotic gut microbiota and its metabolite secretions play a significant role in CRC development and progression. In this study, we identified microbial and metabolic biomarkers applicable to CRC using a meta-analysis of metagenomic datasets from diverse geographical regions. We used LEfSe, random forest (RF), and co-occurrence network methods to identify microbial biomarkers. Geographic dataset-specific markers were identified and evaluated using area under the ROC curve (AUC) scores and random effect size. Co-occurrence networks analysis showed a reduction in the overall microbial associations and the presence of oral pathogenic microbial clusters in CRC networks. Analysis of predicted metabolites from CRC datasets showed the enrichment of amino acids, cadaverine, and creatine in CRC, which were positively correlated with CRC-associated microbes (Peptostreptococcus stomatis, Gemella morbillorum, Bacteroides fragilis, Parvimonas spp., Fusobacterium nucleatum, Solobacterium moorei, and Clostridium symbiosum), and negatively correlated with control-associated microbes. Conversely, butyrate, nicotinamide, choline, tryptophan, and 2-hydroxybutanoic acid showed positive correlations with control-associated microbes (P < 0.05). Overall, our study identified a set of global CRC biomarkers that are reproducible across geographic regions. We also reported significant differential metabolites and microbe-metabolite interactions associated with CRC. This study provided significant insights for further investigations leading to the development of noninvasive CRC diagnostic tools and therapeutic interventions. IMPORTANCE Several studies showed associations between gut dysbiosis and CRC. Yet, the results are not conclusive due to cohort-specific associations that are influenced by genomic, dietary, and environmental stimuli and associated reproducibility issues with various analysis approaches. Emerging evidence suggests the role of microbial metabolites in modulating host inflammation and DNA damage in CRC. However, the experimental validations have been hindered by cost, resources, and cumbersome technical expertise required for metabolomic investigations. In this study, we performed a meta-analysis of CRC microbiota data from diverse geographical regions using multiple methods to achieve reproducible results. We used a computational approach to predict the metabolomic profiles using existing CRC metagenomic datasets. We identified a reliable set of CRC-specific biomarkers from this analysis, including microbial and metabolite markers. In addition, we revealed significant microbe-metabolite associations through correlation analysis and microbial gene families associated with dysregulated metabolic pathways in CRC, which are essential in understanding the vastly sporadic nature of CRC development and progression.

RevDate: 2022-06-29

Van Brussel K, Wang X, Shi M, et al (2022)

The enteric virome of cats with feline panleukopenia differs in abundance and diversity from healthy cats.

Transboundary and emerging diseases [Epub ahead of print].

Feline panleukopenia (FPL) is a severe, often fatal disease caused by feline panleukopenia virus (FPV). How infection with FPV might impact the composition of the entire eukaryotic enteric virome in cats has not been characterized. We used metatranscriptomic and viral particle enrichment metagenomic approaches to characterize the enteric viromes of 23 cats naturally infected with FPV (FPV-cases) and 36 age-matched healthy shelter cats (healthy controls). Sequencing reads from mammalian infecting viral families largely belonged to the Coronaviridae, Parvoviridae and Astroviridae. The most abundant viruses among the healthy control cats were feline coronavirus, Mamastrovirus 2 and Carnivore bocaparvovirus 3 (feline bocavirus), with frequent co-infections of all three. Feline chaphamaparvovirus was only detected in healthy controls (6/36, 16.7%). Among the FPV-cases, in addition to FPV, the most abundant viruses were Mamastrovirus 2, feline coronavirus and Carnivore bocaparvovirus 4 (feline bocaparvovirus 2). The latter and feline bocaparvovirus 3 were detected significantly more frequently in FPV-cases than in healthy controls. Feline calicivirus was present in a higher proportion of FPV-cases (11/23, 47.8%) compared to healthy controls (5/36, 13.9%, p = 0.0067). Feline kobuvirus infections were also common among FPV-cases (9/23, 39.1%) and were not detected in any healthy controls (p<0.0001). While abundant in both groups, astroviruses were more frequently present in FPV-cases (19/23, 82.6%) than in healthy controls (18/36, p = 0.0142). The differences in eukaryotic virome composition revealed here indicate that further investigations are warranted to determine associations between enteric viral co-infections on clinical disease severity in cats with FPL. This article is protected by copyright. All rights reserved.

RevDate: 2022-06-29

Luu T, Khalid R, Rehman T, et al (2022)

Disseminated Nocardia paucivorans Infection Resembling Metastatic Disease in a Kidney Transplant Recipient.

Cureus, 14(5):e25365.

Recipients of solid-organ transplants (SOT) or hematopoietic stem-cell transplants are prone to various complications, including serious infections. Nocardiosis is an opportunistic bacterial infection that primarily affects the lung. It may also cause skin and soft-tissue infection, cerebral abscess, bloodstream infection, or infection involving other organs. We present a case of an immunocompromised kidney transplant recipient who experienced a prolonged history of unexplained indolent constitutional symptoms without a fever. Initial radiographic findings were suggestive of metastatic disease at multiple sites. However, metagenomic next-generation sequencing of microbial cell-free DNA in blood revealed disseminated Nocardia paucivorans infection, and organisms consistent with Nocardia were identified on histopathology of a lung biopsy. It is crucial for healthcare providers to be aware of unusual opportunistic infections to provide appropriate workups and interventions for immunocompromised SOT recipients.

RevDate: 2022-06-29

Goussarov G, Mysara M, Vandamme P, et al (2022)

Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data.

MicrobiologyOpen, 11(3):e1298.

The rise of metagenomics offers a leap forward for understanding the genetic diversity of microorganisms in many different complex environments by providing a platform that can identify potentially unlimited numbers of known and novel microorganisms. As such, it is impossible to imagine new major initiatives without metagenomics. Nevertheless, it represents a relatively new discipline with various levels of complexity and demands on bioinformatics. The underlying principles and methods used in metagenomics are often seen as common knowledge and often not detailed or fragmented. Therefore, we reviewed these to guide microbiologists in taking the first steps into metagenomics. We specifically focus on a workflow aimed at reconstructing individual genomes, that is, metagenome-assembled genomes, integrating DNA sequencing, assembly, binning, identification and annotation.

RevDate: 2022-06-29

Najafpour B, Pinto PIS, Canario AVM, et al (2022)

Quantifying dominant bacterial genera detected in metagenomic data from fish eggs and larvae using genus-specific primers.

MicrobiologyOpen, 11(3):e1274.

The goal of this study was to design genus-specific primers for rapid evaluation of the most abundant bacterial genera identified using amplicon-based sequencing of the 16S rRNA gene in fish-related samples and surrounding water. Efficient genus-specific primers were designed for 11 bacterial genera including Alkalimarinus, Colwellia, Enterovibrio, Marinomonas, Massilia, Oleispira, Phaeobacter, Photobacterium, Polarbacerium, Pseudomonas, and Psychrobium. The specificity of the primers was confirmed by the phylogeny of the sequenced polymerase chain reaction (PCR) amplicons that indicated primers were genus-specific except in the case of Colwellia and Phaeobacter. Copy number of the 16S rRNA gene obtained by quantitative PCR using genus-specific primers and the relative abundance obtained by 16S rRNA gene sequencing using universal primers were well correlated for the five analyzed abundant bacterial genera. Low correlations between quantitative PCR and 16S rRNA gene sequencing for Pseudomonas were explained by the higher coverage of known Pseudomonas species by the designed genus-specific primers than the universal primers used in 16S rRNA gene sequencing. The designed genus-specific primers are proposed as rapid and cost-effective tools to evaluate the most abundant bacterial genera in fish-related or potentially other metagenomics samples.

RevDate: 2022-06-28

Urbaniak C, Morrison MD, Thissen JB, et al (2022)

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station.

Microbiome, 10(1):100.

BACKGROUND: The International Space Station (ISS) is a unique and complex built environment with the ISS surface microbiome originating from crew and cargo or from life support recirculation in an almost entirely closed system. The Microbial Tracking 1 (MT-1) project was the first ISS environmental surface study to report on the metagenome profiles without using whole-genome amplification. The study surveyed the microbial communities from eight surfaces over a 14-month period. The Microbial Tracking 2 (MT-2) project aimed to continue the work of MT-1, sampling an additional four flights from the same locations, over another 14 months.

METHODS: Eight surfaces across the ISS were sampled with sterile wipes and processed upon return to Earth. DNA extracted from the processed samples (and controls) were treated with propidium monoazide (PMA) to detect intact/viable cells or left untreated and to detect the total DNA population (free DNA/compromised cells/intact cells/viable cells). DNA extracted from PMA-treated and untreated samples were analyzed using shotgun metagenomics. Samples were cultured for bacteria and fungi to supplement the above results.

RESULTS: Staphylococcus sp. and Malassezia sp. were the most represented bacterial and fungal species, respectively, on the ISS. Overall, the ISS surface microbiome was dominated by organisms associated with the human skin. Multi-dimensional scaling and differential abundance analysis showed significant temporal changes in the microbial population but no spatial differences. The ISS antimicrobial resistance gene profiles were however more stable over time, with no differences over the 5-year span of the MT-1 and MT-2 studies. Twenty-nine antimicrobial resistance genes were detected across all samples, with macrolide/lincosamide/streptogramin resistance being the most widespread. Metagenomic assembled genomes were reconstructed from the dataset, resulting in 82 MAGs. Functional assessment of the collective MAGs showed a propensity for amino acid utilization over carbohydrate metabolism. Co-occurrence analyses showed strong associations between bacterial and fungal genera. Culture analysis showed the microbial load to be on average 3.0 × 105 cfu/m2 CONCLUSIONS: Utilizing various metagenomics analyses and culture methods, we provided a comprehensive analysis of the ISS surface microbiome, showing microbial burden, bacterial and fungal species prevalence, changes in the microbiome, and resistome over time and space, as well as the functional capabilities and microbial interactions of this unique built microbiome. Data from this study may help to inform policies for future space missions to ensure an ISS surface microbiome that promotes astronaut health and spacecraft integrity. Video Abstract.

RevDate: 2022-06-28

Hu L, Qian Y, Ci M, et al (2022)

Localized intensification of arsenic methylation within landfill leachate-saturated zone.

The Science of the total environment pii:S0048-9697(22)04076-1 [Epub ahead of print].

Leachate-saturated zone (LSZ) of landfills is a complicated biogeochemical hotspot due to the continuous input of electron donors and acceptors from the top refuse layer with leachate migration. In this study, the methylation behavior of the arsenic (As) was investigated. The results indicate that As-methylation processes are influenced by temperature fields in LSZ. The dimethylarsinic acid biotransformation capability can be enhanced with an increase in temperature. Microbial diversity, quantification of functional gene (arsM), and co-occurrence network analysis further characterized the drivers of As methylation in LSZ. As-biogeochemical cycle pathways, as well as As-functional gene distribution among different temperature fields, were modeled on the basis of KEGG annotation. Binning analysis was further employed to assemble As-methylated metagenomes, enabling the identification of novel species for As methylation in landfills. Then, 87 high-quality draft metagenome-assembled genomes (MAGs) were reconstructed from LSZ refuse samples; nearly 15 % (13 of 87) belonged to putative As-methylates functional MAGs. Combined with the model of the As-biogeochemical cycle, nine putative functional species could complete methylation processes alone. The findings of this study highlighted the temperature influence on the As-methylation behavior in LSZ and could facilitate the management of As contamination in landfills.

RevDate: 2022-06-28

Xiu W, Wu M, Nixon SL, et al (2022)

Genome-Resolved Metagenomic Analysis of Groundwater: Insights into Arsenic Mobilization in Biogeochemical Interaction Networks.

Environmental science & technology [Epub ahead of print].

High-arsenic (As) groundwaters, a worldwide issue, are critically controlled by multiple interconnected biogeochemical processes. However, there is limited information on the complex biogeochemical interaction networks that cause groundwater As enrichment in aquifer systems. The western Hetao basin was selected as a study area to address this knowledge gap, offering an aquifer system where groundwater flows from an oxidizing proximal fan (low dissolved As) to a reducing flat plain (high dissolved As). The key microbial interaction networks underpinning the biogeochemical pathways responsible for As mobilization along the groundwater flow path were characterized by genome-resolved metagenomic analysis. Genes associated with microbial Fe(II) oxidation and dissimilatory nitrate reduction were noted in the proximal fan, suggesting the importance of nitrate-dependent Fe(II) oxidation in immobilizing As. However, genes catalyzing microbial Fe(III) reduction (omcS) and As(V) detoxification (arsC) were highlighted in groundwater samples downgradient flow path, inferring that reductive dissolution of As-bearing Fe(III) (oxyhydr)oxides mobilized As(V), followed by enzymatic reduction to As(III). Genes associated with ammonium oxidation (hzsABC and hdh) were also positively correlated with Fe(III) reduction (omcS), suggesting a role for the Feammox process in driving As mobilization. The current study illustrates how genomic sequencing tools can help dissect complex biogeochemical systems, and strengthen biogeochemical models that capture key aspects of groundwater As enrichment.

RevDate: 2022-06-28

Wang Z, Zhang Z, Lu C, et al (2022)

Effects of Sporisorium reiliana polysaccharides and Phoenix dactylifera monosaccharides on the gut microbiota and serum metabolism in mice with fructose-induced hyperuricemia.

Archives of microbiology, 204(7):436.

In recent decades, the prevalence of hyperuricemia has increased, and dietary fructose is an important risk factor for the development of this disease. This study investigated and compared the effects of Sphacelotheca reiliana polysaccharides and Phoenix dactylifera monosaccharides on a series of physiological and biochemical indicators and on the metagenomes and serum metabolites in mice with hyperuricemia caused by a high-fructose diet. S. reiliana polysaccharides inhibited uric acid biosynthesis and promoted uric acid excretion, thereby alleviating the hyperuricemia phenotype. In addition, hyperuricemia was closely related to the gut microbiota. After treatment with S. reiliana polysaccharides, the abundances of Bacteroidetes and Proteobacteria in the mouse intestines were decreased, the expression of genes involved in glycolysis/gluconeogenesis metabolic pathways and purine metabolism was downregulated, and the dysfunction of the gut microbiota was alleviated. With regard to serum metabolism, the abundance of hippuric acid, uridine, kynurenic acid, propionic acid and arachidonoyl decreased, and the abundances of serum metabolites in inflammatory pathways involved in kidney injury and gout, such as bile acid metabolism, purine metabolism and tryptophan metabolism pathways, decreased. P. dactylifera monosaccharides aggravated hyperuricemia. This research provides a valuable reference for the development of sugar applications.

RevDate: 2022-06-28

Roguet A, Newton RJ, Eren AM, et al (2022)

Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure.

mSystems [Epub ahead of print].

Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored. Here, we show that the bacterial assemblages sequenced from untreated wastewater in 71 U.S. cities were highly coherent at a fine sequence level, suggesting that urban infrastructure separated by great spatial distances can give rise to strikingly similar communities. Within the overall microbial community structure, temperature had a discernible impact on the distribution patterns of closely related amplicon sequence variants, resulting in warm and cold ecotypes. Two bacterial genera were dominant in most cities regardless of their size or geographic location; on average, Arcobacter accounted for 11% and Acinetobacter 10% of the entire community. Metagenomic analysis of six cities revealed these highly abundant resident organisms carry clinically important antibiotic resistant genes blaCTX-M, blaOXA, and blaTEM. In contrast, human fecal bacteria account for only ~13% of the community; therefore, antibiotic resistance gene inputs from human sources to the sewer system could be comparatively small, which will impact measurement capabilities when monitoring human populations using wastewater. With growing awareness of the metabolic potential of microbes within these vast networks of pipes and the ability to examine the health of human populations, it is timely to increase our understanding of the ecology of these systems. IMPORTANCE Sewer infrastructure is a relatively new habitat comprised of thousands of kilometers of pipes beneath cities. These wastewater conveyance systems contain large reservoirs of microbial biomass with a wide range of metabolic potential and are significant reservoirs of antibiotic resistant organisms; however, we lack an adequate understanding of the ecology or activity of these communities beyond wastewater treatment plants. The striking coherence of the sewer microbiome across the United States demonstrates that the sewer environment is highly selective for a particular microbial community composition. Therefore, results from more in-depth studies or proven engineering controls in one system could be extrapolated more broadly. Understanding the complex ecology of sewer infrastructure is critical for not only improving our ability to treat human waste and increasing the sustainability of our cities but also to create scalable and effective sewage microbial observatories, which are inevitable investments of the future to monitor health in human populations.

RevDate: 2022-06-28

Borren NZ, AN Ananthakrishnan (2022)

Precision medicine: how multiomics will shape the future of inflammatory bowel disease?.

Current opinion in gastroenterology, 38(4):382-387.

PURPOSE OF REVIEW: In this article, we provide an overview of studies examining multiomic profiling in various clinical scenarios in the management of inflammatory bowel diseases (IBDs).

RECENT FINDINGS: IBD arises as a result of an interplay between genetic, environmental, microbial and immunologic perturbations. The access to high throughput technology as well as the decrease in costs associated with such studies has led to a growing wealth of literature examining the utility of single or multiomic profiles in the management of IBD. Such studies have commonly examined the genome (and less frequently the epigenome), transcriptome, metabolome, proteome and the gut microbial metagenome in the context of overall IBD status or specific clinical scenarios, including the disease progression or response to treatment. The findings have provided important insight into how each of these compartments reflect underlying disease pathophysiologic processes and, in turn, can influence stratification of patients for clinical management.

SUMMARY: Multiomic profiling in IBD has the potential to advance the field of personalized precision medicine in the management of IBDs.

RevDate: 2022-06-28

Qin X, Zhou J, Wang Z, et al (2022)

Metagenomic analysis of the microbiome of the upper reproductive tract: combating ovarian cancer through predictive, preventive, and personalized medicine.

The EPMA journal pii:286 [Epub ahead of print].

Purpose: We investigated whether ovarian cancer could alter the genital microbiota in a specific way with clinical values. Furthermore, we proposed how such changes could be envisioned in a paradigm of predictive, preventive, and personalized medicine (PPPM).

