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28 Sep 2021 at 01:31
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Bibliography on: Metagenomics


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 28 Sep 2021 at 01:31 Created: 


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®)


RevDate: 2021-09-27

Rui M, Zhang X, Huang J, et al (2021)

The baseline oral microbiota predicts the response of locally advanced oral squamous cell carcinoma patients to induction chemotherapy: A prospective longitudinal study.

Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology pii:S0167-8140(21)06736-0 [Epub ahead of print].

PURPOSE: Among oral squamous cell carcinoma (OSCC) patients who receive docetaxel, cisplatin, and 5-fluorouracil (TPF) induction chemotherapy, those with a favorable pathological response tend to obtain satisfactory clinical outcomes, while the total population exhibit no survival benefit. Thus, there is an urgent need to improve the therapeutic effect of TPF by applying personalized treatment according to distinct biomarkers.

METHODS AND MATERIALS: In the present study, we collected oral rinse samples from 44 OSCC patients enrolled in our prospective multicenter random phase II trial before TPF induction chemotherapy to conduct 16S rRNA gene sequencing and metagenomic analysis. Patients were administrated with two cycles of TPF induction chemotherapy (75 mg/m2 cisplatin and 75 mg/m2 docetaxel on day 1 and 750 mg/m2 fluorouracil from the first to the fifth day), and then divided into responsive and nonresponsive groups according to the Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1.

RESULTS: In the 16S rRNA gene sequence analysis, Fusobacterium and Mycoplasma were more enriched in the nonresponsive group, while Slackia was more enriched in the responder group at the genus level. In the metagenomic shotgun sequencing analysis, Fusobacterium nucleatum was more enriched in the nonresponsive group. Functional analysis showed that the platinum drug resistance pathway and microRNAs in cancer and RNA degradation pathways were remarkably associated with patient sensitivity to induction chemotherapy.

CONCLUSIONS: Our data suggest that the oral microbiome may play an important role in the OSCC patient sensitivity to TPF induction chemotherapy and offer novel potential biomarkers for predicting the response to TPF induction chemotherapy.

RevDate: 2021-09-27

Patel V, Lee S, McPhail M, et al (2021)

Rifaximin reduces gut-derived inflammation and mucin degradation in cirrhosis and encephalopathy: RIFSYS randomised controlled trial.

Journal of hepatology pii:S0168-8278(21)02040-7 [Epub ahead of print].

BACKGROUND: Rifaximin is efficacious in the prevention of recurrent hepatic encephalopathy (HE) but its mechanism of action remains unclear. We postulated that rifaximin reduces gut microbiota-derived endotoxemia and systemic inflammation, a known driver of HE.

DESIGN: A randomised placebo-controlled double-blind mechanistic study of rifaximin versus placebo was performed in cirrhotic patients with HE. Rifaximin-α 550mg (TARGAXAN) twice daily (n=19) or placebo (n=19) was administered for 90-days.

PRIMARY OUTCOME: 50% reduction in neutrophil oxidative burst (OB) at 30-days.

SECONDARY OUTCOMES: Psychometric Hepatic Encephalopathy Scale (PHES), shotgun metagenomic sequencing of saliva and faeces, plasma and faecal metabolome, blood bacterial DNA, neutrophil toll-like receptor (TLR)-2/4/9 and interleukin-8 expression, and plasma and faecal cytokine analysis.

RESULTS: Patients were well-matched: median MELD [11 rifaximin-α versus 10 placebo]. Day 30 HE grade normalised on rifaximin-α but not placebo (p=0.014) with an improvement in PHES score; p=0.009. Rifaximin-α reduced circulating neutrophil TLR-4 expression on day-30 (p=0.021) with a reduction in plasma tumour necrosis factor-α (TNF-α); p<0.001. Rifaximin-α suppressed oralisation of the gut, reducing the mucin-degrading sialidase-rich species Streptococcus spp, Veillonella atypica and parvula, Akkermansia and Hungatella. Rifaximin-α promoted a TNF-α and IL-17E enriched intestinal microenvironment augmenting anti-bacterial responses to invading pathobionts and promoting gut barrier repair. Those on rifaximin-α were less likely to develop infection [odds ratio 0.21(0.05-0.96)].

CONCLUSION: Rifaximin-treated patients were less likely to develop infection with resolution of overt and covert HE. Rifaximin-α reduced oralisation of the gut with mucin-degrading species attenuating systemic inflammation. These data link rifaximin-α as having a role in gut barrier repair as a mechanism by which it ameliorates bacterial translocation and systemic endotoxemia in cirrhosis.

LAY SUMMARY: This clinical trial examined the underlying mechanism of action of an antibiotic called rifaximin which has been shown to be an effective treatment for a complication of chronic liver disease which effects the brain (termed encephalopathy). It shows that rifaximin suppresses gut bacteria that translocate from the mouth to the intestine which causes the intestinal wall to become leaky by breaking down the protective mucus barrier. This resolves encephalopathy and reduces inflammation in the blood preventing the development of infection.

CLINICAL TRIAL NUMBER: ClinicalTrials.gov NCT02019784.

RevDate: 2021-09-27

Zhang Y, Hu B, Agwanda B, et al (2021)

Viromes and surveys of RNA viruses in camel-derived ticks revealing transmission patterns of novel tick-borne viral pathogens in Kenya.

Emerging microbes & infections [Epub ahead of print].

Tick-borne viruses (TBVs) capable of transmitting between ticks and hosts have been increasingly recognized as a global public health concern. In this study, Hyalomma ticks and serum samples from camels were collected using recorded sampling correlations in eastern Kenya. Viromes of pooled ticks were profiled by metagenomic sequencing, revealing a diverse community of viruses related to at least 11 families. Five highly abundant viruses, including three novel viruses (Iftin tick virus, Mbalambala tick virus [MATV], and Bangali torovirus [BanToV]) and new strains of previously identified viruses (Bole tick virus 4 [BLTV4] and Liman tick virus [LMTV]), were characterized in terms of genome sequences, organizations, and phylogeny, and their molecular prevalence was investigated in individual ticks. Moreover, viremia and antibody responses to these viruses have been investigated in camels. MATV, BLTV4, LMTV, and BanToV were identified as viral pathogens that can potentially cause zoonotic diseases. The transmission patterns of these viruses were summarized, suggesting three different types according to the sampling relationships between viral RNA-positive ticks and camels positive for viral RNA and/or antibodies. They also revealed the frequent transmission of BanToV and limited but effective transmission of other viruses between ticks and camels. Furthermore, follow-up surveys on TBVs from tick, animal, and human samples with definite sampling relationships are suggested. The findings revealed substantial threats from the emerging TBVs and may guide the prevention and control of TBV-related zoonotic diseases in Kenya and in other African countries.

RevDate: 2021-09-27

Kajitani R, Noguchi H, Gotoh Y, et al (2021)

MetaPlatanus: a metagenome assembler that combines long-range sequence links and species-specific features.

Nucleic acids research pii:6376035 [Epub ahead of print].

De novo metagenome assembly is effective in assembling multiple draft genomes, including those of uncultured organisms. However, heterogeneity in the metagenome hinders assembly and introduces interspecies misassembly deleterious for downstream analysis. For this purpose, we developed a hybrid metagenome assembler, MetaPlatanus. First, as a characteristic function, it assembles the basic contigs from accurate short reads and then iteratively utilizes long-range sequence links, species-specific sequence compositions, and coverage depth. The binning information was also used to improve contiguity. Benchmarking using mock datasets consisting of known bacteria with long reads or mate pairs revealed the high contiguity MetaPlatanus with a few interspecies misassemblies. For published human gut data with nanopore reads from potable sequencers, MetaPlatanus assembled many biologically important elements, such as coding genes, gene clusters, viral sequences, and over-half bacterial genomes. In the benchmark with published human saliva data with high-throughput nanopore reads, the superiority of MetaPlatanus was considerably more evident. We found that some high-abundance bacterial genomes were assembled only by MetaPlatanus as near-complete. Furthermore, MetaPlatanus can circumvent the limitations of highly fragmented assemblies and frequent interspecies misassembles obtained by the other tools. Overall, the study demonstrates that MetaPlatanus could be an effective approach for exploring large-scale structures in metagenomes.

RevDate: 2021-09-27

Karlicki M, Antonowicz S, A Karnkowska (2021)

Tiara: Deep learning-based classification system for eukaryotic sequences.

Bioinformatics (Oxford, England) pii:6375939 [Epub ahead of print].

MOTIVATION: With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step towards a better understanding of eukaryotic diversity.