Methods: The samples were collected using cotton swabs from the cervical, uterine cavity, fallopian tubes, and ovaries of patients subjected to the surgical procedures for the malignant/benign lesions. All samples were then analyzed by metagenomic shotgun sequencing. The distribution patterns and characteristics of the microbiota in the reproductive tract of subjects were analyzed and were interpreted in relation to the clinical outcomes of the subjects.

Results: While the ovarian cancer was able to alter the genital microbiota, the bacteria were the dominant microorganisms in all samples across all cohorts in the study (median 99%). The microbiota of the upper female reproductive tract were mainly from the cervical, identified by low bacterial biomass and high bacterial diversity. Ovarian cancer had a distinct microbiota signature. The tubal ligation affects its microbial distribution. There were no different species on the surface of platinum-sensitive ovarian tissues compared to samples from platinum-resistant patients.

Conclusion: The ovarian cancer-induced changes in microbiota magnify the potential of microbiota as a biotherapeutic modality in the treatment of ovarian cancer in this study and very likely for several malignancies and other conditions. Our findings demonstrated, for the first time, that microbiota could be dissected and applied in more specific fashion based on a predictive, preventive, and personalized medicine (PPPM) model in the treatment of ovarian cancer. Utilizing microbiota portfolio in a PPPM system in ovarian cancer would provide a unique opportunity to a clinically intelligent and novel approach in the treatment of ovarian cancer as well as several other conditions and malignancies.

Supplementary Information: The online version contains supplementary material available at 10.1007/s13167-022-00286-1.

RevDate: 2022-06-28

Modin O, Fuad N, Abadikhah M, et al (2022)

A relationship between phages and organic carbon in wastewater treatment plant effluents.

Water research X, 16:100146 pii:S2589-9147(22)00016-0.

With stringent effluent requirements and the implementation of new processes for micropollutant removal, it is increasingly important for wastewater treatment plants (WWTPs) to understand the factors affecting effluent quality. Phages (viruses infecting prokaryotes) are abundant in the biological treatment processes. They can contribute to organic carbon in the treated effluent both because they are organic in nature and occur in the effluent and because they cause lysis of microorganisms. Today very little is known about the effects of phages on effluent quality. The goal of this study was, therefore, to determine the relationship between phages and organic carbon in WWTP effluents. We also examined the diversity, taxonomy, and host-association of DNA phages using metagenomics. Effluent samples were collected from four WWTPs treating municipal wastewater. Significant differences in both organic carbon and virus-like particle concentrations were observed between the plants and there was a linear relationship between the two parameters. The phage communities were diverse with many members being taxonomically unclassified. Putative hosts were dominated by bacteria known to be abundant in activated sludge systems such as Comamonadaceae. The composition of phages differed between the WWTPs, suggesting that local conditions shape the communities. Overall, our findings suggest that the abundance and composition of phages are related to effluent quality. Thus, there is a need for further research clarifying the association between phage dynamics and WWTP function.

RevDate: 2022-06-28

Zhang J, Liu S, Sun H, et al (2022)

Corrigendum to "Metagenomics-based insights into the microbial community profiling and flavor development potentiality of baijiu Daqu and huangjiu wheat Qu" [Food Res. Int. 152 (2022) 110707].

Food research international (Ottawa, Ont.), 157:111448.

RevDate: 2022-06-28

Zhu Q, Chen L, Peng Z, et al (2022)

Analysis of environmental driving factors on Core Functional Community during Daqu fermentation.

Food research international (Ottawa, Ont.), 157:111286.

Sauce-flavor Daqu determines the quality of Baijiu because its core functional community (CFC) can produce abundant enzymes and aroma. However, complex environmental factors make it difficult to accurately control the fermentation quality of Daqu. In this study, we constructed a functional gene database to identify CFC based on multi-omics technology and explore controllable environmental factors of CFC to improve the quality of Daqu. The results showed that the CFC is mainly composed of 7 bacterial and 4 fungal genera, including Kroppenstedtia, Thermoactinomyces, Bacillus, Acinetobacter, Brevibacterium, Saccharopolyspora, Ochrobactrum, Aspergillus, Byssochlamys, Thermoascus, and Thermomyces. Most of them are thermostable microorganisms that can provide the power of fermentation and saccharification (α-amylase, glucoamylase, and protease). In CFC, Acinetobacter and Saccharopolyspora were strongly positively correlated with typical flavor substances, while fungi were negatively correlated, particularly with furans. Therefore, the bacterial genera contributed more to the significant flavors. The CFC was significantly influenced by high temperature and total titrate acid based on RDA. In addition, high-temperature conditions were also strongly positively correlated with flavors that can be quickly produced at high temperatures, such as 2-Furancarboxaldehyde, 2-Furanmethanol, and Tetramethylpyrazine. As a controllable factor, the temperature can be adjusted to improve the quality of Daqu directionally, which will provide theoretical guidance for the production of high-quality Daqu.

RevDate: 2022-06-28

Kothe CI, Mohellibi N, P Renault (2022)

Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics.

Food research international (Ottawa, Ont.), 157:111265.

Brazilian artisanal cheeses date from the first Portuguese settlers and evolved via local factors, resulting in unique products that are now part of the patrimony and identity of different Brazilian regions. In this study, we combined several culture-independent approaches, including 16S/ITS metagenetics, assembly- and deep profiling-metagenomics to characterize the originality of the microbiota of five varieties of Brazilian artisanal cheeses from the South and Southeast regions of Brazil. Their core microbiota contained mainly lactic acid bacteria (LAB), of which Lactococcus lactis subsp. lactis was the most frequent, followed by Streptococcus thermophilus in the South region. Moreover, several samples from the Southeast region contained, as dominant LAB, two other food Streptococci belonging to a new species of the salivarius group and S. infantarius. Rinds of samples from the Southeast region were dominated by the halotolerant bacterium Corynebacterium variabile, and the yeasts Diutina catenulata, followed by Debaryomyces hansenii and Kodamaea ohmeri. Rinds from the South region contained mainly LAB due to their short ripening time, and the predominant yeast was D. hansenii. Phylogenomic analysis based on L. lactis metagenome-assembled genomes (MAGs) showed that most Brazilian strains are closely related and form a different clade from those whose genomes are available at this time, indicating that they belong to a specific group. Lastly, functional analysis showed that S. infantarius acquired a ∼ 26 kb DNA fragment from S. thermophilus starter strains that carry the LacSZ system, allowing fast lactose assimilation, an adaptation advantage for growth in milk. Finally, our study identified several areas of concern, such as the presence of somatic cell DNA and high levels of antibiotic resistance genes in several cheese microbiota, suggesting that milk from diseased animals may still be used occasionally. Overall, the data from this study highlight the potential value of the traditional and artisanal cheese production network in Brazil, and provide a metagenomic-based scheme to help manage this resource safely.

RevDate: 2022-06-28

Jung MJ, Kim J, Lee SH, et al (2022)

Role of combinated lactic acid bacteria in bacterial, viral, and metabolite dynamics during fermentation of vegetable food, kimchi.

Food research international (Ottawa, Ont.), 157:111261.

Lactic acid bacteria (LAB) in kimchi, a traditional Korean food, are major fermentative microorganisms affecting the quality, safety, and nutritional and organoleptic properties of the final product. In this study, we determined the role of three key LAB strains, Leuconostoc gelidum, Latilactobacillus sakei, Weissella koreensis originated from different raw ingredients during natural fermentation, as opposed to an axenic environment. Starter cultures were inoculated into food with wild indigenous microbial communities, and the dynamics of bacterial communities and metabolites were analyzed during fermentation. As bacteriophages within the food viral community directly affect fermentation by influencing bacterial function and composition, the diversity and composition of DNA viral communities were compared with those of corresponding bacterial communities using a metagenomic approach. Our results provide insights into the ecological role of LAB starters in food fermentation and the potential impact of bacteriophages as modulators of bacterial communities associated with the fermentation properties of kimchi.

RevDate: 2022-06-28

Sequino G, Valentino V, Villani F, et al (2022)

Omics-based monitoring of microbial dynamics across the food chain for the improvement of food safety and quality.

Food research international (Ottawa, Ont.), 157:111242.

The diffusion of high-throughput sequencing has dramatically changed the study of food microbial ecology. Amplicon-based description of the microbial community may be routinary implemented in the food industry to understand how the processing parameters and the raw material quality may affect the microbial community of the final product, as well as how the community changes during the shelf-life. In addition, application of shotgun metagenomics may represent an invaluable resource to understand the functional potential of the microbial community, identifying the presence of spoilage-associated activities or genes related to pathogenesis. Finally, retrieving Metagenome-Assembled Genomes (MAGs) of relevant species may be useful for strain-tracking along the food chain and in case of food poisoning outbreaks. This review gives an overview of the possible applications of sequencing-based approaches in the study of food microbial ecology, highlighting limitations that still prevent the spreading of these techniques to the food industry.

RevDate: 2022-06-28

Wang C, Zhao F, Bai Y, et al (2022)

In vitro digestion mimicking conditions in young and elderly reveals marked differences between profiles and potential bioactivity of peptides from meat and soy proteins.

Food research international (Ottawa, Ont.), 157:111215.

We applied in vitro models of gastrointestinal (GI) digestion simulating the conditions of the GI tract of healthy adults and elderly individuals with achlorhydria (EA) to investigate differences in the digestibility of meat (chicken, beef and pork) and soy proteins. Digestibility was significantly affected by EA alterations. Peptidomics analyses revealed significant differences in peptide profiles between control and EA conditions, including number, length distribution, clustering, and differentially abundant peptides (DAPs). Our results revealed that the differences in meat peptide profiles diminished going from the gastric to intestinal phase. For soy protein, the marked differences between control and EA conditions were maintained in the gastric and intestinal phases. Higher numbers of potentially bioactive peptides were generated under the control condition compared to the EA condition. The present study provides insight into the distinct peptide profiles generated by in vitro digestion of meat and soy proteins under adult and EA GI conditions.

RevDate: 2022-06-28

Yang D, Li C, Li L, et al (2022)

Novel insight into the formation mechanism of umami peptides based on microbial metabolism in Chouguiyu, a traditional Chinese fermented fish.

Food research international (Ottawa, Ont.), 157:111211.

Umami peptides formed by microbial metabolism play an important role in the umami taste of Chouguiyu. In this study, 138 umami peptides and 6 kinds of proteases in two categories from 35 microbial genera were identified from Chouguiyu during the fermentation process by peptidomics and metagenomics analysis, respectively. The interaction network maps between the umami peptides and protease-producing microbial genera in each protease classification were constructed based on Pearson's correlation coefficient after a two-way orthogonal partial least squares (O2PLS) evaluation. The proteases classified in 34 clusters of orthologous groups (COG) from Vagococcus, Peptostreptococcus, Acinetobacter, Psychrobacter, and Enterococcus played a major role in the formation of umami peptides. The core umami peptides with the highest abundance and correlation were mainly derived from troponin and myosin in mandarin fish. The lactic acid bacteria contributed most to the hydrolysis preparation of these umami peptides. This study is beneficial to screen the proteases and related microbial strains to improve the umami taste of Chouguiyu.

RevDate: 2022-06-28

Yasir M, Al-Zahrani IA, Bibi F, et al (2022)

New insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteria.

Food research international (Ottawa, Ont.), 157:111190.

Consumption of fermented foods has grown worldwide due to the purported health benefits. It is thus critical to understand fermented foods microbiome that mainly influences the quality and safety of these foods. This study identified bacterial communities, including functional profiles of probiotics and antimicrobial resistance genes (ARGs), in pickled vegetables commonly consumed in the Middle Eastern, African, and Asian sub-continent regions. Eighteen samples from six pickled vegetables were collected from local markets in Saudi Arabia and analyzed using shotgun metagenomic sequencing. Statistical analyses revealed significant distance and separate clustering of bacterial communities among the different pickle types. Species of Levilactobacillus namurensis, Lentilactobacillus buchneri, Lentilactobacillus parafarraginis, Lactiplantibacillus pentosus, Pectobacterium carotovorum, Leuconostoc carnosum, Weissella confuse were found in a range of dominance in most of the samples. Binning revealed 33 high-quality, metagenome-assembled genomes (MAGs), including 4 MAGs representing putatively novel species of Lactobacillus, Alcanivorax, and Dichelobacter. Moreover, 285 ARGs and variants produce resistance against 20 classes of antibiotics were retrieved, mostly from Enterobacteriaceae contigs. The metagenomes harbored relatively high abundances of carbohydrate fermentation enzymes, as well as metabolic pathways for amino acid metabolism, cofactors and vitamins biosynthesis. Overall, by providing a comprehensive overview of bacterial communities and probiotic bacteria in pickled vegetables, the results suggest the need for more hygienic processing to avoid Enterobacteriaceae contamination and ARG spread.

RevDate: 2022-06-27

She J, Fu L, Zheng X, et al (2022)

Characterization of a new L-carnosine synthase mined from deep-sea sediment metagenome.

Microbial cell factories, 21(1):129.

L-Carnosine is a natural biologically active dipeptide with critical physiological functions, such as antioxidant, antiglycation, and cytoplasmic buffering properties. Direct enzymatic synthesis is a promising way for L-carnosine production. In this study, a new aminopeptidase (gene_236976) with synthetic activity toward L-carnosine was identified by a metagenome mining approach from deep-sea sediment and functionally expressed in Escherichia coli. The enzyme shared a low identity of 14.3% with reported L-carnosine dipeptidase (SmPepD) from Serratia marcescens. β-Alanine methyl ester was proven to be the best substrate for the synthesis, and no ATP was needed for the enzymatic reaction. The enzyme activity was increased by structure-guided rational design. Only the mutant of G310 site gave positive results, and G310A mutant showed the best performance among the site-direct saturation mutagenesis, indicating that the additional CH3 group of mutant G310A was the main factor affecting the enzymatic activity. The engineered enzyme produced about 10 mM L-carnosine was produced from substrates of 50 mM β-alanine methyl ester and 50 mM L-histidine, under a tentatively optimized condition. This study enriched the enzyme resources for developing the microbial synthesis process of L-carnosine production.

RevDate: 2022-06-27

Wynendaele E, Debunne N, Janssens Y, et al (2022)

The quorum sensing peptide EntF* promotes colorectal cancer metastasis in mice: a new factor in the host-microbiome interaction.

BMC biology, 20(1):151.

BACKGROUND: Colorectal cancer, one of the most common malignancies worldwide, is associated with a high mortality rate, mainly caused by metastasis. Comparative metagenome-wide association analyses of healthy individuals and cancer patients suggest a role for the human intestinal microbiota in tumor progression. However, the microbial molecules involved in host-microbe communication are largely unknown, with current studies mainly focusing on short-chain fatty acids and amino acid metabolites as potential mediators. Quorum sensing peptides are not yet considered in this context since their presence in vivo and their ability to affect host cells have not been reported so far.

RESULTS: Here, we show that EntF*, a metabolite of the quorum sensing peptide EntF produced by Enterococcus faecium, is naturally present in mice bloodstream. Moreover, by using an orthotopic mouse model, we show that EntF* promotes colorectal cancer metastasis in vivo, with metastatic lesions in liver and lung tissues. In vitro tests suggest that EntF* regulates E-cadherin expression and consequently the epithelial-mesenchymal transition, via the CXCR4 receptor. In addition, alanine-scanning analysis indicates that the first, second, sixth, and tenth amino acid of EntF* are critical for epithelial-mesenchymal transition and tumor metastasis.

CONCLUSION: Our work identifies a new class of molecules, quorum sensing peptides, as potential regulators of host-microbe interactions. We prove, for the first time, the presence of a selected quorum sensing peptide metabolite in a mouse model, and we demonstrate its effects on colorectal cancer metastasis. We believe that our work represents a starting point for future investigations on the role of microbiome in colorectal cancer metastasis and for the development of novel bio-therapeutics in other disease areas.

RevDate: 2022-06-27

Huang G, Zhou L, Yang N, et al (2022)

Extracorporeal membrane oxygenation rescue for severe pneumocystis pneumonia with the Macklin effect: a case report.

BMC infectious diseases, 22(1):577.

BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) in an immunocompromised host is often associated with the Macklin effect, which can progress to spontaneous pneumomediastinum (SPM), subcutaneous emphysema (SCE), and pneumothorax (PNX). Diagnosing the causative organism of these conditions in non-HIV infected patients and treating hypoxemia while preventing further lung damage can be challenging. This study examines the case of a non-HIV infected male with SPM, SCE, and PNX secondary to severe Pneumocystis jirovecii (PJ) infection.

CASE PRESENTATION: A 53-year-old male with pure red cell aplasia (PRCA) was admitted with fever, dry cough, and shortness of breath. His respiratory function progressively deteriorated due to the development of SPM, SCE, and PNX, eventually requiring endotracheal intubation and invasive ventilation. As a result of high pressure in his airways occasioned by lung recruitment maneuvers, his pulmonary parameters worsened, necessitating veno-venous (VV) extracorporeal membrane oxygenation (ECMO) therapy. The early initiation of VV-ECMO facilitated ultra-protective lung ventilation and prevented the progression of SPM, SCE, and PNX. Traditional diagnostic assays were unrevealing, whereupon the patient resorted to the metagenomic next-generation sequencing technology for uncovering potential pathogens. Consequently, we detected a significantly higher infection by PJ in the patient's bronchoscopy lavage fluid. Finally, the patient was successfully treated with appropriate antimicrobials and was decannulated after nine days of ECMO support.

CONCLUSIONS: SPM, SCE, and PNX are rare clinical manifestations of PJP. However, they can be considered as poor prognostic factors of the infection. Physicians should, therefore, be alert to the possibility of PJP in immunocompromised patients.

RevDate: 2022-06-27

Zhang Z, Zhang Y, Shi Z, et al (2022)

Linking Genome-Centric Metagenomics to Kinetic Analysis Reveals the Regulation Mechanism of Hydroxylamine in Nitrite Accumulation of Biological Denitrification.

Environmental science & technology [Epub ahead of print].