RESULTS: We developed Tiara, a deep-learning-based approach for the identification of eukaryotic sequences in the metagenomic datasets. Its two-step classification process enables the classification of nuclear and organellar eukaryotic fractions and subsequently divides organellar sequences into plastidial and mitochondrial. Using the test dataset, we have shown that Tiara performed similarly to EukRep for prokaryotes classification and outperformed it for eukaryotes classification with lower calculation time. In the tests on the real data, Tiara performed better than EukRep in analysing the small dataset representing eukaryotic cell microbiome and large dataset from the pelagic zone of oceans. Tiara is also the only available tool correctly classifying organellar sequences, which was confirmed by the recovery of nearly complete plastid and mitochondrial genomes from the test data and real metagenomic data.

AVAILABILITY: Tiara is implemented in python 3.8, available at https://github.com/ibe-uw/tiara and tested on Unix-based systems. It is released under an open-source MIT license and documentation is available at https://ibe-uw.github.io/tiara. Version 1.0.1 of Tiara has been used for all benchmarks.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2021-09-27

Ettinger CL, Byrne FJ, Collin MA, et al (2021)

Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease.

G3 (Bethesda, Md.), 11(10):.

Homalodisca vitripennis (Hemiptera: Cicadellidae), known as the glassy-winged sharpshooter, is a xylem feeding leafhopper and an important agricultural pest as a vector of Xylella fastidiosa, which causes Pierce's disease in grapes and a variety of other scorch diseases. The current H. vitripennis reference genome from the Baylor College of Medicine's i5k pilot project is a 1.4-Gb assembly with 110,000 scaffolds, which still has significant gaps making identification of genes difficult. To improve on this effort, we used a combination of Oxford Nanopore long-read sequencing technology combined with Illumina sequencing reads to generate a better assembly and first-pass annotation of the whole genome sequence of a wild-caught Californian (Tulare County) individual of H. vitripennis. The improved reference genome assembly for H. vitripennis is 1.93-Gb in length (21,254 scaffolds, N50 = 650 Mb, BUSCO completeness = 94.3%), with 33.06% of the genome masked as repetitive. In total, 108,762 gene models were predicted including 98,296 protein-coding genes and 10,466 tRNA genes. As an additional community resource, we identified 27 orthologous candidate genes of interest for future experimental work including phenotypic marker genes like white. Furthermore, as part of the assembly process, we generated four endosymbiont metagenome-assembled genomes, including a high-quality near complete 1.7-Mb Wolbachia sp. genome (1 scaffold, CheckM completeness = 99.4%). The improved genome assembly and annotation for H. vitripennis, curated set of candidate genes, and endosymbiont MAGs will be invaluable resources for future research of H. vitripennis.

RevDate: 2021-09-27

Zeng S, Yan WQ, Wu XM, et al (2021)

Case Report: Diagnosis of Klebsiella pneumoniae Invasive Liver Abscess Syndrome With Purulent Meningitis in a Patient From Pathogen to Lesions.

Frontiers in medicine, 8:714916.

As a determinant human pathogen, Klebsiella pneumoniae is known to cause rare K. pneumoniae liver abscess syndrome (KLAS) which was more common in Asia in early-stage and reported increasingly outside Asia now. Patients with KLAS who have septic metastatic ocular or central nervous system (CNS) lesions are associated with high morbidity and mortality. Relatively infrequent adult community-acquired K. pneumoniae meningitis have been documented and most were with poor prognosis. In this paper, we reported a case of KLAS presenting purulent meningitis as disease onset. While negative results were obtained in the bacterial culture of CSF, blood, or liver pus, metagenomic next-generation sequencing (mNGS) of CSF, and blood samples which were synchronously performed demonstrated Klebsiella pneumoniae as the pathogenic microorganism (13,470 and 5,318 unique reads, respectively). The ultimately cured patient benefited from rapid pathogen diagnosis, early percutaneous drainage of the abscess, and prompt appropriate antibiotic administration. Our case highlights the importance of clinicians using mNGS for early pathogen diagnosis of this disease.

RevDate: 2021-09-27

Yu J, Zhang H, Chen L, et al (2021)

Disease-Associated Gut Microbiota Reduces the Profile of Secondary Bile Acids in Pediatric Nonalcoholic Fatty Liver Disease.

Frontiers in cellular and infection microbiology, 11:698852.

Children with nonalcoholic fatty liver disease (NAFLD) display an altered gut microbiota compared with healthy children. However, little is known about the fecal bile acid profiles and their association with gut microbiota dysbiosis in pediatric NAFLD. A total of 68 children were enrolled in this study, including 32 NAFLD patients and 36 healthy children. Fecal samples were collected and analyzed by metagenomic sequencing to determine the changes in the gut microbiota of children with NAFLD, and an ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) system was used to quantify the concentrations of primary and secondary bile acids. The associations between the gut microbiota and concentrations of primary and secondary bile acids in the fecal samples were then analyzed. We found that children with NAFLD exhibited reduced levels of secondary bile acids and alterations in bile acid biotransforming-related bacteria in the feces. Notably, the decrease in Eubacterium and Ruminococcaceae bacteria, which express bile salt hydrolase and 7α-dehydroxylase, was significantly positively correlated with the level of fecal lithocholic acid (LCA). However, the level of fecal LCA was negatively associated with the abundance of the potential pathogen Escherichia coli that was enriched in children with NAFLD. Pediatric NAFLD is characterized by an altered profile of gut microbiota and fecal bile acids. This study demonstrates that the disease-associated gut microbiota is linked with decreased concentrations of secondary bile acids in the feces. The disease-associated gut microbiota likely inhibits the conversion of primary to secondary bile acids.

RevDate: 2021-09-27

Zheng Y, Qiu X, Wang T, et al (2021)

The Diagnostic Value of Metagenomic Next-Generation Sequencing in Lower Respiratory Tract Infection.

Frontiers in cellular and infection microbiology, 11:694756.

Lower respiratory tract infections are associated with high morbidity and mortality and significant clinical harm. Due to the limited ability of traditional pathogen detection methods, anti-infective therapy is mostly empirical. Therefore, it is difficult to adopt targeted drug therapy. In recent years, metagenomic next-generation sequencing (mNGS) technology has provided a promising means for pathogen-specific diagnosis and updated the diagnostic strategy for lower respiratory tract infections. This article reviews the diagnostic value of mNGS for lower respiratory tract infections, the impact of different sampling methods on the detection efficiency of mNGS, and current technical difficulties in the clinical application of mNGS.

RevDate: 2021-09-27

Oh KY, Lee S, Lee MS, et al (2021)

Composition of Vaginal Microbiota in Pregnant Women With Aerobic Vaginitis.

Frontiers in cellular and infection microbiology, 11:677648.

Vaginal dysbiosis, such as bacterial vaginosis (BV) and aerobic vaginitis (AV), is an important cause of premature birth in pregnant women. However, there is very little research on vaginal microbial distribution in AV compared to that in BV. This study aimed to analyze the composition of the vaginal microbiota of pregnant women with AV using microbial community analysis and identify the causative organism using each criterion of the AV scoring system. Also, we compared the quantification of aerobic bacteria using quantitative polymerase chain reaction (qPCR) and their relative abundances (RA) using metagenomics. This prospective case-control study included 228 pregnant Korean women from our previous study. A wet mount test was conducted on 159 women to diagnose AV using the AV scoring system. Vaginal samples were analyzed using metagenomics, Gram staining for Nugent score determination, conventional culture, and qPCR for Staphylococcus spp., Streptococcus spp., and Enterobacteriaceae. The relative abundances (RAs) of eleven species showed significant differences among the three groups (Normal flora (NF), mild AV, and moderate AV). Three species including Lactobacillus crispatus were significantly lower in the AV groups than in the NF group, while eight species were higher in the AV groups, particularly moderate AV. The decrease in the RA of L. crispatus was common in three criteria of the AV scoring system (Lactobacillary, WBC, and background flora grades), while it did not show a significant difference among the three grade groups of the toxic leukocyte criterion. Also, the RAs of anaerobes, such as Gardnerella and Megasphaera, were higher in the AV groups, particularly moderate AV, while the RAs of aerobes were very low (RA < 0.01). Therefore, qPCR was performed for aerobes (Staphylococcus spp., Streptococcus spp., and Enterobacteriaceae); however, their quantification did not show a higher level in the AV groups when compared to that in the NF group. Therefore, AV might be affected by the RA of Lactobacillus spp. and the main anaerobes, such as Gardnerella spp. Activation of leukocytes under specific conditions might convert them to toxic leukocytes, despite high levels of L. crispatus. Thus, the pathogenesis of AV can be evaluated under such conditions.

RevDate: 2021-09-27

Shi Q, Zhang J, Wang J, et al (2021)

Homologous Escherichia coli Identified in Cerebrospinal Fluid and Bloodstream.

Frontiers in cellular and infection microbiology, 11:674235.

Background: Escherichia coli is an opportunistic bacterium that causes a wide range of diseases, such as bloodstream infection and central nervous system infection. The traditional culture-based method to detect E. coli usually takes more than 2 days. The object of this study is to explore the value of metagenomic next-generation sequencing (mNGS) in identifying E. coli from human cerebrospinal fluid. In addition, we investigated the infection source of E. coli through whole genome sequencing and phylogenetic analysis.

Methods: We combined a clinical example to analyze the function of mNGS in pathogen detection from cerebrospinal fluid. NextSeq 550Dx platform was applied for mNGS. Next, whole genome sequencing was performed to obtain the genomic characterization of E. coli. Furthermore, we screened 20 E. coli strains from the National Center for Biotechnology Information and conducted a phylogenetic analysis.

Results: A middle-aged patient who attended our hospital was diagnosed with craniopharyngioma and received surgery. The patient had recurrent fever and persistent lethargy after surgery. Cerebrospinal fluid culture firstly failed to grow the bacteria. Next the cerebrospinal fluid sample was detected by mNGS and the sequence readings of E. coli were identified. Later, E. coli was reported via the second cerebrospinal fluid culture, certifying the result of mNGS. Moreover, we also cultured carbapenem-resistant E. coli from the patient's bloodstream. Through whole genome sequencing and phylogenetic analysis, we found that the E. coli isolated from cerebrospinal fluid and the bloodstream was 100% homologous, indicating the E. coli central nervous system infection was originated from the bloodstream.

Conclusion: Metagenomic next-generation sequencing is a valuable tool to identify the pathogens from cerebrospinal fluid, and seeking the infection source is of great significance in clinical diagnosis and treatment. Furthermore, carbapenem-resistant E. coli is a serious problem as the cause of bloodstream infection and central nervous system infection, and effective and adequate measures to prevent and control the present circumstance are urgent.

RevDate: 2021-09-27

Kumar A, Mukhia S, R Kumar (2021)

Industrial applications of cold-adapted enzymes: challenges, innovations and future perspective.

3 Biotech, 11(10):426.

Extreme cold environments are potential reservoirs of microorganisms producing unique and novel enzymes in response to environmental stress conditions. Such cold-adapted enzymes prove to be valuable tools in industrial biotechnology to meet the increasing demand for efficient biocatalysts. The inherent properties like high catalytic activity at low temperature, high specific activity and low activation energy make the cold-adapted enzymes well suited for application in various industries. The interest in this group of enzymes is expanding as they are the preferred alternatives to harsh chemical synthesis owing to their biodegradable and non-toxic nature. Irrespective of the multitude of applications, the use of cold-adapted enzymes at the industrial level is still limited. The current review presents the unique adaptive features and the role of cold-adapted enzymes in major industries like food, detergents, molecular biology and bioremediation. The review highlights the significance of omics technology i.e., metagenomics, metatranscriptomics and metaproteomics in enzyme bioprospection from extreme environments. It further points out the challenges in using cold-adapted enzymes at the industrial level and the innovations associated with novel enzyme prospection strategies. Documentations on cold-adapted enzymes and their applications are abundant; however, reports on the role of omics tools in exploring cold-adapted enzymes are still scarce. So, the review covers the aspect concerning the novel techniques for enzyme discovery from nature.

RevDate: 2021-09-27

Cao R, Ren Q, Luo J, et al (2021)

Analysis of Microorganism Diversity in Haemaphysalis longicornis From Shaanxi, China, Based on Metagenomic Sequencing.

Frontiers in genetics, 12:723773.

Ticks are dangerous ectoparasites of humans and animals, as they are important disease vectors and serve as hosts for various microorganisms (including a variety of pathogenic microorganisms). Diverse microbial populations coexist within the tick body. Metagenomic next-generation sequencing (mNGS) has been suggested to be useful for rapidly and accurately obtaining microorganism abundance and diversity data. In this study, we performed mNGS to analyze the microbial diversity of Haemaphysalis longicornis from Baoji, Shaanxi, China, with the Illumina HiSeq platform. We identified 189 microbial genera (and 284 species) from ticks in the region; the identified taxa included Anaplasma spp., Rickettsia spp., Ehrlichia spp., and other important tick-borne pathogens at the genus level as well as symbiotic microorganisms such as Wolbachia spp., and Candidatus Entotheonella. The results of this study provide insights into possible tick-borne diseases and reveal new tick-borne pathogens in this region. Additionally, valuable information for the biological control of ticks is provided. In conclusion, this study provides reference data for guiding the development of prevention and control strategies targeting ticks and tick-borne diseases in the region, which can improve the effectiveness of tick and tick-borne disease control.

RevDate: 2021-09-27

Perry MR, Lepper HC, McNally L, et al (2021)

Secrets of the Hospital Underbelly: Patterns of Abundance of Antimicrobial Resistance Genes in Hospital Wastewater Vary by Specific Antimicrobial and Bacterial Family.

Frontiers in microbiology, 12:703560.

Background: Hospital wastewater is a major source of antimicrobial resistance (AMR) outflow into the environment. This study uses metagenomics to study how hospital clinical activity impacts antimicrobial resistance genes (ARGs) abundances in hospital wastewater. Methods: Sewage was collected over a 24-h period from multiple wastewater collection points (CPs) representing different specialties within a tertiary hospital site and simultaneously from community sewage works. High throughput shotgun sequencing was performed using Illumina HiSeq4000. ARG abundances were correlated to hospital antimicrobial usage (AMU), data on clinical activity and resistance prevalence in clinical isolates. Results: Microbiota and ARG composition varied between CPs and overall ARG abundance was higher in hospital wastewater than in community influent. ARG and microbiota compositions were correlated (Procrustes analysis, p=0.014). Total antimicrobial usage was not associated with higher ARG abundance in wastewater. However, there was a small positive association between resistance genes and antimicrobial usage matched to ARG phenotype (IRR 1.11, CI 1.06-1.16, p<0.001). Furthermore, analyzing carbapenem and vancomycin resistance separately indicated that counts of ARGs to these antimicrobials were positively associated with their increased usage [carbapenem rate ratio (RR) 1.91, 95% CI 1.01-3.72, p=0.07, and vancomycin RR 10.25, CI 2.32-49.10, p<0.01]. Overall, ARG abundance within hospital wastewater did not reflect resistance patterns in clinical isolates from concurrent hospital inpatients. However, for clinical isolates of the family Enterococcaceae and Staphylococcaceae, there was a positive relationship with wastewater ARG abundance [odds ratio (OR) 1.62, CI 1.33-2.00, p<0.001, and OR 1.65, CI 1.21-2.30, p=0.006 respectively]. Conclusion: We found that the relationship between hospital wastewater ARGs and antimicrobial usage or clinical isolate resistance varies by specific antimicrobial and bacterial family studied. One explanation, we consider is that relationships observed from multiple departments within a single hospital site will be detectable only for ARGs against parenteral antimicrobials uniquely used in the hospital setting. Our work highlights that using metagenomics to identify the full range of ARGs in hospital wastewater is a useful surveillance tool to monitor hospital ARG carriage and outflow and guide environmental policy on AMR.

RevDate: 2021-09-27

Busing JD, Buendia M, Choksi Y, et al (2021)

Microbiome in Eosinophilic Esophagitis-Metagenomic, Metatranscriptomic, and Metabolomic Changes: A Systematic Review.

Frontiers in physiology, 12:731034.

Background: Our understanding of human gut microbiota has expanded in recent years with the introduction of high-throughput sequencing methods. These technologies allow for the study of metagenomic, metatranscriptomic, and metabolomic bacterial alterations as they relate to human disease. Work in this area has described the human gut microbiome in both healthy individuals and those with chronic gastrointestinal diseases, such as eosinophilic esophagitis (EoE). Objectives: A systematic review of the current available literature on metagenomic, metatranscriptomic, and metabolomic changes in EoE was performed. Methods: This review was performed following the PRISMA guidelines for reporting systematic reviews and meta-analyses. All relevant publications up to March 2021 were retrieved using the search engines PubMed, Google Scholar, and Web of Science. They were then extracted, assessed, and reviewed. Only original studies published in English were included. Results: A total of 46 potential manuscripts were identified for review. Twelve met criteria for further review based on relevance screening and 9 met criteria for inclusion, including 6 studies describing the microbiome in EoE and 3 detailing metabolomic/tissue biochemistry alterations in EoE. No published studies examined metatranscriptomic changes. Samples for microbiome analysis were obtained via esophageal biopsy (n = 3), esophageal string test (n = 1), salivary sampling (n = 1), or stool specimen (n = 1). Samples analyzing tissue biochemistry were obtained via esophageal biopsy (n = 2) and blood plasma (n = 1). There were notable differences in how samples were collected and analyzed. Metabolomic and tissue biochemical alterations were described using Raman spectroscopy, which demonstrated distinct differences in the spectral intensities of glycogen, lipid, and protein content compared to controls. Finally, research in proteomics identified an increase in the pro-fibrotic protein thrombospondin-1 in patients with EoE compared with controls. Conclusions: While there are notable changes in the microbiome, these differ with the collection technique and method of analysis utilized. Techniques characterizing metabolomics and tissue biochemistry are now being utilized to further study patients with EoE. The lack of published data related to the human microbiome, metagenome, metatranscriptome, and metabolome in patients with EoE highlights the need for further research in these areas.