Given hydroxylamine accumulation in various nitrification systems and its potential mechanism in regulating the subsequent denitrification process were unraveled in this study. Hydroxylamine (>0.5 mgN/L) immediately induced nitrite accumulation of activated sludge by inhibiting the activities of nitrite reductases and their electron transport modules (Complex III and cytochrome c). Moreover, long-term exposure to 0.5-2.5 mgN/L hydroxylamine accelerated the functional transformation from denitrification to denitratation under low C/N conditions. However, genome-centric metagenomics indicated that a genotypic complete rather than truncated denitrifier Thauera aminoaromatica TJ127 was enriched and mainly responsible for acetate storage and nitrate reduction of the denitratation community. Interestingly, its enrichment resulted in nitrite production and reduction sequentially but reduced nitrate only to nitrite under carbon-limited conditions (C/N ≤ 3.0). Thus, it showed higher tolerance to hydroxylamine than the concurrent phenotype denitrifiers in activated sludge. Moreover, due to its higher anoxic storage capability in the feast phase, this enrichment became highly specialized by decreasing the feast/famine ratio, and thus a satisfactory denitratation performance was still maintained without hydroxylamine. These results suggested that the transient release of hydroxylamine from nitrification may interfere with subsequent denitrification metabolism, but its continuous accumulation is beneficial for achieving denitratation, which could steadily provide nitrite for mainstream anammox.

RevDate: 2022-06-27

Cui P, Kong K, Yao Y, et al (2022)

Community composition, bacterial symbionts, antibacterial and antioxidant activities of honeybee-associated fungi.

BMC microbiology, 22(1):168.

BACKGROUND: Fungi associated with insects represent one potentially rich source for the discovery of novel metabolites. However, a comprehensive understanding of the fungal communities of Apis mellifera ligustica remains elusive.

RESULTS: Here, we investigated the phylogenetic diversity and community composition of honeybee-associated fungi using combination of culture-dependent and culture-independent approaches. A total of forty-five fungi were isolated and purified from the Apis mellifera ligustica, royal jelly, and honeycomb, which belonged to four classes and eleven different genera. Furthermore, 28 bacterial 16S rRNA gene sequences were obtained by PCR from the fungal metagenome. High-throughput sequencing analyses revealed that the fungal communities were more diverse, a total of 62 fungal genera were detected in the honeybee gut by culture-independent method, whereas only 4 genera were isolated by culture-dependent method. Similarly, 247 fungal genera were detected in the honeycomb, whereas only 4 genera were isolated. In addition, we assessed the antibacterial and antioxidant activities of fungal isolates. Most fungal crude extracts obtained from the cultivation supernatant exhibited antioxidant activities. Only two fungal crude extracts displayed moderate activity against Escherichia coli and Staphylococcus aureus. Chemical analysis of Chaetomium subaffine MFFC22 led to the discovery of three known compounds, including cochliodinol (1), emodin (2), chrysophanol (3). Among them, cochliodinol (1) showed intense DPPH radical scavenging activity with the 50% inhibitory concentration (IC50) of 3.06 μg/mL, which was comparable to that of the positive ascorbic acid (IC50 = 2.25 μg/mL). Compound 2 displayed weak inhibitory activities against Micrococcus tetragenus and S. aureus.

CONCLUSIONS: This research provided a fundamental clue for the complex interactions among honeybees, fungi, bacterial symbionts, and the effects on the honeybee. Furthermore, the diversity of honeybee-associated fungi had great potential in finding the resource of new species and antioxidants.

RevDate: 2022-06-27

Banciu HL, Gridan IM, Zety AV, et al (2022)

Asgard archaea in saline environments.

Extremophiles : life under extreme conditions, 26(2):21.

Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.

RevDate: 2022-06-27

Liu Y, Ji M, Yu T, et al (2022)

A genome and gene catalog of glacier microbiomes.

Nature biotechnology [Epub ahead of print].

Glaciers represent a unique inventory of microbial genetic diversity and a record of evolution. The Tibetan Plateau contains the largest area of low-latitude glaciers and is particularly vulnerable to global warming. By sequencing 85 metagenomes and 883 cultured isolates from 21 Tibetan glaciers covering snow, ice and cryoconite habitats, we present a specialized glacier microbial genome and gene catalog to archive glacial genomic and functional diversity. This comprehensive Tibetan Glacier Genome and Gene (TG2G) catalog includes 883 genomes and 2,358 metagenome-assembled genomes, which represent 968 candidate species spanning 30 phyla. The catalog also contains over 25 million non-redundant protein-encoding genes, the utility of which is demonstrated by the exploration of secondary metabolite biosynthetic potentials, virulence factor identification and global glacier metagenome comparison. The TG2G catalog is a valuable resource that enables enhanced understanding of the structure and functions of Tibetan glacial microbiomes.

RevDate: 2022-06-27

Medvedeva S, Sun J, Yutin N, et al (2022)

Three families of Asgard archaeal viruses identified in metagenome-assembled genomes.

Nature microbiology [Epub ahead of print].

Asgardarchaeota harbour many eukaryotic signature proteins and are widely considered to represent the closest archaeal relatives of eukaryotes. Whether similarities between Asgard archaea and eukaryotes extend to their viromes remains unknown. Here we present 20 metagenome-assembled genomes of Asgardarchaeota from deep-sea sediments of the basin off the Shimokita Peninsula, Japan. By combining a CRISPR spacer search of metagenomic sequences with phylogenomic analysis, we identify three family-level groups of viruses associated with Asgard archaea. The first group, verdandiviruses, includes tailed viruses of the class Caudoviricetes (realm Duplodnaviria); the second, skuldviruses, consists of viruses with predicted icosahedral capsids of the realm Varidnaviria; and the third group, wyrdviruses, is related to spindle-shaped viruses previously identified in other archaea. More than 90% of the proteins encoded by these viruses of Asgard archaea show no sequence similarity to proteins encoded by other known viruses. Nevertheless, all three proposed families consist of viruses typical of prokaryotes, providing no indication of specific evolutionary relationships between viruses infecting Asgard archaea and eukaryotes. Verdandiviruses and skuldviruses are likely to be lytic, whereas wyrdviruses potentially establish chronic infection and are released without host cell lysis. All three groups of viruses are predicted to play important roles in controlling Asgard archaea populations in deep-sea ecosystems.

RevDate: 2022-06-27

Rambo IM, Langwig MV, Leão P, et al (2022)

Genomes of six viruses that infect Asgard archaea from deep-sea sediments.

Nature microbiology [Epub ahead of print].

Asgard archaea are globally distributed prokaryotic microorganisms related to eukaryotes; however, viruses that infect these organisms have not been described. Here, using metagenome sequences recovered from deep-sea hydrothermal sediments, we characterize six relatively large (up to 117 kb) double-stranded DNA (dsDNA) viral genomes that infected two Asgard archaeal phyla, Lokiarchaeota and Helarchaeota. These viruses encode Caudovirales-like structural proteins, as well as proteins distinct from those described in known archaeal viruses. Their genomes contain around 1-5% of genes associated with eukaryotic nucleocytoplasmic large DNA viruses (NCLDVs) and appear to be capable of semi-autonomous genome replication, repair, epigenetic modifications and transcriptional regulation. Moreover, Helarchaeota viruses may hijack host ubiquitin systems similar to eukaryotic viruses. Genomic analysis of these Asgard viruses reveals that they contain features of both prokaryotic and eukaryotic viruses, and provides insights into their potential infection and host interaction mechanisms.

RevDate: 2022-06-27

Faridl M, Mellyani K, Khoirunnisa K, et al (2022)

RNA-seq analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic COVID-19 patients.

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases pii:S1201-9712(22)00368-X [Epub ahead of print].

OBJECTIVES: The characterization of asymptomatic and mildly symptomatic COVID-19 patients by observing changes in gene expression profile and possible bacterial coinfection is relevant to be investigated. We aimed to identify transcriptomic and coinfection profiles in both groups of patients.

METHODS: An RNA-seq analysis on nasopharyngeal swabs were performed using a shotgun sequencing pipeline. Differential gene analysis, viral genome assembly, and metagenomics analysis were further performed using the retrieved data.

RESULTS: Both groups of patients underwent a cilia modification & mRNA splicing. Modulation in macroautophagy, epigenetics, and cell cycle processes was observed specifically in the asymptomatic group. Modulation in the RNA transport was found specifically in the mildly symptomatic group. The mildly symptomatic group showed modulation in the RNA transport and upregulation of autophagy regulator genes and genes in the complement system. No link between viral variants and disease severity was found. Microbiome analysis revealed the elevation of Streptococcus pneumoniae and Veillonella parvula proportion in symptomatic patients.

CONCLUSION: A reduction in the autophagy influx and modification in the epigenetic profile might be involved in halting the disease progression. A global dysregulation of RNA processing and translation might cause more severe outcomes in symptomatic individuals. Coinfection by opportunistic microflora should be taken into account when assessing the possible outcome of SARS-CoV-2 infection.

RevDate: 2022-06-27

Zhang S, Ma X, Sun H, et al (2022)

Semi-continuous mesophilic-thermophilic two-phase anaerobic co-digestion of food waste and spent mushroom substance: Methanogenic performance, microbial, and metagenomic analysis.

Bioresource technology pii:S0960-8524(22)00847-1 [Epub ahead of print].

The methanogenic efficiency and system stability of anaerobic co-digestion of food waste (FW) and spent mushroom substance (SMS) are important for its application. A 90-day semi-continuous study was conducted to compare the co-digestion performance of an ethanologenic-methanogenic two-phase system and an acidogenic-methanogenic system using FW and SMS as substrates. The results showed that the ethanologenic-methanogenic system increased the contents of ethanol and acetate in the hydrolytic acidification phase. Microbial-community analysis showed that ethanologenic-methanogenic system enriched hydrolytic acidifying bacteria and methanogens such as Methanoculleus, resulting in an increase in the average methane yield of methanogenic phase by 1.91-2.43 times at the same organic loading rate (OLR = 3.0-4.0 g-VS·L-1·d-1). Metagenomic analysis indicated that the ethanologenic-methanogenic system increased the abundance of enzyme-encoding genes and promoted the degradation of acetate and CO2/H2, thereby enhancing methanogenic metabolic pathways, compared to the acidogenic-methanogenic system.

RevDate: 2022-06-27

Troci A, Rausch P, Waschina S, et al (2022)

Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis.

Molecular nutrition & food research [Epub ahead of print].

SCOPE: The gut microbiome regulates various metabolic pathways in the host and its dysbiosis is involved in the pathogenesis of diverse diseases. Multiple factors modulate the composition of the microbiome and how it physiologically functions, but one of the major factors triggering gut microbiome establishment is diet. We aim to unravel interactions and changes between diet and gut microbiome over a period of 3 years.

METHODS AND RESULTS: We investigated the relation between 152 dietary factors, in terms of food groups and nutrients, and the microbiome of 75 individuals over a three-year time period. Shotgun metagenomic sequencing was performed to profile gut microbial composition and function. Dietary intake was assessed through food frequency questionnaires. Associations between diet and MAGs, functional KOs and metabolites were explored for each time point. We showed that there were significant changes in gut microbiome taxonomy and functional composition between two time points (Padonis < 0.05) and identified microbial taxa and KO functional units that were differentially expressed over the study period. Whereas microbial taxonomy was found to be highly individualized and unstable, overall microbial functions stayed relatively stable. Moreover, in-silico metabolic modeling of the gut microbial communities indicated that changes in dietary intake of medium-chain saturated fatty acids is accompanied by an altered utilization of amino acids by the gut microbiome.

CONCLUSION: Our study design allowed us to validate functional stability within the gut microbiome of healthy subjects over a three-year period. However, enduring changes in nutrition such as increased alcohol consumption or decreased intake of vegetables come along with enhanced microbial functions that are associated with disease etiology. This article is protected by copyright. All rights reserved.

RevDate: 2022-06-27

Mercado JV, Koyama M, K Nakasaki (2022)

Co-occurrence network analysis reveals loss of microbial interactions in anaerobic digester subjected to repeated organic load shocks.

Water research, 221:118754 pii:S0043-1354(22)00707-2 [Epub ahead of print].

Fluctuations in the anaerobic digestion (AD) organic loading rate (OLR) cause shocks to the AD microbiome, which lead to unstable methane productivity. Managing these fluctuations requires a larger digester, which is impractical for community-scale applications, limiting the potential of AD in advancing a circular economy. To allow operation of small-scale AD while managing OLR fluctuations, we need to tackle the issue through elucidation of the microbial community dynamics via 16S rRNA gene sequencing. This study elucidated the interrelation of the AD performance and the dynamics of the microbial interactions within its microbiome in response to repeated high OLR shocks at different frequencies. The OLR shocks were equivalent to 4 times the baseline OLR of 2 g VS/L/d. We found that less frequent organic load shocks result to deterioration of methane productivity. Co-occurrence network analysis shows that this coincides with the breakdown of the microbiome network structure. This suggests loss of microbial interactions necessary in maintaining stable AD. Identification of species influencing the network structure revealed that a species under the genus Anaerovorax has the greatest influence, while orders Spirochaetales and Synergistales represent the greatest number of the influential species. We inferred that the impact imposed by the OLR shocks shifted the microbiome activity towards biochemical pathways that are not contributing to methane production. Establishing a small-scale AD system that permits OLR fluctuations would require developing an AD microbiome resilient to infrequent organic loading shocks.

RevDate: 2022-06-27

Prieto Riquelme MV, Garner E, Gupta S, et al (2022)

Demonstrating a Comprehensive Wastewater-Based Surveillance Approach That Differentiates Globally Sourced Resistomes.

Environmental science & technology [Epub ahead of print].

Wastewater-based surveillance (WBS) for disease monitoring is highly promising but requires consistent methodologies that incorporate predetermined objectives, targets, and metrics. Herein, we describe a comprehensive metagenomics-based approach for global surveillance of antibiotic resistance in sewage that enables assessment of 1) which antibiotic resistance genes (ARGs) are shared across regions/communities; 2) which ARGs are discriminatory; and 3) factors associated with overall trends in ARGs, such as antibiotic concentrations. Across an internationally sourced transect of sewage samples collected using a centralized, standardized protocol, ARG relative abundances (16S rRNA gene-normalized) were highest in Hong Kong and India and lowest in Sweden and Switzerland, reflecting national policy, measured antibiotic concentrations, and metal resistance genes. Asian versus European/US resistomes were distinct, with macrolide-lincosamide-streptogramin, phenicol, quinolone, and tetracycline versus multidrug resistance ARGs being discriminatory, respectively. Regional trends in measured antibiotic concentrations differed from trends expected from public sales data. This could reflect unaccounted uses, captured only by the WBS approach. If properly benchmarked, antibiotic WBS might complement public sales and consumption statistics in the future. The WBS approach defined herein demonstrates multisite comparability and sensitivity to local/regional factors.

RevDate: 2022-06-27

Muthappa DM, Lamba S, Sivasankaran SK, et al (2022)

16S rRNA Based Profiling of Bacterial Communities Colonizing Bakery-Production Environments.

Foodborne pathogens and disease [Epub ahead of print].

Conventional culture-based techniques are largely inadequate in elucidating the microbiota contained in an environment, due to low recovery within a complex bacterial community. This limitation has been mitigated by the use of next-generation sequencing (NGS)-based approaches thereby facilitating the identification and classification of both culturable and uncultivable microorganisms. Amplicon targeted NGS methods, such as 16S ribosomal RNA (16S rRNA) and shotgun metagenomics, are increasingly being applied in various settings such as in food production environments to decipher the microbial consortium therein. Even though multiple food matrices/food production environments have been studied, the low-moisture environment associated with bakery food production remains to be investigated. To address this knowledge gap, in this study, we investigated the microbiome associated with two bakery production sites (designated as A and B) located in Ireland using 16S rRNA-amplicon-based sequencing. Amplicons corresponding to a hypervariable region contained within the 16S rRNA gene were amplified from DNA samples purified from environmental swabs and ingredients collected at both sites at various stages (preparation, production, postproduction, and storage) across the bakery production chain, over three seasons (winter, spring, and summer). These amplicons were sequenced, and data were analyzed using the mothur pipeline and visualized using MicrobiomeAnalyst and a series of R packages. The top seven bacterial phyla identified at both sites were composed of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Patescibacteria, and Verrucomicrobia. In addition, the phyla Tenericutes (Mycoplasmatota) and Acidobacteria were observed only in samples taken at site B. Different bacterial compositions were identified at each stage of production. These same bacteria were also found to be present in the final processed food suggesting the influence of the environment on the food matrix. This study is the first demonstration of the utility of 16S rRNA amplicon-based sequencing to describe the microbiota associated with bakery processing environments.

RevDate: 2022-06-27

Tang T, Hou S, Fuhrman JA, et al (2022)

Phage-bacterial contig association prediction with a convolutional neural network.

Bioinformatics (Oxford, England), 38(Supplement_1):i45-i52.

MOTIVATION: Phage-host associations play important roles in microbial communities. But in natural communities, as opposed to culture-based lab studies where phages are discovered and characterized metagenomically, their hosts are generally not known. Several programs have been developed for predicting which phage infects which host based on various sequence similarity measures or machine learning approaches. These are often based on whole viral and host genomes, but in metagenomics-based studies, we rarely have whole genomes but rather must rely on contigs that are sometimes as short as hundreds of bp long. Therefore, we need programs that predict hosts of phage contigs on the basis of these short contigs. Although most existing programs can be applied to metagenomic datasets for these predictions, their accuracies are generally low. Here, we develop ContigNet, a convolutional neural network-based model capable of predicting phage-host matches based on relatively short contigs, and compare it to previously published VirHostMatcher (VHM) and WIsH.

RESULTS: On the validation set, ContigNet achieves 72-85% area under the receiver operating characteristic curve (AUROC) scores, compared to the maximum of 68% by VHM or WIsH for contigs of lengths between 200 bps to 50 kbps. We also apply the model to the Metagenomic Gut Virus (MGV) catalogue, a dataset containing a wide range of draft genomes from metagenomic samples and achieve 60-70% AUROC scores compared to that of VHM and WIsH of 52%. Surprisingly, ContigNet can also be used to predict plasmid-host contig associations with high accuracy, indicating a similar genetic exchange between mobile genetic elements and their hosts.

The source code of ContigNet and related datasets can be downloaded from https://github.com/tianqitang1/ContigNet.

RevDate: 2022-06-27

Liu S, D Koslicki (2022)

CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices.

Bioinformatics (Oxford, England), 38(Supplement_1):i28-i35.