RevDate: 2021-09-27

Ikemura T, Iwasaki Y, Wada K, et al (2021)

AI for the collective analysis of a massive number of genome sequences: various examples from the small genome of pandemic SARS-CoV-2 to the human genome.

Genes & genetic systems [Epub ahead of print].

In genetics and related fields, huge amounts of data, such as genome sequences, are accumulating, and the use of artificial intelligence (AI) suitable for big data analysis has become increasingly important. Unsupervised AI that can reveal novel knowledge from big data without prior knowledge or particular models is highly desirable for analyses of genome sequences, particularly for obtaining unexpected insights. We have developed a batch-learning self-organizing map (BLSOM) for oligonucleotide compositions that can reveal various novel genome characteristics. Here, we explain the data mining by the BLSOM: an unsupervised AI. As a specific target, we first selected SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) because a large number of viral genome sequences have been accumulated via worldwide efforts. We analyzed more than 0.6 million sequences collected primarily in the first year of the pandemic. BLSOMs for short oligonucleotides (e.g., 4-6-mers) allowed separation into known clades, but longer oligonucleotides further increased the separation ability and revealed subgrouping within known clades. In the case of 15-mers, there is mostly one copy in the genome; thus, 15-mers that appeared after the epidemic started could be connected to mutations, and the BLSOM for 15-mers revealed the mutations that contributed to separation into known clades and their subgroups. After introducing the detailed methodological strategies, we explain BLSOMs for various topics, such as the tetranucleotide BLSOM for over 5 million 5-kb fragment sequences derived from almost all microorganisms currently available and its use in metagenome studies. We also explain BLSOMs for various eukaryotes, including fishes, frogs and Drosophila species, and found a high separation ability among closely related species. When analyzing the human genome, we found enrichments in transcription factor-binding sequences in centromeric and pericentromeric heterochromatin regions. The tDNAs (tRNA genes) could be separated according to their corresponding amino acid.

RevDate: 2021-09-26

Shen L, Tian XJ, Liang RZ, et al (2021)

[Clinical and imaging features of Chlamydia psittaci pneumonia: an analysis of 48 cases in China].

Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases, 44(10):886-891.

Objective: To explore the clinical characteristics, imaging findings, laboratory tests and treatment strategies for Chlamydia psittaci pneumonia. Methods: From January 1, 2019 to January 20, 2021, 48 cases of Psittacosis from 11 hospitals in China were diagnosed via metagenomic next-generation sequencing(mNGS). The data of all patients on occupational history, clinical manifestations, laboratory tests, chest computed tomography(CT)findings, treatment outcomes and prognosis were retrospectively analyzed. Results: Among the 48 patients, there were 29 males and 19 females, with a mean age of (57.1±10.3) years. Thirty patients had a confirmed history of exposure to poultry. The onset to admission interval was (6.5±3.2) days, and hospital stay was (12.4±4.8) days. Clinical manifestations included fever (100%, 48/48), relative bradycardia (71%, 34/48), cough (54.2%, 26/48), sputum (27.1%, 13/48), fatigue (16.7%, 8/48), headache and delirium (20.8%, 9/48), and gastrointestinal symptoms (16.7%, 8/48). Laboratory data showed that white blood cells were (8.0±3.8)×109/L, and the proportion of neutrophils increased in 44 patients. The level of C-reactive protein was (155.3±74.1)mg/L, and that of procalcitonin (PCT)in 59.5% of patients was more than 0.5 μg/L. Percentages of patients with increased lactate dehydrogenase and creatine kinase were 82.9% and 45.2%, respectively. Chest CT scans showed unilateral lung involvement in 34 cases(70.8%) and single lobe involvement in 27 cases(56.3%).The most common imaging change was consolidation, with 38 cases (79.2%) showing lobar consolidation. In terms of treatment, 25 patients were treated with fluoroquinolones alone, 6 patients with doxycycline alone, and 13 patients with combined treatment. The combined-treatment group and the doxycycline alone group were similar in the course of defervescence. The combined treatment group and the doxycycline alone group were both superior to the fluoroquinolones alone group. However, 11 patients were admitted to ICU, all of them received artificial ventilation, and 5 cases developed shock, and one died. Conclusions: Chlamydia psittaci pneumonia is an animal-derived infectious disease with unique features in clinical symptoms, laboratory tests and chest imaging. Appropriate treatment is able to significantly shorten the course of disease and improve the prognosis.

RevDate: 2021-09-26

Gómez-Albarrán C, Melguizo C, Patiño B, et al (2021)

Diversity of Mycobiota in Spanish Grape Berries and Selection of Hanseniaspora uvarum U1 to Prevent Mycotoxin Contamination.

Toxins, 13(9): pii:toxins13090649.

The occurrence of mycotoxins on grapes poses a high risk for food safety; thus, it is necessary to implement effective prevention methods. In this work, a metagenomic approach revealed the presence of important mycotoxigenic fungi in grape berries, including Aspergillus flavus, Aspergillus niger aggregate species, or Aspergillus section Circumdati. However, A. carbonarius was not detected in any sample. One of the samples was not contaminated by any mycotoxigenic species, and, therefore, it was selected for the isolation of potential biocontrol agents. In this context, Hanseniaspora uvarum U1 was selected for biocontrol in vitro assays. The results showed that this yeast is able to reduce the growth rate of the main ochratoxigenic and aflatoxigenic Aspergillus spp. occurring on grapes. Moreover, H. uvarum U1 seems to be an effective detoxifying agent for aflatoxin B1 and ochratoxin A, probably mediated by the mechanisms of adsorption to the cell wall and other active mechanisms. Therefore, H. uvarum U1 should be considered in an integrated approach to preventing AFB1 and OTA in grapes due to its potential as a biocontrol and detoxifying agent.

RevDate: 2021-09-26

Chiu K, Bashir ST, Gao L, et al (2021)

Subacute Exposure to an Environmentally Relevant Dose of Di-(2-ethylhexyl) Phthalate during Gestation Alters the Cecal Microbiome, but Not Pregnancy Outcomes in Mice.

Toxics, 9(9): pii:toxics9090215.

Di-2-ethylhexyl phthalate (DEHP) is a plasticizer commonly found in polyvinyl chloride, medical equipment, and food packaging. DEHP has been shown to target the reproductive system and alter the gut microbiome in humans and experimental animals. However, very little is known about the impact of DEHP-induced microbiome changes and its effects during pregnancy. Thus, the objective of this study was to investigate the effects of DEHP exposure during pregnancy on the cecal microbiome and pregnancy outcomes. Specifically, this study tested the hypothesis that subacute exposure to DEHP during pregnancy alters the cecal microbiome in pregnant mice, leading to changes in birth outcomes. To test this hypothesis, pregnant dams were orally exposed to corn oil vehicle or 20 µg/kg/day DEHP for 10 days and euthanized 21 days after their last dose. Cecal contents were collected for 16S Illumina and shotgun metagenomic sequencing. Fertility studies were also conducted to examine whether DEHP exposure impacted birth outcomes. Subacute exposure to environmentally relevant doses of DEHP in pregnant dams significantly increased alpha diversity and significantly altered beta diversity. Furthermore, DEHP exposure during pregnancy significantly increased the relative abundance of Bacteroidetes and decreased the relative abundance of Firmicutes and Deferribacteres compared with controls. The affected taxonomic families included Deferribacteraceae, Lachnospiraceae, and Mucisprillum. In addition to changes in the gut microbiota, DEHP exposure significantly altered 14 functional pathways compared with the control. Finally, DEHP exposure did not significantly impact the fertility and birth outcomes compared with the control. Collectively, these data indicate that DEHP exposure during pregnancy shifts the cecal microbiome, but the shifts do not impact fertility and birth outcomes.

RevDate: 2021-09-26

Buchy P, Buisson Y, Cintra O, et al (2021)

COVID-19 pandemic: lessons learned from more than a century of pandemics and current vaccine development for pandemic control.

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases pii:S1201-9712(21)00752-9 [Epub ahead of print].

Pandemic dynamics and health care responses are markedly different during the COVID-19 pandemic than in earlier outbreaks. Compared with established infectious disease such as influenza, we currently know relatively little about the origin, reservoir, cross-species transmission and evolution of SARS-CoV-2. Health care services, drug availability, laboratory testing, research capacity and global governance are more advanced than during 20th century pandemics, although COVID-19 has highlighted significant gaps. The risk of zoonotic transmission and an associated new pandemic is rising substantially. COVID-19 vaccine development has been done at unprecedented speed, with the usual sequential steps done in parallel. The pandemic has illustrated the feasibility of this approach and the benefits of a globally coordinated response and infrastructure. Some of the COVID-19 vaccines recently developed or currently in development might offer flexibility or sufficiently broad protection to swiftly respond to antigenic drift or emergence of new coronaviruses. Yet many challenges remain, including the large-scale production of sufficient quantity of vaccines, delivery of vaccines to all countries and ensuring vaccination of relevant age groups. This wide vaccine technology approach will be best employed in tandem with active surveillance for emerging variants or new pathogens using antigen mapping, metagenomics and next generation sequencing.

RevDate: 2021-09-26

Park SY, Faraci G, Nanda S, et al (2021)

Gut microbiome in people living with HIV is associated with impaired thiamine and folate syntheses.

Microbial pathogenesis pii:S0882-4010(21)00483-6 [Epub ahead of print].

People living with HIV have a high incidence of cardiovascular and neurological diseases as comorbid disorders that are commonly linked to inflammation. While microbial translocation can augment inflammation during HIV infection, functional microbiome shifts that may increase pro-inflammatory responses have not been fully characterized. In addition, defining HIV-induced microbiome changes has been complicated by high variability among individuals. Here we conducted functional annotation of previously-published 16 S ribosomal RNA gene sequences of 305 HIV positive and 249 negative individuals, with adjustment for geographic region, sex, sexual behavior, and age. Metagenome profiles were inferred from these individuals'16 S data. HIV infection was associated with impaired microbial vitamin B synthesis; around half of the gene families in thiamine and folate biosynthesis pathways were significantly less abundant in the HIV positive group than the negative control. These results are consistent with the high prevalence of thiamine and folate deficiencies in HIV infections. These HIV-induced microbiota shifts have the potential to influence cardiovascular and neurocognitive diseases, given the documented associations between B-vitamin deficiencies, inflammation, and these diseases. We also observed that most essential amino acid biosynthesis pathways were downregulated in the microbiome of HIV-infected individuals. Microbial vitamin B and amino acid synthesis pathways were not significantly recovered by antiretroviral treatment when we compared 262 ART positive and 184 ART negative individuals. Our meta-analysis provides a new outlook for understanding vitamin B and amino acid deficiencies in HIV patients, suggesting that interventions for reversing HIV-induced microbiome shifts may aid in lessening the burdens of HIV comorbidities.

RevDate: 2021-09-26

Turjeman S, O Koren (2021)

ARGuing the case for (or against) probiotics.

Trends in microbiology pii:S0966-842X(21)00215-8 [Epub ahead of print].

Antibiotic resistance is one of the leading medical challenges with which we are currently faced. Antibiotics, while powerful medical tools, also wreak havoc on the endogenous microbiota. Many believe that probiotics can restore the microbiota following antibiotic treatment and might even suppress the spread of antibiotic-resistance genes, but a recent study (Montassier et al.) suggests otherwise.

RevDate: 2021-09-27
CmpDate: 2021-09-27

Garcia-Lopez E, Alcazar P, C Cid (2021)

Identification of Biomolecules Involved in the Adaptation to the Environment of Cold-Loving Microorganisms and Metabolic Pathways for Their Production.

Biomolecules, 11(8):.

Cold-loving microorganisms of all three domains of life have unique and special abilities that allow them to live in harsh environments. They have acquired structural and molecular mechanisms of adaptation to the cold that include the production of anti-freeze proteins, carbohydrate-based extracellular polymeric substances and lipids which serve as cryo- and osmoprotectants by maintaining the fluidity of their membranes. They also produce a wide diversity of pigmented molecules to obtain energy, carry out photosynthesis, increase their resistance to stress and provide them with ultraviolet light protection. Recently developed analytical techniques have been applied as high-throughoutput technologies for function discovery and for reconstructing functional networks in psychrophiles. Among them, omics deserve special mention, such as genomics, transcriptomics, proteomics, glycomics, lipidomics and metabolomics. These techniques have allowed the identification of microorganisms and the study of their biogeochemical activities. They have also made it possible to infer their metabolic capacities and identify the biomolecules that are parts of their structures or that they secrete into the environment, which can be useful in various fields of biotechnology. This Review summarizes current knowledge on psychrophiles as sources of biomolecules and the metabolic pathways for their production. New strategies and next-generation approaches are needed to increase the chances of discovering new biomolecules.

RevDate: 2021-09-27
CmpDate: 2021-09-27

Neafsey DE, Taylor AR, BL MacInnis (2021)

Advances and opportunities in malaria population genomics.

Nature reviews. Genetics, 22(8):502-517.

Almost 20 years have passed since the first reference genome assemblies were published for Plasmodium falciparum, the deadliest malaria parasite, and Anopheles gambiae, the most important mosquito vector of malaria in sub-Saharan Africa. Reference genomes now exist for all human malaria parasites and nearly half of the ~40 important vectors around the world. As a foundation for genetic diversity studies, these reference genomes have helped advance our understanding of basic disease biology and drug and insecticide resistance, and have informed vaccine development efforts. Population genomic data are increasingly being used to guide our understanding of malaria epidemiology, for example by assessing connectivity between populations and the efficacy of parasite and vector interventions. The potential value of these applications to malaria control strategies, together with the increasing diversity of genomic data types and contexts in which data are being generated, raise both opportunities and challenges in the field. This Review discusses advances in malaria genomics and explores how population genomic data could be harnessed to further support global disease control efforts.

RevDate: 2021-09-27
CmpDate: 2021-09-27

Choi DH, Park J, Choi JK, et al (2020)

Association between the microbiomes of tonsil and saliva samples isolated from pediatric patients subjected to tonsillectomy for the treatment of tonsillar hyperplasia.

Experimental & molecular medicine, 52(9):1564-1573.

Oral microbes have the capacity to spread throughout the gastrointestinal system and are strongly associated with multiple diseases. Given that tonsils are located between the oral cavity and the laryngopharynx at the gateway of the alimentary and respiratory tracts, tonsillar tissue may also be affected by microbiota from both the oral cavity (saliva) and the alimentary tract. Here, we analyzed the distribution and association of the microbial communities in the saliva and tonsils of Korean children subjected to tonsillectomy because of tonsil hyperplasia (n = 29). The microbiome profiles of saliva and tonsils were established via 16S rRNA gene sequencing. Based on the alpha diversity indices, the microbial communities of the two groups showed high similarities. According to Spearman's ranking correlation analysis, the distribution of Treponema, the causative bacterium of periodontitis, in saliva and tonsils was found to have a significant positive correlation. Two representative microbes, Prevotella in saliva and Alloprevotella in tonsils, were negatively correlated, while Treponema 2 showed a strong positive correlation between saliva and tonsils. Taken together, strong similarities in the microbial communities of the tonsils and saliva are evident in terms of diversity and composition. The saliva microbiome is expected to significantly affect the tonsil microbiome. Furthermore, we suggest that our study creates an opportunity for tonsillar microbiome research to facilitate the development of novel microbiome-based therapeutic strategies.

RevDate: 2021-09-25

Hakim JA, Green GBH, Watts SA, et al (2021)

Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics.

Current issues in molecular biology, 43(2):978-995 pii:cimb43020070.

This paper describes the microbial community composition and genes for key metabolic genes, particularly the nitrogen fixation of the mucous-enveloped gut digesta of green (Lytechinus variegatus) and purple (Strongylocentrotus purpuratus) sea urchins by using the shotgun metagenomics approach. Both green and purple urchins showed high relative abundances of Gammaproteobacteria at 30% and 60%, respectively. However, Alphaproteobacteria in the green urchins had higher relative abundances (20%) than the purple urchins (2%). At the genus level, Vibrio was dominant in both green (~9%) and purple (~10%) urchins, whereas Psychromonas was prevalent only in purple urchins (~24%). An enrichment of Roseobacter and Ruegeria was found in the green urchins, whereas purple urchins revealed a higher abundance of Shewanella, Photobacterium, and Bacteroides (q-value < 0.01). Analysis of key metabolic genes at the KEGG-Level-2 categories revealed genes for amino acids (~20%), nucleotides (~5%), cofactors and vitamins (~6%), energy (~5%), carbohydrates (~13%) metabolisms, and an abundance of genes for assimilatory nitrogen reduction pathway in both urchins. Overall, the results from this study revealed the differences in the microbial community and genes designated for the metabolic processes in the nutrient-rich sea urchin gut digesta, suggesting their likely importance to the host and their environment.