MOTIVATION: K-mer-based methods are used ubiquitously in the field of computational biology. However, determining the optimal value of k for a specific application often remains heuristic. Simply reconstructing a new k-mer set with another k-mer size is computationally expensive, especially in metagenomic analysis where datasets are large. Here, we introduce a hashing-based technique that leverages a kind of bottom-m sketch as well as a k-mer ternary search tree (KTST) to obtain k-mer-based similarity estimates for a range of k values. By truncating k-mers stored in a pre-built KTST with a large k=kmax value, we can simultaneously obtain k-mer-based estimates for all k values up to kmax. This truncation approach circumvents the reconstruction of new k-mer sets when changing k values, making analysis more time and space-efficient.

RESULTS: We derived the theoretical expression of the bias factor due to truncation. And we showed that the biases are negligible in practice: when using a KTST to estimate the containment index between a RefSeq-based microbial reference database and simulated metagenome data for 10 values of k, the running time was close to 10× faster compared to a classic MinHash approach while using less than one-fifth the space to store the data structure.

A python implementation of this method, CMash, is available at https://github.com/dkoslicki/CMash. The reproduction of all experiments presented herein can be accessed via https://github.com/KoslickiLab/CMASH-reproducibles.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2022-06-27

Alanko JN, Slizovskiy IB, Lokshtanov D, et al (2022)

Syotti: scalable bait design for DNA enrichment.

Bioinformatics (Oxford, England), 38(Supplement_1):i177-i184.

MOTIVATION: Bait enrichment is a protocol that is becoming increasingly ubiquitous as it has been shown to successfully amplify regions of interest in metagenomic samples. In this method, a set of synthetic probes ('baits') are designed, manufactured and applied to fragmented metagenomic DNA. The probes bind to the fragmented DNA and any unbound DNA is rinsed away, leaving the bound fragments to be amplified for sequencing. Metsky et al. demonstrated that bait-enrichment is capable of detecting a large number of human viral pathogens within metagenomic samples.

RESULTS: We formalize the problem of designing baits by defining the Minimum Bait Cover problem, show that the problem is NP-hard even under very restrictive assumptions, and design an efficient heuristic that takes advantage of succinct data structures. We refer to our method as Syotti. The running time of Syotti shows linear scaling in practice, running at least an order of magnitude faster than state-of-the-art methods, including the method of Metsky et al. At the same time, our method produces bait sets that are smaller than the ones produced by the competing methods, while also leaving fewer positions uncovered. Lastly, we show that Syotti requires only 25 min to design baits for a dataset comprised of 3 billion nucleotides from 1000 related bacterial substrains, whereas the method of Metsky et al. shows clearly super-linear running time and fails to process even a subset of 17% of the data in 72 h.

https://github.com/jnalanko/syotti.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2022-06-27

Saito D, Lemos LN, Ferreira ATRN, et al (2022)

Draft Genome Sequences of Five Putatively Novel Saccharibacteria Species Assembled from the Human Oral Metagenome.

Microbiology resource announcements [Epub ahead of print].

We report the draft metagenome-assembled genomes (MAGs) of five putatively novel Saccharibacteria strains retrieved from the oral microbiome. MAGs were obtained from nonstimulated saliva samples from hosts with various clinical statuses and correspond to distinct species taxonomically placed within the Saccharimonadaceae family, as determined by genome-wide analysis against previously described TM7 genomes.

RevDate: 2022-06-27

Li Y, Cao L, Ye M, et al (2022)

Plasma Virome Reveals Blooms and Transmission of Anellovirus in Intravenous Drug Users with HIV-1, HCV, and/or HBV Infections.

Microbiology spectrum [Epub ahead of print].

Intravenous drug users (IDUs) are a high-risk group for HIV-1, hepatitis C virus (HCV), and hepatitis B virus (HBV) infections, which are the leading causes of death in IDUs. However, the plasma virome of IDUs and how it is influenced by above viral infections remain unclear. Using viral metagenomics, we determined the plasma virome of IDUs and its association with HIV-1, HCV, and/or HBV infections. Compared with healthy individuals, IDUs especially those with major viral infections had higher viral abundance and diversity. Anelloviridae dominated plasma virome. Coinfections of multiple anelloviruses were common, and anelloviruses from the same genus tended to coexist together. In this study, 4,487 anellovirus ORF1 sequences were identified, including 1,620 (36.1%) with less than 69% identity to any known sequences, which tripled the current number. Compared with healthy controls (HC), more anellovirus sequences were observed in neg-IDUs, and HIV-1, HCV, and/or HBV infections further expanded the sequence number in IDUs, which was characterized by the emergence of novel divergent taxons and blooms of resident anelloviruses. Pegivirus was mainly identified in infected IDUs. Five main pegivirus transmission clusters (TCs) were identified by phylogenetic analysis, suggesting a transmission link. Similar anellovirus profiles were observed in IDUs within the same TC, suggesting transmission of anellome among IDUs. Our data suggested that IDUs suffered higher plasma viral burden especially anelloviruses, which was associated with HIV-1, HCV, and/or HBV infections. Blooms in abundance and unprecedented diversity of anellovirus highlighted active evolution and replication of this virus in blood circulation, and an uncharacterized role it may engage with the host. IMPORTANCE Virome is associated with immune status and determines or influences disease progression through both pathogenic and resident viruses. Increased viral burden in IDUs especially those with major viral infections indicated the suboptimal immune status and high infection risks of these population. Blooms in abundance and unprecedented diversity of anellovirus highlighted its active evolution and replication in the blood circulation, and sensitive response to other viral infections. In addition, transmission cluster analysis revealed the transmission link of pegivirus among IDUs, and the individuals with transmission links shared similar anellome profiles. In-depth monitoring of the plasma virome in high-risk populations is not only needed for surveillance for emerging viruses and transmission networks of major and neglected bloodborne viruses, but also important for a better understanding of commensal viruses and their role it may engage with immune system.

RevDate: 2022-06-27

Chang HW, Yan D, Singh R, et al (2022)

Multiomic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host‒Microbe Associations.

JID innovations : skin science from molecules to population health, 2(3):100115 pii:S2667-0267(22)00023-6.

Psoriasis is a chronic, inflammatory skin disease that affects 2‒3% of the global population. Besides skin manifestations, patients with psoriasis have increased susceptibility to a number of comorbidities, including psoriatic arthritis, cardiovascular disease, and inflammatory bowel disease. To understand the systemic component of psoriasis pathogenesis, we performed a pilot study to examine the fecal metagenome, host colonic transcriptome, and host peripheral blood immune profiles of patients with psoriasis and healthy controls. Our study showed increased functional diversity in the gut microbiome of patients with psoriasis. In addition, we identified microbial species that preferentially associate with patients with psoriasis and which have been previously found to associate with other autoimmune diseases. Intriguingly, our data revealed three psoriasis subgroups that have distinct microbial and host features. Integrating these features revealed host‒microbe associations that are specific to psoriasis or particular psoriasis subgroups. Our findings provide insight into the factors that may affect the development of comorbidities in patients with psoriasis and may hold diagnostic potential for early identification of patients with psoriasis at risk for these comorbidities.

RevDate: 2022-06-27

Tran DM (2022)

Taxonomic and functional profiles of Coffea canephora endophytic microbiome in the Central Highlands region, Vietnam, revealed by analysis of 16S rRNA metagenomics sequence data.

Data in brief, 43:108372 pii:S2352-3409(22)00569-8.

Vietnam is the largest producer of Robusta coffee (Coffea canephora L.) [1]. Among regions in Vietnam, the Central Highlands is the capital of the coffee plantation and production [2]. Previous works have established a dataset of rhizospheric microbial diversity and its functionality to develop sustainable Robusta coffee production techniques in this region [3], [4], [5], [6]; however, a dataset of the endophytic microbiome of this plant species has been found is still unknown. The work presented here is the first report on the microbial and functional diversity of the endophytic microbiome of Coffea canephora L. grown in the region. A representative root sample was obtained by mixing five different root samples collected from a 6-year-old Robusta coffee field in Dak Lak Province, the Central Highlands, on 30 October 2021. After that, 16S rRNA metagenomic next-generation sequencing was conducted on the sample using the Illumina MiSeq platform. The raw sequence of endophytic microbiome data in this work was uploaded in Fastq format on NCBI with Bioproject PRJNA821717 and can be accessed at https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA821717. The dataset can be useful for understanding basic information about the prokaryotic ecology of this important plant in the Central Highlands, Vietnam. The data can also be valuable for developing cultivation techniques for sustainable Coffea canephora L. production by applying indigenous microbial resources.

RevDate: 2022-06-27

Wu X, Guo M, Shi S, et al (2022)

Efficacy and Safety of Shenqisuxin Granule for Non-ST-segment Elevation Acute Coronary Syndrome: Study Protocol for a Randomized, Double-Blinded, Placebo-Controlled Trial.

Frontiers in cardiovascular medicine, 9:888724.

Introduction: The Chinese herbal compound formula, Shenqisuxin granule (SQSX), promotes neovascularization and prevents in-stent restenosis in modern pharmaceutical studies and is expected to provide an effective strategy for non-ST-segment elevation acute coronary syndrome (NSTEACS). Thus, this study aims to examine the efficacy and safety of SQSX for NSTEACS and initially reveal its mechanism.

Methods/Design: The study is a randomized, double-blinded and placebo-controlled trial. A total of 66 participants will be randomly allocated to one of the following two groups. Participants in the SQSX group will receive conventional treatment plus SQSX, while the placebo group will receive conventional treatment plus placebo, both for 14 days. The primary outcome, hs-CRP, and secondary outcome the Seattle Angina Questionnaire (SAQ) will be assessed at baseline, 7 ± 3 days and 14 ± 3 days. At all visit windows, other indicators including creatine kinase (CK), creatine kinase-myocardial band (CK-MB), cardiac troponins I (cTnI), 12-lead electrocardiograph and the syndrome scores of Qi deficiency and blood stasis will be tested and metagenomic sequencing for intestinal flora will be performed. Echocardiography and safety assessment will be performed at baseline and 14 ± 3 days. Adverse events will be monitored during the trial.

Discussion: The purpose of the study is to examine the efficacy and safety of SQSX to improve NSTEACS and initially reveal its mechanism.

Trial Registration: China Clinical Trial Registry, ChiCTR2000029226. Registered on January 19, 2020.

RevDate: 2022-06-27

Chavan S, Sarangdhar V, N Vigneshwaran (2022)

Nanopore-based metagenomic analysis of the impact of nanoparticles on soil microbial communities.

Heliyon, 8(6):e09693 pii:S2405-8440(22)00981-1.

The current trend of using nanotechnology products in all spheres of human life, including for crop improvement may have a possible impact on soil microorganisms which influence soil and plant health. Nanopore-based metagenomic study reported here used full-length 16S rRNA gene sequences to assess shifts in community composition of soil microorganisms when treated with silver, titanium dioxide and zinc oxide nanoparticles (S-NP, T-NP, Z-NP, respectively). Firmicutes and Proteobacteria were the two dominant phyla in this soil, and there were no significant differences (p < 0.05) observed in these phyla across treatments. However, in the phylum Firmicutes, the abundance of the order Clostridiales showed a significant decrease (p < 0.05) in the presence of S-NP. Similarly, in the phylum Proteobacteria, a significant decrease in the presence of S-NP was seen for two orders, Vibrionales (p < 0.05) and Rhodobacterales (p < 0.01). Analysis at a further depth revealed that abundance of the genus Clostridium (order Clostridiales) decreased in the presence of both S-NP (p < 0.01) and T-NP (p < 0.05). The abundance of the genus Vibrio (order Vibrionales) was likewise impacted in the presence of all the three NPs - S-NP (p < 0.01), T-NP (p < 0.05) and Z-NP (p < 0.05). Analyses at high taxon ranks such as phyla may not give a good representation of the nature of microbial community shifts, and at times may paint an erroneous picture. The use of full-length 16S rRNA gene sequences here yielded a greater taxonomic depth, and some shifts at the lower ranks were discernible.

RevDate: 2022-06-27

Vernocchi P, Ristori MV, Guerrera S, et al (2022)

Gut Microbiota Ecology and Inferred Functions in Children With ASD Compared to Neurotypical Subjects.

Frontiers in microbiology, 13:871086.

Autism spectrum disorders (ASDs) is a multifactorial neurodevelopmental disorder. The communication between the gastrointestinal (GI) tract and the central nervous system seems driven by gut microbiota (GM). Herein, we provide GM profiling, considering GI functional symptoms, neurological impairment, and dietary habits. Forty-one and 35 fecal samples collected from ASD and neurotypical children (CTRLs), respectively, (age range, 3-15 years) were analyzed by 16S targeted-metagenomics (the V3-V4 region) and inflammation and permeability markers (i.e., sIgA, zonulin lysozyme), and then correlated with subjects' metadata. Our ASD cohort was characterized as follows: 30/41 (73%) with GI functional symptoms; 24/41 (58%) picky eaters (PEs), with one or more dietary needs, including 10/41 (24%) with food selectivity (FS); 36/41 (88%) presenting high and medium autism severity symptoms (HMASSs). Among the cohort with GI symptoms, 28/30 (93%) showed HMASSs, 17/30 (57%) were picky eaters and only 8/30 (27%) with food selectivity. The remaining 11/41 (27%) ASDs without GI symptoms that were characterized by HMASS for 8/11 (72%) and 7/11 (63%) were picky eaters. GM ecology was investigated for the overall ASD cohort versus CTRLs; ASDs with GI and without GI, respectively, versus CTRLs; ASD with GI versus ASD without GI; ASDs with HMASS versus low ASSs; PEs versus no-PEs; and FS versus absence of FS. In particular, the GM of ASDs, compared to CTRLs, was characterized by the increase of Proteobacteria, Bacteroidetes, Rikenellaceae, Pasteurellaceae, Klebsiella, Bacteroides, Roseburia, Lactobacillus, Prevotella, Sutterella, Staphylococcus, and Haemophilus. Moreover, Sutterella, Roseburia and Fusobacterium were associated to ASD with GI symptoms compared to CTRLs. Interestingly, ASD with GI symptoms showed higher value of zonulin and lower levels of lysozyme, which were also characterized by differentially expressed predicted functional pathways. Multiple machine learning models classified correctly 80% overall ASDs, compared with CTRLs, based on Bacteroides, Lactobacillus, Prevotella, Staphylococcus, Sutterella, and Haemophilus features. In conclusion, in our patient cohort, regardless of the evaluation of many factors potentially modulating the GM profile, the major phenotypic determinant affecting the GM was represented by GI hallmarks and patients' age.

RevDate: 2022-06-27

Haryono MAS, Law YY, Arumugam K, et al (2022)

Recovery of High Quality Metagenome-Assembled Genomes From Full-Scale Activated Sludge Microbial Communities in a Tropical Climate Using Longitudinal Metagenome Sampling.

Frontiers in microbiology, 13:869135.

The analysis of metagenome data based on the recovery of draft genomes (so called metagenome-assembled genomes, or MAG) has assumed an increasingly central role in microbiome research in recent years. Microbial communities underpinning the operation of wastewater treatment plants are particularly challenging targets for MAG analysis due to their high ecological complexity, and remain important, albeit understudied, microbial communities that play ssa key role in mediating interactions between human and natural ecosystems. Here we consider strategies for recovery of MAG sequence from time series metagenome surveys of full-scale activated sludge microbial communities. We generate MAG catalogs from this set of data using several different strategies, including the use of multiple individual sample assemblies, two variations on multi-sample co-assembly and a recently published MAG recovery workflow using deep learning. We obtain a total of just under 9,100 draft genomes, which collapse to around 3,100 non-redundant genomic clusters. We examine the strengths and weaknesses of these approaches in relation to MAG yield and quality, showing that co-assembly may offer advantages over single-sample assembly in the case of metagenome data obtained from closely sampled longitudinal study designs. Around 1,000 MAGs were candidates for being considered high quality, based on single-copy marker gene occurrence statistics, however only 58 MAG formally meet the MIMAG criteria for being high quality draft genomes. These findings carry broader broader implications for performing genome-resolved metagenomics on highly complex communities, the design and implementation of genome recoverability strategies, MAG decontamination and the search for better binning methodology.

RevDate: 2022-06-27

Chen S, Yu M, Zhang W, et al (2022)

Metagenomic and Microscopic Analysis of Magnetotactic Bacteria in Tangyin Hydrothermal Field of Okinawa Trough.

Frontiers in microbiology, 13:887136.

Magnetotactic bacteria (MTB) have been found in a wide variety of marine habitats, ranging from intertidal sediments to deep-sea seamounts. Deep-sea hydrothermal fields are rich in metal sulfides, which are suitable areas for the growth of MTB. However, MTB in hydrothermal fields have never been reported. Here, the presence of MTB in sediments from the Tangyin hydrothermal field was analyzed by 16S rRNA gene amplicon analysis, metagenomics, and transmission electron microscopy. Sequencing 16S rRNA gene yielded a total of 709 MTB sequences belonging to 20 OTUs, affiliated with Desulfobacterota, Alphaproteobacteria, and Nitrospirae. Three shapes of magnetofossil were identified by transmission electron microscopy: elongated-prismatic, bullet-shaped, and cuboctahedron. All of these structures were composed of Fe3O4. A total of 121 sequences were found to be homologous to the published MTB magnetosome-function-related genes, and relevant domains were identified. Further analysis revealed that diverse MTB are present in the Tangyin hydrothermal field, and that multicellular magnetotactic prokaryote (MMPs) might be the dominant MTB.

RevDate: 2022-06-27

Rchiad Z, Dai M, Hamel C, et al (2022)

Soil Depth Significantly Shifted Microbial Community Structures and Functions in a Semiarid Prairie Agroecosystem.

Frontiers in microbiology, 13:815890.

The North American Great Plains cover a large area of the Nearctic ecozone, and an important part of this biome is semiarid. The sustainable intensification of agriculture that is necessary to produce food for an ever-increasing world population requires knowledge of the taxonomic and functional structure of the soil microbial community. In this study, we investigated the influence of soil depth on the composition and functions of the microbial communities hosted in agricultural soils of a semiarid agroecosystem, using metagenomic profiling, and compared them to changes in soil chemical and physical properties. Shotgun sequencing was used to determine the composition and functions of the soil microbial community of 45 soil samples from three soil depths (0-15 cm, 15-30 cm, and 30-60 cm) under different agricultural land use types (native prairie, seeded prairie, and cropland) in southwest Saskatchewan. Analysis of community composition revealed the declining abundance of phyla Verrucomicrobia, Bacteroidetes, Chlorophyta, Bacillariophyta, and Acidobacteria with soil depth, whereas the abundance of phyla Ascomycota, Nitrospirae, Planctomycetes, and Cyanobacteria increased with soil depth. Soil functional genes related to nucleosides and nucleotides, phosphorus (P) metabolism, cell division and cell cycle, amino acids and derivatives, membrane transport, and fatty acids were particularly abundant at 30-60 cm. In contrast, functional genes related to DNA and RNA metabolism, metabolism of nitrogen, sulfur and carbohydrates, and stress response were more abundant in the top soil depth. The RDA analysis of functional genes and soil physico-chemical properties revealed a positive correlation between phages and soil organic P concentrations. In the rooting zone of this semiarid agroecosystem, soil microbes express variable structural patterns of taxonomic and functional diversity at different soil depths. This study shows that the soil microbial community is structured by soil depth and physicochemical properties, with the middle soil depth being an intermediate transition zone with a higher taxonomic diversity. Our results suggest the co-existence of various microbial phyla adapted to upper and lower soil depths in an intermediate-depth transition zone.

RevDate: 2022-06-27

Garrison CE, Roozbehi S, Mitra S, et al (2022)

Coastal Microbial Communities Disrupted During the 2018 Hurricane Season in Outer Banks, North Carolina.

Frontiers in microbiology, 13:816573.

Hurricane frequencies and intensities are expected to increase under warming climate scenarios, increasing potential to disrupt microbial communities from steady-state conditions and alter ecosystem function. This study shows the impact of hurricane season on microbial community dynamics within the barrier island system of Outer Banks, North Carolina. We found that the passage of two sequential energetic hurricanes in 2018 (Florence and Michael) were correlated with shifts in total and active (DNA and RNA) portions of bacterial communities but not in archaeal communities, and within surface waters but not within the sediment. These microbial community shifts were distinct from non-hurricane season conditions, suggesting significant implications for nutrient cycling in nearshore and offshore environments. Hurricane-influenced marine sites in the coastal North Atlantic region had lower microbial community evenness and Shannon diversity, in addition to increased relative abundance of copiotrophic microbes compared to non-hurricane conditions. The abundance of functional genes associated with carbon and nitrogen cycling pathways were also correlated with the storm season, potentially shifting microbial communities at offshore sites from autotroph-dominated to heterotroph-dominated and leading to impacts on local carbon budgets. Understanding the geographic- and system-dependent responses of coastal microbial communities to extreme storm disturbances is critical for predicting impacts to nutrient cycling and ecosystem stability in current and future climate scenarios.

RevDate: 2022-06-27

Lu M, Schneider D, R Daniel (2022)

Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern.

Frontiers in microbiology, 13:851969.

Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integrated classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.

RevDate: 2022-06-27

Shah D, Brown JR, Lee JCD, et al (2022)

Use of a sample-to-result shotgun metagenomics platform for the detection and quantification of viral pathogens in paediatric immunocompromised patients.

Journal of clinical virology plus, 2(2):None.

Background: Infections by several DNA viruses can severely impact outcomes in paediatric immunocompromised patients. Current testing, which is generally limited to singleplex qPCR assays, can miss both common and rarer viruses if they are not targeted.

Objectives: To evaluate the performance of the Galileo Viral Panel (Galileo), a sample-to-result shotgun metagenomics platform for the detection and quantification of 12 DNA viruses, compared to standard of care qPCR assays.

Study design: A clinical performance evaluation was carried out using 43 prospectively collected EDTA plasma samples positive for one or more DNA viruses. Agreement between assays was assessed by overall, positive, and negative percent agreement, as well as quantitative agreement by linear regression and Bland-Altman analysis.

Results: Overall positive percent agreement was 84% (95% CI: 76%-90%), and negative percent agreement was 95% (95% CI: 92%-97%). There was a high correlation between Galileo and qPCR for ADV, CMV, EBV, and VZV (R2 = 0.91) and a mean difference by Bland Altman of -0.43 log10 IU or cp/ml (95% limits of agreement, -1.37 to 0.51). In addition, there was a high correlation between Galileo Signal Score and qPCR for TTV (R2 = 0.85).

Conclusion: We observed high qualitative and quantitative agreement between qPCR and Galileo. Galileo identified additional viruses that were not tested with routine qPCR and could impact clinical outcomes.

RevDate: 2022-06-27

Su J, Han X, Xu X, et al (2022)

Simultaneous Detection of Pathogens and Tumors in Patients With Suspected Infections by Next-Generation Sequencing.

Frontiers in cellular and infection microbiology, 12:892087.

Background: Differential diagnosis of patients with suspected infections is particularly difficult, but necessary for prompt diagnosis and rational use of antibiotics. A substantial proportion of these patients have non-infectious diseases that include malignant tumors. This study aimed to explore the clinical value of metagenomic next-generation sequencing (mNGS) for tumor detection in patients with suspected infections.

Methods: A multicenter, prospective case study involving patients diagnosed with suspected infections was conducted in four hospitals in Shanghai, China between July 2019 and January 2020. Based upon mNGS technologies and chromosomal copy number variation (CNV) analysis on abundant human genome, a new procedure named Onco-mNGS was established to simultaneously detect pathogens and malignant tumors in all of the collected samples from patients.

Results: Of 140 patients screened by Onco-mNGS testing, 115 patients were diagnosed with infections; 17 had obvious abnormal CNV signals indicating malignant tumors that were confirmed clinically. The positive percent agreement and negative percent agreement of mNGS testing compared to clinical diagnosis was 53.0% (61/115) and 60% (15/25), vs. 20.9% (24/115) and 96.0% (24/25), respectively, for conventional microbiological testing (both P <0.01). Klebsiella pneumoniae (14.8%, 9/61) was the most common pathogen detected by mNGS, followed by Escherichia coli (11.5%, 7/61) and viruses (11.5%, 7/61). The chromosomal abnormalities of the 17 cases included genome-wide variations and local variations of a certain chromosome. Five of 17 patients had a final confirmed with malignant tumors, including three lung adenocarcinomas and two hematological tumors; one patient was highly suspected to have lymphoma; and 11 patients had a prior history of malignant tumor.

Conclusion: This preliminary study demonstrates the feasibility and clinical value of using Onco-mNGS to simultaneously search for potential pathogens and malignant tumors in patients with suspected infections.

RevDate: 2022-06-27

Tan J, Liu Y, Ehnert S, et al (2022)

The Effectiveness of Metagenomic Next-Generation Sequencing in the Diagnosis of Prosthetic Joint Infection: A Systematic Review and Meta-Analysis.

Frontiers in cellular and infection microbiology, 12:875822.

Background: A prosthetic joint infection (PJI) is a devastating complication following total joint arthroplasties with poor prognosis. Identifying an accurate and prompt diagnostic method is particularly important for PJI. Recently, the diagnostic value of metagenomic next-generation sequencing (mNGS) in detecting PJI has attracted much attention, while the evidence of its accuracy is quite limited. Thus, this study aimed to evaluate the accuracy of mNGS for the diagnosis of PJI.

Methods: We summarized published studies to identify the potential diagnostic value of mNGS for PJI patients by searching online databases using keywords such as "prosthetic joint infection", "PJI", and "metagenomic sequencing". Ten of 380 studies with 955 patients in total were included. The included studies provided sufficient data for the completion of 2-by-2 tables. We calculated the sensitivity, specificity, and area under the SROC curve (AUC) to evaluate mNGS for PJI diagnosis.

Results: We found that the pooled diagnostic sensitivity and specificity of mNGS for PJI were 0.93 (95% CI, 0.83 to 0.97) and 0.95 (95% CI, 0.92 to 0.97), respectively. Positive and negative likelihood ratios were 18.3 (95% CI, 10.9 to 30.6) and 0.07 (95% CI, 0.03 to 0.18), respectively. The area under the curve was 0.96 (95% CI, 0.93 to 0.97).

Conclusion: Metagenomic next-generation sequencing displays high accuracy in the diagnosis of PJI, especially for culture-negative cases.

RevDate: 2022-06-27

Sun Q, Li Z, Wang P, et al (2022)

Unveiling the Pathogenic Bacteria Causing Descending Necrotizing Mediastinitis.

Frontiers in cellular and infection microbiology, 12:873161.

The combination of maxillofacial infections (MI) with descending necrotizing mediastinitis (DNM) is a complex disease characterized by rapid development and high mortality. Here, we performed metagenomic next-generation sequencing (mNGS) using samples from 21 patients with MI and eight patients with DNM. In this study, we found that the species richness of the DNM group was higher than that of the MI group, and the species diversity of the DNM group was higher than that of the MI group, with no statistically significant differences between groups (P > 0.05). LefSE analysis revealed that the main species differing between groups were Bacillus, Lactobacillus, Streptococcaceae, and Streptococcus (S. constellatus and S. anginosus). In addition, the PLS-DA analysis revealed that the dominant groups in the DNM group at the species level were S. constellatus, S. anginosus, Streptococcus intermedius, Prevotella oris, Mogibacterium timidum, and Eubacterium nodatum. Next, we correlated the clinical characteristics of the patients with the relative abundance of the pathogens identified in the LefSe and PLS-DA analyses. The relative abundance of S. anginosus was positively correlated with C-reactive protein (CRP) and calcitoninogen (PCT) but negatively correlated with the percentage of lymphocytes (Lymph%) (P < 0.05). On the other hand, M. timidum was positively correlated with the percentage of neutrophils (Neut%) and glycated hemoglobin (GLU) (P < 0.05), and Parvimonas micra was positively correlated with CRP (P < 0.05).

RevDate: 2022-06-27

Proffitt C, Bidkhori G, Lee S, et al (2022)

Genome-scale metabolic modelling of the human gut microbiome reveals changes in the glyoxylate and dicarboxylate metabolism in metabolic disorders.

iScience, 25(7):104513 pii:S2589-0042(22)00784-2.

The human gut microbiome has been associated with metabolic disorders including obesity, type 2 diabetes, and atherosclerosis. Understanding the contribution of microbiome metabolic changes is important for elucidating the role of gut bacteria in regulating metabolism. We used available metagenomics data from these metabolic disorders, together with genome-scale metabolic modeling of key bacteria in the individual and community-level to investigate the mechanistic role of the gut microbiome in metabolic diseases. Modeling predicted increased levels of glutamate consumption along with the production of ammonia, arginine, and proline in gut bacteria common across the disorders. Abundance profiles and network-dependent analysis identified the enrichment of tartrate dehydrogenase in the disorders. Moreover, independent plasma metabolite levels showed associations between metabolites including proline and tyrosine and an increased tartrate metabolism in healthy obese individuals. We, therefore, propose that an increased tartrate metabolism could be a significant mediator of the microbiome metabolic changes in metabolic disorders.

RevDate: 2022-06-26

Privitera GF, Alaimo S, Ferro A, et al (2022)

Virus finding tools: current solutions and limitations.

Briefings in bioinformatics pii:6618234 [Epub ahead of print].

MOTIVATION: The study of the Human Virome remains challenging nowadays. Viral metagenomics, through high-throughput sequencing data, is the best choice for virus discovery. The metagenomics approach is culture-independent and sequence-independent, helping search for either known or novel viruses. Though it is estimated that more than 40% of the viruses found in metagenomics analysis are not recognizable, we decided to analyze several tools to identify and discover viruses in RNA-seq samples.

RESULTS: We have analyzed eight Virus Tools for the identification of viruses in RNA-seq data. These tools were compared using a synthetic dataset of 30 viruses and a real one. Our analysis shows that no tool succeeds in recognizing all the viruses in the datasets. So we can conclude that each of these tools has pros and cons, and their choice depends on the application domain.

AVAILABILITY: Synthetic data used through the review and raw results of their analysis can be found at https://zenodo.org/record/6426147. FASTQ files of real data can be found in GEO (https://www.ncbi.nlm.nih.gov/gds) or ENA (https://www.ebi.ac.uk/ena/browser/home). Raw results of their analysis can be downloaded from https://zenodo.org/record/6425917.

RevDate: 2022-06-27
CmpDate: 2022-06-27

Javaid N, Olwagen C, Nzenze S, et al (2022)

Population genomics of pneumococcal carriage in South Africa following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) immunization.

Microbial genomics, 8(6):.

Streptococcus pneumoniae is a major human pathogen responsible for over 317000 deaths in children <5 years of age with the burden of the disease being highest in low- and middle-income countries including South Africa. Following the introduction of the 7-valent and 13-valent pneumococcal conjugate vaccine (PCV) in South Africa in 2009 and 2011, respectively, a decrease in both invasive pneumococcal infections and asymptomatic carriage of vaccine-type pneumococci were reported. In this study, we described the changing epidemiology of the pneumococcal carriage population in South Africa, by sequencing the genomes of 1825 isolates collected between 2009 and 2013. Using these genomic data, we reported the changes in serotypes, Global Pneumococcal Sequence Clusters (GPSCs), and antibiotic resistance before and after the introduction of PCV13. The pneumococcal carriage population in South Africa has a high level of diversity, comprising of 126 GPSCs and 49 serotypes. Of the ten most prevalent GPSCs detected, six were predominantly found in Africa (GPSC22, GPSC21, GPSC17, GPSC33, GPSC34 and GPSC52). We found a significant decrease in PCV7 serotypes (19F, 6B, 23F and 14) and an increase in non-vaccine serotypes (NVT) (16F, 34, 35B and 11A) among children <2 years of age. The increase in NVTs was driven by pneumococcal lineages GPSC33, GPSC34, GPSC5 and GPSC22. Overall, a decrease in antibiotic resistance for 11 antimicrobials was detected in the PCV13 era. Further, we reported a higher resistance prevalence among vaccine types (VTs), as compared to NVTs; however, an increase in penicillin resistance among NVT was observed between the PCV7 and PCV13 eras. The carriage isolates from South Africa predominantly belonged to pneumococcal lineages, which are endemic to Africa. While the introduction of PCV resulted in an overall reduction of resistance in pneumococcal carriage isolates, an increase in penicillin resistance among NVTs was detected in children aged between 3 and 5 years, driven by the expansion of penicillin-resistant clones associated with NVTs in the PCV13 era.

RevDate: 2022-06-25

Jangid A, Fukuda S, Seki M, et al (2022)

Gut microbiota alternation under the intestinal epithelium-specific knockout of mouse Piga gene.

Scientific reports, 12(1):10812.

Crosstalk between the gut microbiota and intestinal epithelium shapes the gut environment and profoundly influences the intestinal immune homeostasis. Glycosylphosphatidylinositol anchored proteins (GPI - APs) contribute to a variety of gut-associated immune functions, including microbial surveillance and defense, and epithelial cell polarity. Properly polarised epithelial cells are essential for the establishment of the barrier function of gut epithelia. The Piga gene is one among seven genes that encode for an enzyme which is involved in the first step of GPI-anchor biosynthesis. This is the first study reporting a knockout of the intestinal epithelial cell-specific Piga gene (Piga-/-) and its association with the gut microbiota in mice using a whole metagenome shotgun-based sequencing approach. An overall reduced microbiota diversity has been observed in the Piga-/- group as compared to the control group (ANOVA p = 0.34). The taxonomic biomarkers, namely: Gammaproteobacteria (class), Enterobacterales (order), Enterobacteriaceae (family), Escherichia (genus), Proteus (genus) and Escherichia coli (species), increased more in the Piga-/- mice as compared to in the control group. Further, the pathogenic E. coli strains, namely E. coli O157:H7 str. EDL 933 (EHEC), E. coli CFT073 (UPEC) and E. coli 536 (UPEC), were found in the Piga-/- mice which also harbored virulence factor transporters. In addition, the taxa responsible for short chain fatty acid production were decreased in the Piga-/- group. The Piga-/- mice gut harbored an increased number of microbial functions responsible for the survival of pathogens in the inflamed gut environment. Our observations clearly indicate that the Piga-/- mice gut might have an overall enhancement in pathogenic behaviour and reduced capabilities beneficial to health.

RevDate: 2022-06-25

Lemos LN, de Carvalho FM, Santos FF, et al (2022)

Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans.

Scientific data, 9(1):366.

The One Health concept is a global strategy to study the relationship between human and animal health and the transfer of pathogenic and non-pathogenic species between these systems. However, to the best of our knowledge, no data based on One Health genome-centric metagenomics are available in public repositories. Here, we present a dataset based on a pilot-study of 2,915 metagenome-assembled genomes (MAGs) of 107 samples from the human (N = 34), cattle (N = 28), swine (N = 15) and poultry (N = 30) gut microbiomes. Samples were collected from the five Brazilian geographical regions. Of the draft genomes, 1,273 were high-quality drafts (≥90% of completeness and ≤5% of contamination), and 1,642 were medium-quality drafts (≥50% of completeness and ≤10% of contamination). Taxonomic predictions were based on the alignment and concatenation of single-marker genes, and the most representative phyla were Bacteroidota, Firmicutes, and Proteobacteria. Many of these species represent potential pathogens that have already been described or potential new families, genera, and species with potential biotechnological applications. Analyses of this dataset will highlight discoveries about the ecology and functional role of pathogens and uncultivated Archaea and Bacteria from food-producing animals and humans. Furthermore, it also represents an opportunity to describe new species from underrepresented taxonomic groups.

RevDate: 2022-06-25

Lee SA, Kim M, Esterhuizen M, et al (2022)

An acceleration of carotenoid production and growth of Haematococcus lacustris induced by host-microbiota network interaction.

Microbiological research, 262:127097 pii:S0944-5013(22)00137-9 [Epub ahead of print].