RevDate: 2021-09-25

Ploszaj T, Brauncajs M, Traczyk-Borszynska M, et al (2021)

The value of bacterial metagenomic analysis in post-surgical examination of gallstones.

Archives of microbiology [Epub ahead of print].

Gallstone disease is one of the most common causes of hospitalization for gastrointestinal diseases in the world. Recent studies have examined the presence of bacteria in the formation of stones. Our main goal was to determine the overall composition of gallstone microflora. Gallstones were obtained from 24 patients during laparoscopic cholecystectomy from which DNA were extracted. Composition of bacterial flora was evaluated on 16 s rDNA sequencing technique. In the vast majority of samples, bacteria were present, and four groups could be differentiated regarding the flora. Overall composition shows that 87% of the stones were cholesterol/mixed type of gallstone. Additionally, potentially harmful microorganisms (Streptococcus, Clostridium and Kocuria) that could cause post-surgery complications were identified in several patients. The obtained results indicate that this technique may be useful in analyzing the type of stones and in pinpointing the presence of pathogenic bacteria.

RevDate: 2021-09-25

Kumpitsch C, Fischmeister FPS, Mahnert A, et al (2021)

Reduced B12 uptake and increased gastrointestinal formate are associated with archaeome-mediated breath methane emission in humans.

Microbiome, 9(1):193.

BACKGROUND: Methane is an end product of microbial fermentation in the human gastrointestinal tract. This gas is solely produced by an archaeal subpopulation of the human microbiome. Increased methane production has been associated with abdominal pain, bloating, constipation, IBD, CRC or other conditions. Twenty percent of the (healthy) Western populations innately exhale substantially higher amounts (>5 ppm) of this gas. The underlying principle for differential methane emission and its effect on human health is not sufficiently understood.

RESULTS: We assessed the breath methane content, the gastrointestinal microbiome, its function and metabolome, and dietary intake of one-hundred healthy young adults (female: n = 52, male: n = 48; mean age =24.1). On the basis of the amount of methane emitted, participants were grouped into high methane emitters (CH4 breath content 5-75 ppm) and low emitters (CH4 < 5 ppm). The microbiomes of high methane emitters were characterized by a 1000-fold increase in Methanobrevibacter smithii. This archaeon co-occurred with a bacterial community specialized on dietary fibre degradation, which included members of Ruminococcaceae and Christensenellaceae. As confirmed by metagenomics and metabolomics, the biology of high methane producers was further characterized by increased formate and acetate levels in the gut. These metabolites were strongly correlated with dietary habits, such as vitamin, fat and fibre intake, and microbiome function, altogether driving archaeal methanogenesis.

CONCLUSIONS: This study enlightens the complex, multi-level interplay of host diet, genetics and microbiome composition/function leading to two fundamentally different gastrointestinal phenotypes and identifies novel points of therapeutic action in methane-associated disorders. Video Abstract.

RevDate: 2021-09-24

Ferretti MV, Hussien RA, Ballicora MA, et al (2021)

The ADP-glucose pyrophosphorylase from Melainabacteria: A comparative study between photosynthetic and non-photosynthetic bacterial sources.

Biochimie pii:S0300-9084(21)00223-6 [Epub ahead of print].

Until recently, the cyanobacterial phylum only included oxygenic photosynthesizer members. The discovery of Melainabacteria as a group of supposed non-photosynthetic cyanobacteria asked to revisit such scenario. From metagenomic data, we were able to identify sequences encoding putative ADP-glucose pyrophosphorylases (ADP-GlcPPase) from free-living and intestinal Melainabacteria. The respective genes were de novo synthesized and over-expressed in Escherichia coli. The purified recombinant proteins from both Melainabacteria species were active as ADP-GlcPPases, exhibiting Vmax values of 2.3 (free-living) and 7.1 U/mg (intestinal). The enzymes showed similar S0.5 values (∼0.3 mM) for ATP, while the one from the intestinal source exhibited a 6-fold higher affinity toward glucose-1P. Both recombinant ADP-GlcPPases were sensitive to glucose-6P activation (A0.5-0.3 mM) and Pi and ADP inhibition (I0.5 between 0.2 and 3 mM). Interestingly, the enzymes from Melainabacteria were insensitive to 3-phosphoglycerate, which is the principal activator of ADP-GlcPPases from photosynthetic cyanobacteria. As far as we know, this is the first biochemical characterization of an active enzyme from Melainabacteria. This work contributes to a better understanding of the evolution of allosteric regulation in the ADP-GlcPPase family, which is critical for synthesizing the main reserve polysaccharide in prokaryotes (glycogen) and plants (starch). In addition, our results offer further information to discussions regarding the phylogenetic position of Melainabacteria.

RevDate: 2021-09-24

Tanaka T, Matsuno Y, Torisu T, et al (2021)

Gastric microbiota in patients with Helicobacter pylori-negative gastric MALT lymphoma.

Medicine, 100(38):e27287.

ABSTRACT: To investigate the mucosal microbiota in the stomach of patients with Helicobacter pylori-negative mucosa-associated lymphoid tissue (MALT) lymphoma by means of metagenomic analysis.Although some gastric MALT lymphomas are associated with the presence of H. pylori, other gastric MALT lymphomas occur independently of H. pylori infection. The pathogenesis of H. pylori-negative MALT lymphoma remains unclear.Mucosal biopsy specimens were collected from the gastric body from 33 MALT lymphoma patients with gastric lesions, including both H. pylori-infection naïve patients and posteradication patients, as well as 27 control participants without H. pylori infection or cancer. Subsequently, the samples were subjected to 16S rRNA gene sequencing. Quantitative insights into microbial ecology, linear discriminant analysis effect size, and phylogenetic investigation of communities by reconstruction of unobserved states softwares were used to analyze the participants' microbiota.H. pylori-negative MALT lymphoma patients had significantly lower alpha diversity (P = .04), compared with control participants. Significant differences were evident in the microbial composition (P = .04), as determined by comparison of beta diversity between the 2 groups. Taxonomic composition analysis indicated that the genera Burkholderia and Sphingomonas were significantly more abundant in MALT lymphoma patients, while the genera Prevotella and Veillonella were less abundant. Functional microbiota prediction showed that the predicted gene pathways "replication and repair," "translation," and "nucleotide metabolism" were downregulated in MALT lymphoma patients.H. pylori-negative MALT lymphoma patients exhibited altered gastric mucosal microbial compositions, suggesting that altered microbiota might be involved in the pathogenesis of H. pylori-negative MALT lymphoma.

RevDate: 2021-09-24

Fei X, Li S, Wang L, et al (2021)

Impact of light on anoxic/oxic reactors: performance, quorum sensing, and metagenomic characteristics.

Water science and technology : a journal of the International Association on Water Pollution Research, 84(6):1452-1463.

The effect of light has raised attention on wastewater treatment. However, little research has concentrated on the influences of light on activated sludge. In this study, the influences of light on the performance, quorum sensing (QS) and metagenomic characteristics of anoxic/oxic reactors were investigated. The reactor without light (AO1) showed higher total nitrogen (TN) removal (79.15 ± 1.69%) than the reactor with light (AO2) (74.54 ± 1.30%), and significant differences were observed. It was observed that light facilitated the production of protein-like and tryptophan-like substances by employing parallel factor analysis for extracellular polymeric substance (EPS), resulting in more EPS production in AO2, indicating light was beneficial to EPS production. The concentrations of N-acyl-homoserine lactones (AHLs) were various in the two reactors, so the AHLs-mediated QS behaviors in both reactors were also different. These results revealed that light significantly influenced nitrogen removal, EPS, and QS. Metagenomic analysis based on Tax4Fun demonstrated that light reduced the denitrification, stimulated the polysaccharide and protein biosynthesis pathways and down-regulated the AHLs synthesis pathway, resulting in lower TN removal, more EPS production, and lower AHLs concentrations. Based on the above, the likely mechanism was proposed for the influences of light on the reactor.

RevDate: 2021-09-25

Hinsu A, Dumadiya A, Joshi A, et al (2021)

To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere.