Haematococcus lacustris is a chlamydomonadalean with high biotechnological interest owing to its capacity to produce astaxanthin, a valuable secondary carotenoid with extraordinary antioxidation properties. However, its prolonged growth has limited its utility commercially. Thus, rapid growth to attain high densities of H. lacustris cells optimally producing astaxanthin is an essential biotechnological target to facilitate profitable commercialisation. Our study focused on characterising the bacterial communities associated with the alga's phycosphere by metagenomics. Subsequently, we altered the bacterial consortia in combined co-culture with key beneficial bacteria to optimise the growth of H. lacustris. The algal biomass increased by up to 2.1-fold in co-cultures, leading to a 1.6-fold increase in the astaxanthin yield. This study attempted to significantly improve the H. lacustris growth rate and biomass yield via Next-Generation Sequencing analysis and phycosphere bacterial augmentation, highlighting the possibility to overcome the hurdles associated with astaxanthin production by H. lacustris at a commercial scale.

RevDate: 2022-06-25

Su H, Hu X, Xu W, et al (2022)

Metagenomic analysis of the abundances, diversity, and distribution of antibiotic resistance genes and their potential bacterial hosts in two types of shrimp-rearing farms in South China.

Ecotoxicology and environmental safety, 241:113801 pii:S0147-6513(22)00641-8 [Epub ahead of print].

Antibiotic resistance genes (ARGs) are attracting increasing concern worldwide. Many previous studies have investigated the occurrence and concentrations of ARGs in aquaculture. However, the sources of ARGs and the links with their potential bacterial hosts have not yet been explored. This study investigated the abundances and diversity of ARGs in two types of shrimp farms in South China through metagenomic sequencing. In total, 14 ARG types were detected. Tetracycline was the dominant ARG type. The abundances of ARGs in samples decreased in the order of duck feces > water source > sediment > shrimp gut > pond water. The samples from the duck-shrimp integrated farm contained 1.29-3.81-fold more abundant ARGs than those from the shrimp monoculture farm (p < 0.05). Several ARGs, that were most predominant in the duck feces samples, were also the most predominant in the shrimp gut samples from the duck-shrimp integrated farm. Redundancy analysis indicated that the abundances and distribution of ARGs formed three clusters: duck feces, water samples, and sediment and shrimp gut samples. The dominant genera in duck feces known as human pathogenic bacteria were potential hosts of ARGs, and were also dominant in the shrimp gut samples in the duck-shrimp integrated farm. Additionally, the abundances of dominant genera in the shrimp gut samples of the duck-shrimp integrated farm were 1.74-35.07-fold higher than those in the shrimp monoculture farm (p < 0.01). The duck-shrimp integrated farm had 3.36-fold and 4.94-fold higher abundances of ARGs and mobile genetic elements in the shrimp gut samples than those from the shrimp monoculture farm, respectively (p < 0.05). The results indicate that duck feces may be a crucial source of diverse and abundant ARGs spreading to reared shrimps in duck-shrimp integrated farms, posing a severe risk to public health.

RevDate: 2022-06-24

Fritsch DA, Jackson MI, Wernimont SM, et al (2022)

Microbiome function underpins the efficacy of a fiber-supplemented dietary intervention in dogs with chronic large bowel diarrhea.

BMC veterinary research, 18(1):245.

BACKGROUND: Chronic large bowel diarrhea is a common occurrence in pet dogs. While nutritional intervention is considered the primary therapy, the metabolic and gut microfloral effects of fiber and polyphenol-enriched therapeutic foods are poorly understood.

METHODS: This prospective clinical study enrolled 31 adult dogs from private veterinary practices with chronic, active large bowel diarrhea. Enrolled dogs received a complete and balanced dry therapeutic food containing a proprietary fiber bundle for 56 days. Metagenomic and metabolomic profiling were performed on fecal samples at Days 1, 2, 3, 14, 28, and 56; metabolomic analysis was conducted on serum samples taken at Days 1, 2, 3, 28, and 56.

RESULTS: The dietary intervention improved clinical signs and had a clear effect on the gut microfloral metabolic output of canines with chronic diarrhea, shifting gut metabolism from a predominantly proteolytic to saccharolytic fermentative state. Microbial metabolism of tryptophan to beneficial indole postbiotics and the conversion of plant-derived phenolics into bioavailable postbiotics were observed. The intervention altered the endocannabinoid, polyunsaturated fatty acid, and sphingolipid profiles, suggesting a modulation in gastrointestinal inflammation. Changes in membrane phospholipid and collagen signatures were indicative of improved gut function and possible alleviation of the pathophysiology related to chronic diarrhea.

CONCLUSIONS: In dogs with chronic diarrhea, feeding specific dietary fibers increased gut saccharolysis and bioavailable phenolic and indole-related compounds, while suppressing putrefaction. These changes were associated with improved markers of gut inflammation and stool quality.

RevDate: 2022-06-24

Xiong X, Rao Y, Tu X, et al (2022)

Gut archaea associated with bacteria colonization and succession during piglet weaning transitions.

BMC veterinary research, 18(1):243.

BACKGROUND: Host-associated gut microbial communities are key players in shaping the fitness and health of animals. However, most current studies have focused on the gut bacteria, neglecting important gut fungal and archaeal components of these communities. Here, we investigated the gut fungi and archaea community composition in Large White piglets using shotgun metagenomic sequencing, and systematically evaluated how community composition association with gut microbiome, functional capacity, and serum metabolites varied across three weaning periods.

RESULTS: We found that Mucoromycota, Ascomycota and Basidiomycota were the most common fungi phyla and Euryarchaeota was the most common archaea phyla across individuals. We identified that Methanosarcina siciliae was the most significantly different archaea species among three weaning periods, while Parasitella parasitica, the only differential fungi species, was significantly and positively correlated with Methanosarcina siciliae enriched in day 28 group. The random forest analysis also identified Methanosarcina siciliae and Parasitella parasitica as weaning-biased archaea and fungi at the species level. Additionally, Methanosarcina siciliae was significantly correlated with P. copri and the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, characteristic successional alterations in gut archaea, fungi, bacteria, and serum metabolites with each weaning step revealed a weaning transition coexpression network, e.g., Methanosarcina siciliae and P. copri were positively and significantly correlated with 15-HEPE, 8-O-Methyloblongine, and Troxilin B3.

CONCLUSION: Our findings provide a deep insight into the interactions among gut archaea, fungi, bacteria, and serum metabolites and will present a theoretical framework for understanding gut bacterial colonization and succession association with archaea during piglet weaning transitions.

RevDate: 2022-06-24

Maeda Y, Motooka D, Kawasaki T, et al (2022)

Longitudinal alterations of the gut mycobiota and microbiota on COVID-19 severity.

BMC infectious diseases, 22(1):572.

BACKGROUND: The impact of SARS-CoV-2 infection on the gut fungal (mycobiota) and bacterial (microbiota) communities has been elucidated individually. This study analyzed both gut mycobiota and microbiota and their correlation in the COVID-19 patients with severe and mild conditions and follow-up to monitor their alterations after recovery.

METHODS: We analyzed the gut mycobiota and microbiota by bacterial 16S and fungal ITS1 metagenomic sequencing of 40 severe patients, 38 mild patients, and 30 healthy individuals and reanalyzed those of 10 patients with severe COVID-19 approximately 6 months after discharge.

RESULTS: The mycobiota of the severe and mild groups showed lower diversity than the healthy group, and in some, characteristic patterns dominated by a single fungal species, Candida albicans, were detected. Lower microbial diversity in the severe group was observed, but no differences in its diversity or community structure were detected between the mild and healthy groups. The microbiota of the severe group was characterized by an increase in Enterococcus and Lactobacillus, and a decrease in Faecalibacterium and Bacteroides. The abundance of Candida was positively correlated with that of Enterococcus in patients with COVID-19. After the recovery of severe patients, alteration of the microbiota remained, but the mycobiota recovered its diversity comparable to that of mild and healthy groups.

CONCLUSION: In mild cases, the microbiota is stable during SARS-CoV-2 infection, but in severe cases, alterations persist for 6 months after recovery.

RevDate: 2022-06-24

Li J, Zhao Q, Huang JP, et al (2022)

The functional microbiota of on- and off-year moso bamboo (Phyllostachys edulis) influences the development of the bamboo pest Pantana phyllostachysae.

BMC plant biology, 22(1):307.

BACKGROUND: Development of Pantana phyllostachysae, a moso bamboo pest, is affected by its diet. Understanding the mechanism underlying the different insect-resistant capacities of on- and off-year moso bamboo fed by P. phyllostachysae is crucial for managing pest outbreaks. As microbes were proven to influence plant immunity, we compared gut microbial communities of P. phyllostachysae with different diets by metabarcoding sequencing. By using sterilization assay, microbes were removed from leaf surfaces, and thus we confirmed that microbes inhabiting moso bamboo leaves impact the weight of P. phyllostachysae larva. Furthermore, the gut microbial communities of P. phyllostachysae fed on on- and off-year bamboo leaves were compared, to identify the functional microbial communities that impact the interaction between bamboo leaves and P. phyllostachysae.

RESULTS: We found that species from orders Lactobacillales and Rickettsiales are most effective within functional microbiota. Functional prediction revealed that gut microbes of larva fed on on-year leaves were related to naphthalene degradation, while those fed on off-year leaves were related to biosynthesis of ansamycins, polyketide sugar unit biosynthesis, metabolism of xenobiotics, and tetracycline biosynthesis. Most functional microbes are beneficial to the development of larva that feed on on-year bamboo leaves, but damage the balance of intestinal microenvironment and immune systems of those larva that feed on off-year leaves.

CONCLUSIONS: This work developed an efficient strategy for microbiome research of Lepidopteran insects and provided insights into microbiota related to the interaction between host plants and P. phyllostachysae. We provided microbial candidates for the ecological control of P. phyllostachysae according to the function of effective microbiota.

RevDate: 2022-06-24

Rout AK, Dehury B, Parida PK, et al (2022)

Taxonomic profiling and functional gene annotation of microbial communities in sediment of river Ganga at Kanpur, India: insights from whole-genome metagenomics study.

Environmental science and pollution research international [Epub ahead of print].

The perennial river Ganga is recognized as one of India's largest rivers of India, but due to continuous anthropogenic activities, the river's ecosystem is under threat. Next-generation sequencing technology has transformed metagenomics in the exploration of microbiome and their imperative function in diverse aquatic ecosystems. In this study, we have uncovered the structure of community microbiome and their functions in sediments of river Ganga at Kanpur, India, at three polluted stretches through a high-resolution metagenomics approach using Illumina HiSeq 2500. Among the microbes, bacteria dominate more than 82% in the three polluted sediment samples of river Ganga. Pseudomonadota (alpha, beta, and gamma) is the major phylum of bacteria that dominates in three sediment samples. Genes involved in degradation of xenobiotic compounds involving nitrotoluene, benzoate, aminobenzoate, chlorocyclohexane, and chlorobenzene were significantly enriched in the microbiome of polluted stretches. Pathway analysis using KEGG database revealed a higher abundance of genes involved in energy metabolism such as oxidative phosphorylation, nitrogen, methane, sulfur, and carbon fixation pathways in the sediment metagenome data from the river Ganga. A higher abundance of pollutant degrading enzymes like 4-hydroxybenzoate 3-monooxygenase, catalase-peroxidase, and altronate hydrolase in the polluted microbiome indicates their role in degradation of plastics and dyes. Overall, our study has provided bacterial diversity and their dynamics in community structure and function from polluted river microbiome, which is expected to open up better avenues for exploration of novel functional genes/enzymes with potential application in health and bioremediation.

RevDate: 2022-06-24

Kelly MS, Bunyavanich S, Phipatanakul W, et al (2022)

The Environmental Microbiome, Allergic Disease and Asthma.

The journal of allergy and clinical immunology. In practice pii:S2213-2198(22)00591-8 [Epub ahead of print].

The environmental microbiome represents the entirety of the microbes and their metabolites that we encounter in our environments. A growing body of evidence supports the role of the environmental microbiome in risk for and severity of allergic diseases and asthma. The environmental microbiome represents a ubiquitous, lifelong exposure to non-self antigens. During the critical window between birth and one year of life, interactions between our early immune system and the environmental microbiome have two consequences: our individual microbiome is populated by environmental microbes, and our immune system is trained regarding which antigens to tolerate. During this time, a diversity of exposures appears largely protective, dramatically decreasing the risk of developing allergic diseases and asthma. As we grow older, our interactions with the environmental microbiome change. While it continues to exert influence over the composition of the human microbiome, the environmental microbiome becomes increasingly a source for antigenic stimulation and infection. The same microbial exposure protective against disease development may exacerbate disease severity. While much has been learned about the importance of the environmental microbiome in allergic disease, much more remains to be understood about these complicated interactions between our environment, our microbiome, our immune system and disease.

RevDate: 2022-06-24

Dong C, Yang Y, Wang Y, et al (2022)

Gut Microbiota Combined with Metabolites Reveals Unique Features of Acute Myocardial Infarction Patients Different from Stable Coronary Artery Disease.

Journal of advanced research pii:S2090-1232(22)00146-1 [Epub ahead of print].

INTRODUCTION: Acute myocardial infarction (AMI) accounts for the majority of deaths caused by coronary artery disease (CAD). Early warning of AMI, especially for patients with stable coronary artery disease (sCAD), is urgently needed. Our previous study showed that alterations in the gut microbiota were correlated with CAD severity.

OBJECTIVES: Herein, we tried to discover accurate and convenient biomarkers for AMI by combination of gut microbiota and fecal/blood/urinary metabolomics.

METHODS: We recruited 190 volunteers including 93 sCAD patients, 49 AMI patients, and 48 subjects with normal coronary artery (NCA), and measured their blood biochemical parameters, 16S rRNA-based gut microbiota and NMR-based fecal/blood/urinary metabolites. We further selected 20 subjects from each group and analyzed their gut microbiota by whole-metagenome shotgun sequencing.

RESULTS: Multi-omic analyses revealed that AMI patients exhibited specific changes in gut microbiota and serum/urinary/fecal metabolites as compared to subjects with sCAD or NCA. Fourteen bacterial genera and 30 metabolites (11 in feces, 10 in blood, 9 in urine) were closely related to AMI phenotypes and could accurately distinguish AMI patients from sCAD patients. Some species belonging to Alistipes, Streptococcus, Ruminococcus, Lactobacillus and Faecalibacterium were effective to distinguish AMI from sCAD and their predictive ability was confirmed in an independent cohort of CAD patients. We further selected nine indicators including 4 bacterial genera, 3 fecal and 2 urinary metabolites as a noninvasive biomarker set which can distinguish AMI from sCAD with an AUC of 0.932.

CONCLUSION: Combination of gut microbiota and fecal/urinary metabolites provided a set of potential useful and noninvasive predictive biomarker for AMI from sCAD.

RevDate: 2022-06-24

Isidro J, Borges V, Pinto M, et al (2022)

Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus.

Nature medicine pii:10.1038/s41591-022-01907-y [Epub ahead of print].

The largest monkeypox virus (MPXV) outbreak described so far in non-endemic countries was identified in May 20221-6. Here, shotgun metagenomics allowed the rapid reconstruction and phylogenomic characterization of the first MPXV outbreak genome sequences, showing that this MPXV belongs to clade 3 and that the outbreak most likely has a single origin. Although 2022 MPXV (lineage B.1) clustered with 2018-2019 cases linked to an endemic country, it segregates in a divergent phylogenetic branch, likely reflecting continuous accelerated evolution. An in-depth mutational analysis suggests the action of host APOBEC3 in viral evolution as well as signs of potential MPXV human adaptation in ongoing microevolution. Our findings also indicate that genome sequencing may provide resolution to track the spread and transmission of this presumably slow-evolving dsDNA virus.

RevDate: 2022-06-24

Huang Y, Zou K, Qing T, et al (2022)

Metagenomics and metatranscriptomics analyses of antibiotic synthesis in activated sludge.

Environmental research pii:S0013-9351(22)01068-4 [Epub ahead of print].

The generic of antibiotics is considered to be a main reason for the generation of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). However, little has been reported about the antibiotic biosynthesis by activated sludge. In this study, the distribution and expression of antibiotic biosynthetic genes (ABGs) in the floc sludge and biofilm from two WWTPs were deciphered using metagenomics and metatranscriptomics. The results showed that 2% of the community were in general well-linked to antibiotic production based on 16S rRNA analysis, indicating a non-negligible antibiotic synthetic ability of WWTPs. 93 ABGs belonging to 26 antibiotics were determined, among which aminoglycosides, β-lactams, ansamycins, peptides, macrolides were majority. The relative abundances of detected ABGs had a large interval, ranging from 0.000006% to 0.042%. The predominant antibiotic types of synthetic genes with higher relative expression levels were monobactams, penicillin & cephalosporins, streptomycin and vancomycin, primarily belonging to β-lactams and aminoglycosides. The hypothetical synthetic pathways of streptomycin synthesis and penicillin & cephalosporin synthesis were proposed. And the coexistence of ABGs and ARGs for these two antibiotics was also pronounced in activated sludge from meta-omics data. These findings for the first time demonstrated the antibiotic synthetic potential in activated sludges, revealing new sources of antibiotics and resistance genes in WWTPs, and thereby aggravating environmental pollution.

RevDate: 2022-06-24

Gaio D, DeMaere MZ, Anantanawat K, et al (2022)

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig.

PloS one, 17(6):e0270372 pii:PONE-D-22-05513.

Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.

RevDate: 2022-06-24

Apiwatsiri P, Pupa P, Sirichokchatchawan W, et al (2022)

Metagenomic analysis of the gut microbiota in piglets either challenged or not with enterotoxigenic Escherichia coli reveals beneficial effects of probiotics on microbiome composition, resistome, digestive function and oxidative stress responses.

PloS one, 17(6):e0269959 pii:PONE-D-22-04406.

This study used metagenomic analysis to investigate the gut microbiota and resistome in piglets that were or were not challenged with enterotoxigenic Escherichia coli (ETEC) and had or had not received dietary supplementation with microencapsulated probiotics. The 72 piglets belonged to six groups that were either non-ETEC challenged (groups 1-3) or ETEC challenged (receiving 5ml of 109 CFU/ml pathogenic ETEC strain L3.2 one week following weaning at three weeks of age: groups 4-6). On five occasions at 2, 5, 8, 11, and 14 days of piglet age, groups 2 and 5 were supplemented with 109 CFU/ml of multi-strain probiotics (Lactiplantibacillus plantarum strains 22F and 25F, and Pediococcus acidilactici 72N) while group 4 received 109 CFU/ml of P. acidilactici 72N. Group 3 received 300mg/kg chlortetracycline in the weaner diet to mimic commercial conditions. Rectal faecal samples were obtained for metagenomic and resistome analysis at 2 days of age, and at 12 hours and 14 days after the timing of post-weaning challenge with ETEC. The piglets were all euthanized at 42 days of age. The piglets in groups 2 and 5 were enriched with several desirable microbial families, including Lactobacillaceae, Lachnospiraceae and Ruminococcaceae, while piglets in group 3 had increases in members of the Bacteroidaceae family and exhibited an increase in tetW and tetQ genes. Group 5 had less copper and multi-biocide resistance. Mobile genetic elements IncQ1 and IncX4 were the most prevalent replicons in antibiotic-fed piglets. Only groups 6 and 3 had the integrase gene (intl) class 2 and 3 detected, respectively. The insertion sequence (IS) 1380 was prevalent in group 3. IS3 and IS30, which are connected to dietary intake, were overrepresented in group 5. Furthermore, only group 5 showed genes associated with detoxification, with enrichment of genes associated with oxidative stress, glucose metabolism, and amino acid metabolism compared to the other groups. Overall, metagenomic analysis showed that employing a multi-strain probiotic could transform the gut microbiota, reduce the resistome, and boost genes associated with food metabolism.

RevDate: 2022-06-24

Claro IM, Romano CM, Candido DDS, et al (2022)

Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022.

Revista do Instituto de Medicina Tropical de Sao Paulo, 64:e48 pii:S0036-46652022000100224.

Monkeypox virus (MPXV), a zoonotic virus endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of the first confirmed case of MPXV in Brazil. Shotgun metagenomic sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation.

RevDate: 2022-06-24

Aaron J, van Zyl LJ, LMT Dicks (2022)

Isolation and Characterization of Lytic Proteus Virus 309.

Viruses, 14(6): pii:v14061309.

Proteus mirabilis is frequently associated with complicated urinary tract infections (UTIs) and is the main cause of catheter-associated urinary tract infections (CAUTIs). Treatment of such infections is complicated and challenging due to the biofilm forming abilities of P. mirabilis. If neglected or mistreated, infections may lead to life-threating conditions such as cystitis, pyelonephritis, kidney failure, and bacteremia that may progress to urosepsis. Treatment with antibiotics, especially in cases of recurring and persistent infections, leads to the development of resistant strains. Recent insights into phage therapy and using phages to coat catheters have been evaluated with many studies showing promising results. Here, we describe a highly lytic bacteriophage, Proteus_virus_309 (41,740 bp), isolated from a wastewater treatment facility in Cape Town, South Africa. According to guidelines of the International Committee on Taxonomy of Viruses (ICTV), bacteriophage 309 is a species within the genus Novosibovirus. Similar to most members of the genus, bacteriophage 309 is strain-specific and lyse P. mirabilis in less than 20 min.

RevDate: 2022-06-24

Zakotnik S, Knap N, Bogovič P, et al (2022)

Complete Genome Sequencing of Tick-Borne Encephalitis Virus Directly from Clinical Samples: Comparison of Shotgun Metagenomic and Targeted Amplicon-Based Sequencing.

Viruses, 14(6): pii:v14061267.

The clinical presentation of tick-borne encephalitis virus (TBEV) infection varies from asymptomatic to severe meningoencephalitis or meningoencephalomyelitis. The TBEV subtype has been suggested as one of the most important risk factors for disease severity, but TBEV genetic characterization is difficult. Infection is usually diagnosed in the post-viremic phase, and so relevant clinical samples of TBEV are extremely rare and, when present, are associated with low viral loads. To date, only two complete TBEV genomes sequenced directly from patient clinical samples are publicly available. The aim of this study was to develop novel protocols for the direct sequencing of the TBEV genome, enabling studies of viral genetic determinants that influence disease severity. We developed a novel oligonucleotide primer scheme for amplification of the complete TBEV genome. The primer set was tested on 21 clinical samples with various viral loads and collected over a 15-year period using the two most common sequencing platforms. The amplicon-based strategy was compared to direct shotgun sequencing. Using the novel primer set, we successfully obtained nearly complete TBEV genomes (>90% of genome) from all clinical samples, including those with extremely low viral loads. Comparison of consensus sequences of the TBEV genome generated using the novel amplicon-based strategy and shotgun sequencing showed no difference. We conclude that the novel primer set is a powerful tool for future studies on genetic determinants of TBEV that influence disease severity and will lead to a better understanding of TBE pathogenesis.

RevDate: 2022-06-24

Mastriani E, Bienes KM, Wong G, et al (2022)

PIMGAVir and Vir-MinION: Two Viral Metagenomic Pipelines for Complete Baseline Analysis of 2nd and 3rd Generation Data.

Viruses, 14(6): pii:v14061260.

The taxonomic classification of viral sequences is frequently used for the rapid identification of pathogens, which is a key point for when a viral outbreak occurs. Both Oxford Nanopore Technologies (ONT) MinION and the Illumina (NGS) technology provide efficient methods to detect viral pathogens. Despite the availability of many strategies and software, matching them can be a very tedious and time-consuming task. As a result, we developed PIMGAVir and Vir-MinION, two metagenomics pipelines that automatically provide the user with a complete baseline analysis. The PIMGAVir and Vir-MinION pipelines work on 2nd and 3rd generation data, respectively, and provide the user with a taxonomic classification of the reads through three strategies: assembly-based, read-based, and clustering-based. The pipelines supply the scientist with comprehensive results in graphical and textual format for future analyses. Finally, the pipelines equip the user with a stand-alone platform with dedicated and various viral databases, which is a requirement for working in field conditions without internet connection.

RevDate: 2022-06-24

Velasco-Rodríguez Ó, Fil M, Heggeset TMB, et al (2022)

Characterization of Microbial Diversity in Decayed Wood from a Spanish Forest: An Environmental Source of Industrially Relevant Microorganisms.

Microorganisms, 10(6): pii:microorganisms10061249.

Rotting wood is inhabited by a large diversity of bacteria, fungi, and insects with complex environmental relationships. The aim of this work was to study the composition of the microbiota (bacteria and fungi) in decaying wood from a northwest Spanish forest as a source of industrially relevant microorganisms. The analyzed forest is situated in a well-defined biogeographic area combining Mediterranean and temperate macrobioclimates. Bacterial diversity, determined by metagenome analyses, was higher than fungal heterogeneity. However, a total of 194 different cultivable bacterial isolates (mainly Bacillaceae, Streptomycetaceae, Paenibacillaceae, and Microbacteriaceae) were obtained, in contrast to 343 fungal strains (mainly Aspergillaceae, Hypocreaceae, and Coniochaetaceae). Isolates traditionally known as secondary metabolite producers, such as Actinobacteria and members of the Penicillium genus, were screened for their antimicrobial activity by the detection of antibiotic biosynthetic clusters and competitive bioassays against fungi involved in wood decay. In addition, the ability of Penicillium isolates to degrade cellulose and release ferulic acid from wood was also examined. These results present decaying wood as an ecologically rich niche and a promising source of biotechnologically interesting microorganisms.

RevDate: 2022-06-24

Baltazar-Díaz TA, González-Hernández LA, Aldana-Ledesma JM, et al (2022)

Escherichia/Shigella, SCFAs, and Metabolic Pathways-The Triad That Orchestrates Intestinal Dysbiosis in Patients with Decompensated Alcoholic Cirrhosis from Western Mexico.

Microorganisms, 10(6): pii:microorganisms10061231.

Gut microbiota undergoes profound alterations in alcohol cirrhosis. Microbiota-derived products, e.g., short chain fatty acids (SCFA), regulate the homeostasis of the gut-liver axis. The objective was to evaluate the composition and functions of the intestinal microbiota in patients with alcohol-decompensated cirrhosis. Fecal samples of 18 patients and 18 healthy controls (HC) were obtained. Microbial composition was characterized by 16S rRNA amplicon sequencing, SCFA quantification was performed by gas chromatography (GC), and metagenomic predictive profiles were analyzed by PICRUSt2. Gut microbiota in the cirrhosis group revealed a significant increase in the pathogenic/pathobionts genera Escherichia/Shigella and Prevotella, a decrease in beneficial bacteria, such as Blautia, Faecalibacterium, and a decreased α-diversity (p < 0.001) compared to HC. Fecal SCFA concentrations were significantly reduced in the cirrhosis group (p < 0.001). PICRUSt2 analysis indicated a decrease in acetyl-CoA fermentation to butyrate, as well as an increase in pathways related to antibiotics resistance, and aromatic amino acid biosynthesis. These metabolic pathways have been poorly described in the progression of alcohol-related decompensated cirrhosis. The gut microbiota of these patients possesses a pathogenic/inflammatory environment; therefore, future strategies to balance intestinal dysbiosis should be implemented. These findings are described for the first time in the population of western Mexico.

RevDate: 2022-06-24

Senn S, Bhattacharyya S, Presley G, et al (2022)

The Functional Biogeography of eDNA Metacommunities in the Post-Fire Landscape of the Angeles National Forest.

Microorganisms, 10(6): pii:microorganisms10061218.

Wildfires have continued to increase in frequency and severity in Southern California due in part to climate change. To gain a further understanding of microbial soil communities' response to fire and functions that may enhance post-wildfire resilience, soil fungal and bacterial microbiomes were studied from different wildfire areas in the Gold Creek Preserve within the Angeles National Forest using 16S, FITS, 18S, 12S, PITS, and COI amplicon sequencing. Sequencing datasets from December 2020 and June 2021 samplings were analyzed using QIIME2, ranacapa, stats, vcd, EZBioCloud, and mixomics. Significant differences were found among bacterial and fungal taxa associated with different fire areas in the Gold Creek Preserve. There was evidence of seasonal shifts in the alpha diversity of the bacterial communities. In the sparse partial least squares analysis, there were strong associations (r > 0.8) between longitude, elevation, and a defined cluster of Amplicon Sequence Variants (ASVs). The Chi-square test revealed differences in fungi-bacteria (F:B) proportions between different trails (p = 2 × 10-16). sPLS results focused on a cluster of Green Trail samples with high elevation and longitude. Analysis revealed the cluster included the post-fire pioneer fungi Pyronema and Tremella. Chlorellales algae and possibly pathogenic Fusarium sequences were elevated. Bacterivorous Corallococcus, which secretes antimicrobials, and bacterivorous flagellate Spumella were associated with the cluster. There was functional redundancy in clusters that were differently composed but shared similar ecological functions. These results implied a set of traits for post-fire resiliency. These included photo-autotrophy, mineralization of pyrolyzed organic matter and aromatic/oily compounds, potential pathogenicity and parasitism, antimicrobials, and N-metabolism.

RevDate: 2022-06-24

Ledormand P, Desmasures N, Midoux C, et al (2022)

Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage.

Microorganisms, 10(6): pii:microorganisms10061203.

Phageomes are known to play a key role in the functioning of their associated microbial communities. The phageomes of fermented foods have not been studied thoroughly in fermented foods yet, and even less in fermented beverages. Two approaches were employed to investigate the presence of phages in cider, a fermented beverage made from apple, during a fermentation process of two cider tanks, one from an industrial producer and one from a hand-crafted producer. The phageome (free lytic phages) was explored in cider samples with several methodological developments for total phage DNA extraction, along with single phage isolation. Concentration methods, such as tangential flow filtration, flocculation and classical phage concentration methods, were employed and tested to extract free phage particles from cider. This part of the work revealed a very low occurrence of free lytic phage particles in cider. In parallel, a prophage investigation during the fermentation process was also performed using a metagenomic approach on the total bacterial genomic DNA. Prophages in bacterial metagenomes in the two cider tanks seemed also to occur in low abundance, as a total of 1174 putative prophages were identified in the two tanks overtime, and only two complete prophages were revealed. Prophage occurrence was greater at the industrial producer than at the hand-crafted producer, and different dynamics of prophage trends were also observed during fermentation. This is the first report dealing with the investigation of the phageome and of prophages throughout a fermentation process of a fermented beverage.

RevDate: 2022-06-24

Murray B, Ertekin E, Dailey M, et al (2022)

Adaptation of Cyanobacteria to the Endolithic Light Spectrum in Hyper-Arid Deserts.

Microorganisms, 10(6): pii:microorganisms10061198.

In hyper-arid deserts, endolithic microbial communities survive in the pore spaces and cracks of rocks, an environment that enhances water retention and filters UV radiation. The rock colonization zone is enriched in far-red light (FRL) and depleted in visible light. This poses a challenge to cyanobacteria, which are the primary producers of endolithic communities. Many species of cyanobacteria are capable of Far-Red-Light Photoacclimation (FaRLiP), a process in which FRL induces the synthesis of specialized chlorophylls and remodeling of the photosynthetic apparatus, providing the ability to grow in FRL. While FaRLiP has been reported in cyanobacteria from various low-light environments, our understanding of light adaptations for endolithic cyanobacteria remains limited. Here, we demonstrated that endolithic Chroococcidiopsis isolates from deserts around the world synthesize chlorophyll f, an FRL-specialized chlorophyll when FRL is the sole light source. The metagenome-assembled genomes of these isolates encoded chlorophyll f synthase and all the genes required to implement the FaRLiP response. We also present evidence of FRL-induced changes to the major light-harvesting complexes of a Chroococcidiopsis isolate. These findings indicate that endolithic cyanobacteria from hyper-arid deserts use FRL photoacclimation as an adaptation to the unique light transmission spectrum of their rocky habitat.

RevDate: 2022-06-24

Tang L, Gao Y, Yan L, et al (2022)

Comparative Analysis of Microbiome Metagenomics in Reintroduced Wild Horses and Resident Asiatic Wild Asses in the Gobi Desert Steppe.

Microorganisms, 10(6): pii:microorganisms10061166.

The gut microbiome offers important ecological benefits to the host; however, our understanding of the functional microbiome in relation to wildlife adaptation, especially for translocated endangered species, is lagging. In this study, we adopted a comparative metagenomics approach to test whether the microbiome diverges for translocated and resident species with different adaptive potentials. The composition and function of the microbiome of sympatric Przewalski's horses and Asiatic wild asses in desert steppe were compared for the first time using the metagenomic shotgun sequencing approach. We identified a significant difference in microbiome composition regarding the microbes present and their relative abundances, while the diversity of microbe species was similar. Furthermore, the functional profile seemed to converge between the two hosts, with genes related to core metabolism function tending to be more abundant in wild asses. Our results indicate that sympatric wild equids differ in their microbial composition while harboring a stable microbial functional core, which may enable them to survive in challenging habitats. A higher abundance of beneficial taxa, such as Akkermansia, and genes related to metabolism pathways and enzymes, such as lignin degradation, may contribute to more diverse diet choices and larger home ranges of wild asses.

RevDate: 2022-06-24

Tsakeng CUB, Tanekou TTM, Soffack SF, et al (2022)

Assessing the Tsetse Fly Microbiome Composition and the Potential Association of Some Bacteria Taxa with Trypanosome Establishment.

Microorganisms, 10(6): pii:microorganisms10061141.

The tsetse flies, biological vectors of African trypanosomes, harbour a variety of bacteria involved in their vector competence that may help in developing novel vector control tools. This study provides an inventory of tsetse bacterial communities in Cameroon and explores their possible associations with trypanosome establishment in Glossina palpalis palpalis. High throughput sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene, with subsequent metagenomic, multivariate, and association analyses, were used to investigate the levels and patterns of microbial diversity in four tsetse species. Overall, 31 bacterial genera and four phyla were identified. The primary symbiont Wigglesworthia dominated almost all the samples, with an overall relative abundance of 47.29%, and seemed to be replaced by Serratia or Burkholderia in some G. tachinoides flies. Globally, significant differences were observed in the microbiome diversity and composition among tsetse species and between teneral and non-teneral flies, or between flies displaying or not displaying mature trypanosome infections. In addition, differential abundance testing showed some OTUs, or some bacteria taxa, associated with trypanosome maturation in tsetse flies. These bacteria could be further investigated for an understanding of their mechanism of action and alternatively, transformed and used to block trypanosome development in tsetse flies.

RevDate: 2022-06-24

Zhou M, Liu Z, Wang J, et al (2022)

Sphingomonas Relies on Chemotaxis to Degrade Polycyclic Aromatic Hydrocarbons and Maintain Dominance in Coking Sites.

Microorganisms, 10(6): pii:microorganisms10061109.

Polycyclic aromatic hydrocarbons (PAHs) are organic pollutants widely present in industrial sites. Microbial degradation is an effective method of removing PAHs. The identification of microorganisms that have important ecological functions at the site is of great significance for PAH removal. We collected soil samples at three depths in the range of 0-100 cm at 70-day intervals at the coking site and explored the degradation of PAHs. We combined molecular ecology networking, metagenomics, and genome assembly to search for microorganisms that persist, dominate, and affect the microbial community construction in the degradation process and analyzed their adaptation strategies. The results showed that 15.78 mg/kg of PAHs naturally decayed, and 13.33 mg/kg of PAHs migrated from 30-100 cm to 0-30 cm in the soil. Sphingomonas, which occupied a niche advantage, was both the core and keystone microorganism, and its spatial distribution pattern and temporal change dynamics were consistent with those of PAHs. We assembled the genome of Sphingomonas sp., revealing its multiple potential for degrading PAHs and other pollutants. Additionally, flagellar assembly and bacterial chemotaxis genes ranked high in the assembled genome of Sphingomonas sp., which might help it obtain a competitive advantage in the soil. The findings underscored the strategy of Sphingomonas to maintain dominance, enriched the understanding of PAH-degrading microorganisms in site soil, and provided references for the remediation of PAHs.

RevDate: 2022-06-24

García-Mato E, Martínez-Lamas L, Álvarez-Fernández M, et al (2022)

Molecular Detection of Streptococcus downii sp. nov. from Dental Plaque Samples from Patients with Down Syndrome and Non-Syndromic Individuals.

Microorganisms, 10(6): pii:microorganisms10061098.