PeerJ, 9:e12035.

Background: Sequencing driven metagenomics studies have been instrumental in various aspects of microbiology including identification of newer taxa. While this culture-independent approach has its own merits and demerits, several studies have focussed on comparing it with traditional culture-dependent (CD) approach. However, most of these comparative studies rely on Sanger sequencing of complete 16S rRNA gene from pure culture colonies to determine the culturable bacterial diversity. This approach undercounts culturable diversity as only fewer isolates are selected, sequenced, and identified.

Methods: In this study, we have used an Illumina based partial 16S sequencing to identify all the microbes growing on the media and directly comparing with its culture-independent (CI) counterpart. Eight different media were used to target different organisms from soil. Diversity on these media were compared with their CI counterpart. The NGS data was analysed using DADA2 to provide more resolution to the data.

Results: In line with studies of similar nature, current study presented higher bacterial diversity in CI approach. However, the current study reflected that a greater number of sequence variants were missed out in CI approach as compared to number of sequence variants shared with CD approach. We observed around 322 (5.98%) ASVs (Amplicon Sequence Variants) exclusively present in CD samples while, 234 (4.35%) ASVs were shared between both approaches. Most of these 322 CD exclusive ASVs were classified as Enterobacteriaceae family and Bacillus genus, with several ASVs annotated at the species level as well, and these organisms are more commonly observed in soil and were also detected in CI approach. Furthermore, 22 genera were exclusively detected in CD samples, most of which were reported from soil and water.

RevDate: 2021-09-24

Belstrøm D, Constancias F, Drautz-Moses DI, et al (2021)

Periodontitis associates with species-specific gene expression of the oral microbiota.

NPJ biofilms and microbiomes, 7(1):76.

The purpose of the present investigation was to characterize species-specific bacterial activity of the oral microbiota in periodontitis. We tested the hypotheses that chronic inflammation, i.e., periodontitis, associates with bacterial gene expression of the oral microbiota. Oral microbial samples were collected from three oral sites-subgingival plaque, tongue, and saliva from patients with periodontitis and healthy controls. Paired metagenomics and metatranscriptomics were used to perform concomitant characterization of taxonomic composition and to determine species-specific bacterial activity as expressed by the ratio of specific messenger RNA reads to their corresponding genomic DNA reads. Here, we show the association of periodontitis with bacterial gene expression of the oral microbiota. While oral site was the main determinant of taxonomic composition as well as bacterial gene expression, periodontitis was significantly associated with a reduction of carbohydrate metabolism of the oral microbiota at three oral sites (subgingival plaque, tongue, and saliva). Data from the present study revealed the association of periodontitis with bacterial gene expression of the oral microbiota. Conditions of periodontitis was associated with bacterial activity of local subgingival plaque, but also on tongue and the salivary microbiota. Collectively, data suggest that periodontitis associates with impaired carbohydrate metabolism of the oral microbiota. Future longitudinal and interventional studies are warranted to evaluate the potential pathogenic role of impaired bacterial carbohydrate metabolism not only in periodontitis but also in other diseases with low-grade inflammation, such as type 2 diabetes mellitus.

RevDate: 2021-09-24

Wu HH, Feng LF, SY Fang (2021)

Application of metagenomic next-generation sequencing in the diagnosis of severe pneumonia caused by Chlamydia psittaci.

BMC pulmonary medicine, 21(1):300.

PURPOSE: Psittacosis is a zoonotic infectious disease caused by the transmission of the bacterium Chlamydia psittaci (C. psittaci) from birds to humans. Infections in humans mainly present as community-acquired pneumonia (CAP). However, most cases are treated without diagnostic testing, and the importance of Chlamydia psittaci infection as a cause of CAP is therefore unclear. Diagnostic tools, including culture, serologic test, and PCR-based methods, are available but prone to false negative results. Metagenomic next-generation sequencing (mNGS) has been increasingly used in the diagnosis of infectious diseases, particularly when conventional diagnostic approaches have limitation. Detection of nucleic acid sequence of C. psittaci in respiratory tract samples by metagenomic next-generation sequencing (mNGS) is effective for early diagnosis of severe C. psittaci pneumonia. Timely treatment based on tetracycline can reduce unnecessary use of antibiotics and improve prognosis of patients with severe C. psittaci pneumonia.

METHODS: Clinical data of thirteen patients with severe C. psittaci pneumonia diagnosed by mNGS were collected. Clinical manifestations, treatment and prognosis of patients were summarized.

RESULTS: The typical symptoms of pneumonia caused by C. psittaci include fever, headache, myalgia, cough, and dyspnea. In the current study, all patients met the criteria for severe C. psittaci pneumonia and received mechanical ventilation, including noninvasive mechanical ventilation (five/thirteen) and invasive mechanical ventilation (eight/thirteen). The findings showed that patients with C. psittaci pneumonia presented with normal or slightly increased leucocytes and procalcitonin, and high C-reactive protein levels. Computed tomography manifestations included consolidation of lung parenchyma, with air bronchogram and pleural effusion in some patients. mNGS analysis results were obtained within 48-72 h. Eleven patients fully recovered after targeted treatment, however, two patients died from secondary multidrug-resistant Pseudomonas aeruginosa infection.

CONCLUSIONS: The findings of the current study show that mNGS is effective in diagnosis of C. psittaci pneumonia, and has significant diagnosis value in patients with severe infection. Patients responds well to the timely use of appropriate antibiotics.

RevDate: 2021-09-23

McDaniel EA, Wahl SA, Ishii S, et al (2021)

Prospects for multi-omics in the microbial ecology of water engineering.

Water research, 205:117608 pii:S0043-1354(21)00803-4 [Epub ahead of print].

Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.

RevDate: 2021-09-23

Pérez-Sautu U, Wiley MR, Prieto K, et al (2021)

Novel viruses in hard ticks collected in the Republic of Korea unveiled by metagenomic high-throughput sequencing analysis.

Ticks and tick-borne diseases, 12(6):101820 pii:S1877-959X(21)00173-4 [Epub ahead of print].

Ticks are vectors of a wide range of zoonotic viruses of medical and veterinary importance. Recently, metagenomics studies demonstrated that they are also the source of potentially pathogenic novel viruses. During the period from 2015 to 2017, questing ticks were collected by dragging the vegetation from geographically distant locations in the Republic of Korea (ROK) and a target-independent high-throughput sequencing method was utilized to study their virome. A total of seven viruses, including six putative novel viral entities, were identified. Genomic analysis showed that the novel viruses were most closely related to members in the orders Jingchuvirales and Bunyavirales. Phylogenetic reconstruction showed that the Bunyavirales-like viruses grouped in the same clade with other viruses within the Nairovirus and Phlebovirus genera, while the novel Jingchuvirales-like virus grouped together with other viruses within the family Chuviridae. Real-time RT-PCR was used to determine the geographic distribution and prevalence of these viruses in adult ticks. These novel viruses have a wide geographic distribution in the ROK with prevalences ranging from 2% to 18%. Our study expands the knowledge about the composition of the tick virome and highlights the wide diversity of viruses they harbor in the ROK. The discovery of novel viruses associated with ticks in the ROK highlights the need for an active tick-borne disease surveillance program to identify possible reservoirs of putative novel human pathogens.

RevDate: 2021-09-26

Devrim-Lanpir A, İlktaç HY, Wirnitzer K, et al (2021)

Vegan vs. omnivore diets paradox: A whole-metagenomic approach for defining metabolic networks during the race in ultra-marathoners- a before and after study design.

PloS one, 16(9):e0255952.

BACKGROUND: The effect of vegan diets on metabolic processes in the body is still controversial in ultra endurance athletes. The study aims to determine gut microbiome adaptation to extreme exercise according to vegan or omnivore diet consumed in ultra-marathoners. We also seek to evaluate long-term vegan diets' effects on redox homeostasis, and muscle fatigue, and assess energy availability.

METHODS: Seventy participants will be assigned to the study, including 35 vegan ultra-marathoners and 35 omnivores competing in the Sri-Chinmoy ultra marathon race. Research data will be collected from the participants at four steps (three visits to the research laboratory and the race day) throughout the study. At the first visit (seven days before the race), fecal samples, and anthropometric measurements will be collected. Body composition will be measured using DXA. Participants will be informed about keeping detailed food records and will be asked to record their diet data and activity logs during the entire study period. At second visit, maximum oxygen consumption will be measured on treadmill. On race day, blood samples will be collected immediately before, and 0. min, 2 hours, and 24 hours after the race. Body weight will be measured before and after the race. The blood and fecal samples will be stored at -80 C until analysis. Plasma malondialdehyde, reactive oxygen metabolites, total antioxidant capacity, Heatshockprotein-70, and serum Orosomucoid-1 will be analyzed in blood samples. Fecal samples will be analyzed with shotgun metagenomic analysis and interpreted using bioinformatics pipeline (HumanN2). Statistical tests will be analyzed using SPSS version 23.0 and R Software.