A new bacterial species has recently been identified in the dental plaque of an adolescent with Down syndrome. The species is known as Streptococcus downii sp. nov. (abbreviated to S. downii), and it inhibits the growth of S. mutans and certain periodontal pathogens. The aim of this study was to determine the distribution of S. downii in the oral cavity of individuals with Down syndrome. Methods: A specific polymerase chain reaction for the operon of bacteriocin (class IIb lactobin A/cerein 7B family) was designed to detect S. downii in individuals with Down syndrome (n = 200) and in the general population (n = 100). We also compared the whole genome of S. downii and the regions related to its bacteriocins against 127 metagenomes of supragingival plaque of the "Human Microbiome Project". Results: We detected the specific gene of the S. downii bacteriocin in an individual with Down syndrome (Cq, 34.52; GE/μL, 13.0) and in an individual of the non-syndromic control group (Cq, 34.78 Cq; GE/μL, 4.93). The prevalence of S. downii was ≤1% both in Down syndrome and in the general population, which did not allow for clinical-microbiological correlations to be established. This result was confirmed by detecting only one metagenome with an ANIm with approximately 95% homology and with 100% homology with ORFs that code class IIb lactobiocin A/cerein 7B bacteriocins among the 127 metagenomes of the "Human Microbiome Project" tested. Conclusions: The detection rate of S. downii in the supragingival dental plaque was very low, both in the Down syndrome individuals and in the non-syndromic controls. A clinical-microbiological correlation could therefore not be established.

RevDate: 2022-06-24

Doytchinov VV, SG Dimov (2022)

Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach.

Life (Basel, Switzerland), 12(6): pii:life12060916.

Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.

RevDate: 2022-06-24

Tsukamoto Y, T Kakegawa (2022)

Mineralogical and Genomic Constraints on the Origin of Microbial Mn Oxide Formation in Complexed Microbial Community at the Terrestrial Hot Spring.

Life (Basel, Switzerland), 12(6): pii:life12060816.

Manganese (Mn) oxides are widespread on the surface environments of the modern Earth. The role of microbial activities in the formation of Mn oxides has been discussed for several decades. However, the mechanisms of microbial Mn oxidation, and its role in complex microbial communities in natural environments, remain uncertain. Here, we report the geochemical, mineralogical, and metagenomic evidence for biogenic Mn oxides, found in Japanese hot spring sinters. The low crystallinity of Mn oxides, and their spatial associations with organic matter, support the biogenic origin of Mn oxides. Specific multicopper oxidases (MCOs), which are considered Mn-oxidizing enzymes, were identified using metagenomic analyses. Nanoscale nuggets of copper sulfides were, also, discovered in the organic matter in Mn-rich sinters. A part of these copper sulfides most likely represents traces of MCOs, and this is the first report of traces of Mn-oxidizing enzyme in geological samples. Metagenomic analyses, surprisingly, indicated a close association of Mn oxides, not only in aerobic but also in anaerobic microbial communities. These new findings offer the unique and unified positions of Mn oxides, with roles that have not been ignored, to sustain anaerobic microbial communities in hot spring environments.

RevDate: 2022-06-24

Fulci V (2022)

Meta'omics: Challenges and Applications.

International journal of molecular sciences, 23(12): pii:ijms23126486.

Metagenomics and metatranscriptomics are emerging as key disciplines towards a fully understanding the complex relationships between living organisms belonging to different kingdoms [...].

RevDate: 2022-06-24

Wyszkowska J, Borowik A, J Kucharski (2022)

The Role of Grass Compost and Zea Mays in Alleviating Toxic Effects of Tetracycline on the Soil Bacteria Community.

International journal of environmental research and public health, 19(12): pii:ijerph19127357.

Given their common use for disease treatment in humans, and particularly in animals, antibiotics pose an exceptionally serious threat to the soil environment. This study aimed to determine the response of soil bacteria and oxidoreductases to a tetracycline (Tc) contamination, and to establish the usability of grass compost (G) and Zea mays (Zm) in mitigating adverse Tc effects on selected microbial properties of the soil. The scope of microbiological analyses included determinations of bacteria with the conventional culture method and new-generation sequencing method (NGS). Activities of soil dehydrogenases and catalase were determined as well. Tc was found to reduce counts of organotrophic bacteria and actinobacteria in the soils as well as the activity of soil oxidoreductases. Soil fertilization with grass compost (G) and Zea mays (Zm) cultivation was found to alleviate the adverse effects of tetracycline on the mentioned group of bacteria and activity of oxidoreductases. The metagenomic analysis demonstrated that the bacteria belonging to Acidiobacteria and Proteobacteria phyla were found to prevail in the soil samples. The study results recommend soil fertilization with G and Zm cultivation as successful measures in the bioremediation of tetracycline-contaminated soils and indicate the usability of the so-called core bacteria in the bioaugmentation of such soils.

RevDate: 2022-06-24

Islam SMS, Ryu HM, S Sohn (2022)

Tetragenococcus halophilus Alleviates Intestinal Inflammation in Mice by Altering Gut Microbiota and Regulating Dendritic Cell Activation via CD83.

Cells, 11(12): pii:cells11121903.

Ulcerative colitis (UC) is one of the major subtypes of inflammatory bowel disease with unknown etiology. Probiotics have recently been introduced as a treatment for UC. Tetragenococcus halophilus (T. halophilus) is a lactic acid-producing bacterium that survives in environments with high salt concentrations, though little is known about its immunomodulatory function as a probiotic. The purpose of this study is to determine whether T. halophilus exerts an anti-inflammatory effect on intestinal inflammation in mice. Colitis was induced in C57BL/6J mice by feeding 4% DSS in drinking water for 7 days. T. halophilus was orally administered with DSS. Anti-inflammatory functions were subsequently evaluated by flow cytometry, qRT-PCT, and ELISA. Gut microbial composition was analyzed by 16S rRNA metagenomic analysis. DSS-induced colitis mice treated with T. halophilus showed less weight loss and significantly suppressed colonic shortening compared to DSS-induced colitis mice. T. halophilus significantly reduced the frequency of the dendritic cell activation molecule CD83 in peripheral blood leukocytes and intestinal epithelial lymphocytes. Frequencies of CD8+NK1.1+ cells decreased in mice with colitis after T. halophilus treatment and IL-1β levels were also reduced. Alteration of gut microbiota was observed in mice with colitis after administration of T. halophilus. These results suggest T. halophilus is effective in alleviating DSS-induced colitis in mice by altering immune regulation and gut microbiome compositions.

RevDate: 2022-06-24

Yang Y, Li T, Liu P, et al (2022)

The formation of specific bacterial communities contributes to the enrichment of antibiotic resistance genes in the soil plastisphere.

Journal of hazardous materials, 436:129247.

Soil serves as a major reservoir of both antibiotic resistance genes (ARGs) and microplastics. However, the characteristics of the antibiotic resistome in the soil plastisphere remain largely unknown. In this study, we used metagenomic approaches to reveal the changing patterns of ARGs and the bacterial community and their associations in response to three types of microplastics (light density polyethylene, LDPE; polypropylene, PP; polystyrene, PS) using particles 550 µm or 75 µm in diameter. The total ARG abundances significantly increased in the plastisphere and varied across plastic types. The LDPE plastisphere had the highest ARG total abundance and lowest Shannon diversity index, indicating that this plastic had the most severe negative impact on soil bacterial diversity. The PP plastisphere contained higher relative abundances of the pathogenic bacteria Acinetobacter johnsonii and Escherichia coli, demonstrating the higher pathogenic risk of the microbial communities enriched in the plastisphere. Specifically, multidrug resistance genes (ceoB and MuxB) co-existed with more than four microbial taxa, increasing the potential risk of ARG spread in pathogenic bacteria. These findings implied that the plastisphere acts as a hotspot for acquiring and spreading antibiotic resistance and may have long-term negative effects on the soil ecosystem and human health.

RevDate: 2022-06-24

Murphy CWM, Davis GB, Rayner JL, et al (2022)

The role of predicted chemotactic and hydrocarbon degrading taxa in natural source zone depletion at a legacy petroleum hydrocarbon site.

Journal of hazardous materials, 430:128482.

Petroleum hydrocarbon contamination is a global problem which can cause long-term environmental damage and impacts water security. Natural source zone depletion (NSZD) is the natural degradation of such contaminants. Chemotaxis is an aspect of NSZD which is not fully understood, but one that grants microorganisms the ability to alter their motion in response to a chemical concentration gradient potentially enhancing petroleum NSZD mass removal rates. This study investigates the distribution of potentially chemotactic and hydrocarbon degrading microbes (CD) across the water table of a legacy petroleum hydrocarbon site near Perth, Western Australia in areas impacted by crude oil, diesel and jet fuel. Core samples were recovered and analysed for hydrocarbon contamination using gas chromatography. Predictive metagenomic profiling was undertaken to infer functionality using a combination of 16 S rRNA sequencing and PICRUSt2 analysis. Naphthalene contamination was found to significantly increase the occurrence of potential CD microbes, including members of the Comamonadaceae and Geobacteraceae families, which may enhance NSZD. Further work to explore and define this link is important for reliable estimation of biodegradation of petroleum hydrocarbon fuels. Furthermore, the outcomes suggest that the chemotactic parameter within existing NSZD models should be reviewed to accommodate CD accumulation in areas of naphthalene contamination, thereby providing a more accurate quantification of risk from petroleum impacts in subsurface environments, and the scale of risk mitigation due to NSZD.

RevDate: 2022-06-24

Li YJ, Chuang CH, Cheng WC, et al (2022)

A metagenomics study of hexabromocyclododecane degradation with a soil microbial community.

Journal of hazardous materials, 430:128465.

Hexabromocyclododecanes (HBCDs) are globally prevalent and persistent organic pollutants (POPs) listed by the Stockholm Convention in 2013. They have been detected in many environmental media from waterbodies to Plantae and even in the human body. Due to their highly bioaccumulative characterization, they pose an urgent public health issue. Here, we demonstrate that the indigenous microbial community in the agricultural soil in Taiwan could decompose HBCDs with no additional carbon source incentive. The degradation kinetics reached 0.173 day-1 after the first treatment and 0.104 day-1 after second exposure. With additional C-sources, the rate constants decreased to 0.054-0.097 day-1. The hydroxylic debromination metabolites and ring cleavage long-chain alkane metabolites were identified to support the potential metabolic pathways utilized by the soil microbial communities. The metagenome established by Nanopore sequencing showed significant compositional alteration in the soil microbial community after the HBCD treatment. After ranking, comparing relative abundances, and performing network analyses, several novel bacterial taxa were identified to contribute to HBCD biotransformation, including Herbaspirillum, Sphingomonas, Brevundimonas, Azospirillum, Caulobacter, and Microvirga, through halogenated / aromatic compound degradation, glutathione-S-transferase, and hydrolase activity. We present a compelling and applicable approach combining metagenomics research, degradation kinetics, and metabolomics strategies, which allowed us to decipher the natural attenuation and remediation mechanisms of HBCDs.

RevDate: 2022-06-23

Sumithra TG, Sharma SRK, Gayathri S, et al (2022)

Comparative evaluation of fish larval preservation methods on microbiome profiles to aid in metagenomics research.

Applied microbiology and biotechnology [Epub ahead of print].

Applications of microbiome research through metagenomics promise to generate microbiome manipulation strategies for improved larval survival in aquaculture. However, existing lacunae on the effects of sample preservation methods in metagenome profiles hinder the successful application of this technique. In this context, four preservation methods were scrutinized to identify reliable methods for fish larval microbiome research. The results showed that a total of ten metagenomics metrics, including DNA yield, taxonomic and functional microbiome profiles, and diversity measures, were significantly (P < 0.05) influenced by the preservation method. Activity ranking based on the performance and reproducibility showed that three methods, namely immediate direct freezing, room temperature preservation in absolute ethanol, and preservation at - 20 °C in lysis, storage, and transportation buffer, could be recommended for larval microbiome research. Furthermore, as there was an apparent deviation of the microbiome profiles of ethanol preserved samples at room temperature, the other methods are preferred. Detailed analysis showed that this deviation was due to the bias towards Vibrionales and Rhodobacterales. The microbial taxa responsible for the dissimilarity across different methods were identified. Altogether, the paper sheds light on the preservation protocols of fish larval microbiome research for the first time. The results can help in cross-comparison of future and past larval microbiome studies. Furthermore, this is the first report on the activity ranking of preservation methods based on metagenomics metrics. Apart from methodological perspectives, the paper provides for the first time certain insights into larval microbial profiles of Rachycentron canadum, a potential marine aquaculture species. KEY POINTS: • First report on effects of preservation methods on fish larval microbiome profiles. • First report on activity ranking of preservation methods based on metagenomics metrics. • Storage methods influenced DNA yield, taxonomic and functional microbiome profiles.

RevDate: 2022-06-23

Lockwood S, Greening C, Baltar F, et al (2022)

Global and seasonal variation of marine phosphonate metabolism.

The ISME journal [Epub ahead of print].

Marine microbial communities rely on dissolved organic phosphorus (DOP) remineralisation to meet phosphorus (P) requirements. We extensively surveyed the genomic and metagenomic distribution of genes directing phosphonate biosynthesis, substrate-specific catabolism of 2-aminoethylphosphonate (2-AEP, the most abundant phosphonate in the marine environment), and broad-specificity catabolism of phosphonates by the C-P lyase (including methylphosphonate, a major source of methane). We developed comprehensive enzyme databases by curating publicly available sequences and then screened metagenomes from TARA Oceans and Munida Microbial Observatory Time Series (MOTS) to assess spatial and seasonal variation in phosphonate metabolism pathways. Phosphonate cycling genes were encoded in diverse gene clusters by 35 marine bacterial and archaeal classes. More than 65% of marine phosphonate cycling genes mapped to Proteobacteria with production demonstrating wider taxonomic diversity than catabolism. Hydrolysis of 2-AEP was the dominant phosphonate catabolism strategy, enabling microbes to assimilate carbon and nitrogen alongside P. Genes for broad-specificity catabolism by the C-P lyase were far less widespread, though enriched in the extremely P-deplete environment of the Mediterranean Sea. Phosphonate cycling genes were abundant in marine metagenomes, particularly from the mesopelagic zone and winter sampling dates. Disparity between prevalence of substrate-specific and broad-specificity catabolism may be due to higher resource expenditure from the cell to build and retain the C-P lyase. This study is the most comprehensive metagenomic survey of marine microbial phosphonate cycling to date and provides curated databases for 14 genes involved in phosphonate cycling.

RevDate: 2022-06-23

Gosai HB, Panseriya HZ, Patel PG, et al (2022)

Exploring bacterial communities through metagenomics during bioremediation of polycyclic aromatic hydrocarbons from contaminated sediments.

The Science of the total environment pii:S0048-9697(22)03891-8 [Epub ahead of print].

The goal of this study was to evaluate the degradation effectiveness of PAHs degrading bacteria at the mesocosm level, including Stenotrophomonas maltophilia (SC), mixed culture (MC), and enriched native microflora (EC) at the mesocosm level. Maximum degradation was found in the mesocosm MC (26.67 %), followed by SC (25.08 %) and EC (18.25 %) after 60 days. Thus, mixed culture and Stenotrophomonas maltophilia could be a game changer in the PAHs bioremediation at the chronically contaminated sites. MiSeq sequencing has revealed dominancy of γ-Proteobacteria, α-Proteobacteria, β-Proteobacteria at class level and Sphingomonadales, oceanospirillales, Rhodothermales at Order level. Families Alcanivoracaceae, Alteromonadaceae, Nocardiaceae, Rhodospirillaceae and genus Stenotrophomonas, Alcanivorax, Methylophaga, Fluviicola and Rhodoplanes were considerably increased which play key role in the PAHs degradation. Dominant bacterial communities have revealed resilience community to enable potential PAHs degradation process in all the mesocosms. To the best our knowledge this is the first ever attempt in PAHs biodegradation study conducted at the mesocosm level mimicking natural environmental conditions. Consequently, this study could be a benchmark against which future progress studies for the policy makers and stakeholders to design appropriate bioremediation study for the historically PAHs polluted contaminate sites.

RevDate: 2022-06-23

Ali S, Xie J, Zada S, et al (2022)

Bacterial community structure and bacterial isolates having antimicrobial potential in shrimp pond aquaculture.

AMB Express, 12(1):82.

Diseases outbreaks in pond aquaculture have resulted in huge losses to the aquaculture industry. The emergence of non-antimicrobial and environment friendly agents (probiotics) is the potential consideration for the healthy shrimp aquaculture. The present study was aimed to compare the bacterial community compositions in shrimp ponds and surrounding seawater, as well as isolate probiotic bacteria from the shrimp ponds. Based on the high-throughput of 16S rRNA gene sequencing, all sequences were assigned to 3584 unique operational taxonomic units (OTUs) at 97% similarity levels, which were affiliated with 24 phyla, 54 classes, 235 families, and 367 genera. The 10 most abundant phyla were Bacteroidota, Proteobacteria, Actinobacteriota, Planctomycetota, Cyanobacteria, Chloroflexi, Firmicutes, Desulfobacterota, Patescibacteria and Verrucomicrobiota. Notably, the alpha diversity (Shannon diversity) of shrimp ponds was significantly differences (P < 0.05) with that of surrounding seawater. There were 2498 and 791 unique OTUs in shrimp ponds and surrounding seawater, respectively. A total of 15 isolates were obtained in the culturable bacterial diversity, and the antibacterial activities were recorded for potential probiotic bacterial isolates against different tested bacterial isolates including pathogenic bacteria. An isolate Hallobacillus marinus HMALI004 showed strong inhibitory effects against three pathogenic bacteria, Vibrio cholerae CECT 514, non AHPND V. parahaemolyticus BCRC12959 and AHPND V. parahaemolyticus PD-2. The isolates Algophigus sanaruensis AGALI005, Algoriphagus taiwanensis ATALI009 and Bacillus aequororis BAALI008 were also identified as potential probiotics strains.

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RJR Experience and Expertise

Researcher

Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.

Educator

Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.

Administrator

Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.

Technologist

Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.

Publisher

While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.

Speaker

Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.

Facilitator

Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.

Designer

Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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Although we can't usually see them, microbes are essential for every part of human life—indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying—one at a time—the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.

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Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

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Curriculum Vitae for R J Robbins

long standard version

RJR Picks from Around the Web (updated 11 MAY 2018 )