DISCUSSION: Study findings will determine the effects of the vegan diet on sports performance, revealing the multiple interactions between host and gut microbiome at the whole metagenomic level. Additionally, results will show the possible adaptation throughout the race by analyzing blood and fecal samples. Furthermore, by assessing energy availability and determining host-metabolite crosstalk for ultra-endurance athletes, possible nutritional deficiencies can be identified. Thus, advanced nutritional strategies can be developed based on metabolic needs.

TRIAL REGISTRATION: Current controlled trials, ISRCTN registry 69541705. Registered on 8 December 2019.

RevDate: 2021-09-24

Fung C, Rusling M, Lampeter T, et al (2021)

Automation of QIIME2 Metagenomic Analysis Platform.

Current protocols, 1(9):e254.

QIIME is a widely used, open-source microbiome analysis software package that converts raw sequence data into interpretable visualizations and statistical results. QIIME2 has recently succeeded QIIME1, becoming the most updated platform. The protocols in this article describe our effort in automating core functions of QIIME2, using datasets available at docs.qiime2.org. While these specific examples are microbial 16S rRNA gene sequences, our automation can be easily applied to other types of QIIME2 analysis. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparing files and folders Support Protocol 1: Preparing your data for QAP Support Protocol 2: Understanding automated options Basic Protocol 2: Importing into QIIME Basic Protocol 3: DADA2: Filtering, trimming, merging pairs Basic Protocol 4: Performing core metrics Basic Protocol 5: Sample filtering by metadata Basic Protocol 6: Alpha diversity metrics Basic Protocol 7: Cross-sectional beta diversity Basic Protocol 8: Longitudinal feature volatility Basic Protocol 9: Sample classification.

RevDate: 2021-09-23

Sumbula V, Kurian PS, Girija D, et al (2021)

Impact of foliar application of fungicides on tomato leaf fungal community structure revealed by metagenomic analysis.

Folia microbiologica [Epub ahead of print].

Fungicides are commonly used to manage plant pathogens. However, little is known about their effects on the non-target fungal communities that inhabit inside and outside the plant. These fungicides may have adverse effects on beneficial microbial communities with possible consequences for plant health and productivity. Hence, a metagenomic approach, based on the ITS2 region of fungal rDNA, was used to study the impact of foliar application of two fungicides (propineb and iprodione + carbendazim) on non-target tomato leaf fungal communities, in the context of early blight disease management. Metagenomic analysis revealed that the richness and diversity of tomato leaf fungal populations were adversely affected by the chemical treatments tested. Among the two fungicides, propineb (contact fungicide) imparted less non-targeted microorganisms than iprodione + carbendazim (systemic fungicide). In addition, all samples showed association of pathogenic genera Cladosporium, Corynespora, Pseudocercospora along with early blight pathogen Alternaria on tomato leaves that otherwise were undetected. Metagenomic studies also revealed a new mode of action for fungicides and bioagents besides their direct effect that is shifting the microbial community structure so that it provides greater resistance against the pathogen.

RevDate: 2021-09-24

Hause BM, Nelson E, J Christopher-Hennings (2021)

Identification of a novel statovirus in a faecal sample from a calf with enteric disease.

The Journal of general virology, 102(9):.

A novel clade of RNA viruses was identified in the mammalian gastrointestinal tract by next-generation sequencing. Phylogenetically, these viruses are related to the genera Tombusviridae (plant viruses) and Flaviviridae, which includes mammalian, avian and insect hosts. Named in line with their characterization as stool-associated Tombus-like viruses, it is unclear if statoviruses infect mammals or are dietary in origin. Here, metagenomic sequencing of faecal material collected from a 10-week-old calf with enteric disease found that 20 % of the reads mapped to a de novo-assembled 4 kb contig with homology to statoviruses. Phylogenetic analysis of the statovirus genome found a clear evolutionary relationship with statovirus A, but, with only 47 % similarity, we propose that the statovirus sequence presents a novel species, statovirus F. A TaqMan PCR targeting statovirus F performed on faecal material found a cycle threshold of 11, suggesting a high titre of virus shed from the calf with enteric disease. A collection of 48 samples from bovine enteric disease diagnostic submissions were assayed by PCR to investigate statovirus F prevalence and 6 of 48 (12.5 %) were positive. An ELISA to detect antibodies to the coat protein found that antibodies to statovirus F were almost ubiquitous in bovine serum. Combined, the PCR and ELISA results suggest that statovirus F commonly infects cattle. Further research is needed to elucidate the aetiological significance of statovirus infection.

RevDate: 2021-09-24

Martinez JN, Nishihara A, S Haruta (2021)

Metagenome-Assembled Genome Sequences Recovered from Epilithic River Biofilm in the Tama River, Japan.

Microbiology resource announcements, 10(38):e0066421.

Draft genome sequences of putatively novel bacteria were assembled from the metagenome of epilithic biofilm samples collected from the Tama River (Tokyo, Japan). The metagenome contains 44,630,724 sequences, 44,792 contigs, and 48% G+C content. Binning resulted in 31 metagenome-assembled genomes (MAGs) with ≥50% completeness.

RevDate: 2021-09-23

Karunatillaka I, Jaroszewski L, A Godzik (2021)

Novel putative polyethylene terephthalate (PET) plastic degrading enzymes from the environmental metagenome.

Proteins [Epub ahead of print].

Several plastic degrading enzymes have been described in the literature, most notably PETases that are capable of hydrolyzing polyethylene terephthalate (PET) plastic. One of them, the PETase from Ideonella sakaiensis, a bacterium isolated from environmental samples within a PET bottle recycling site, was a subject of extensive studies. To test how widespread PETase functionality is in other bacterial communities, we used a cascade of BLAST searches in the JGI metagenomic datasets and showed that close homologs of I. sakaiensis PETase can also be found in other metagenomic environmental samples from both human-affected and relatively pristine sites. To confirm their classification as putative PETases, we verified that the newly identified proteins have the PETase sequence signatures common to known PETases and that phylogenetic analyses group them with the experimentally characterized PETases. Additionally, docking analysis was performed in order to further confirm the functional assignment of the putative environmental PETases.

RevDate: 2021-09-23

Shokoohi E, Mashela PW, RAR Machado (2021)

Bacterial communities associated with Zeldia punctata, a bacterivorous soil-borne nematode.

International microbiology : the official journal of the Spanish Society for Microbiology [Epub ahead of print].

Soil inhabiting organisms are important determinants of agroecosystem productivity. Understanding the composition, the abundance, and the type of interactions established by soil microorganisms is therefore crucial to design strategies to improve agricultural practices and agroecosystem management. In this study, we collected Zeldia punctata nematodes in maize fields in South Africa and profiled their associated bacterial communities using next-generation sequencing. We observed that Z. punctata nematodes establish associations with ecologically diverse bacterial species. The most abundant species observed are Pseudomonas syringae, a phytopathogenic bacterial complex; Lactobacillus paraplantarum, a broadly distributed bacterial species that is present in soils, water bodies, and animal intestinal tracts and has certain probiotic and antimicrobial properties; and Melissococcus plutonius, a serious pathogenic bacterial species that causes brood disease in honeybees. Our study contributes to a better understanding of the soil bacterial communities associated with nematodes in maize agricultural soils in South Africa and unravels the presence of diverse detrimental and beneficial nematode-associated bacteria.

RevDate: 2021-09-23

Li L, Kang Q, Zhang S, et al (2021)

The complete genome sequence of a novel chrysovirus from the entomopathogenic fungus Beauveria bassiana Vuillemin.

Archives of virology [Epub ahead of print].

Beauveria bassiana, an entomopathogenic fungus, is used for arthropod pest control worldwide. Here, we report the discovery and characterization of a novel double-stranded RNA (dsRNA) mycovirus, Beauveria bassiana chrysovirus 2 (BbCV-2), isolated from a Chinese B. bassiana strain. The genome sequence of the virus was determined by metagenomic sequencing, RT-PCR, and RACE cloning and was found to consist of four dsRNA segments that are 3441 bp, 2779 bp, 2925 bp, and 2688 bp long, respectively. Each dsRNA segment contains a single ORF. The ORF of dsRNA1 encodes a 1114-amino-acid (aa) protein (123.4 kDa) with a conserved RNA-dependent RNA polymerase (RdRp) motif, the sequence of which showed the highest identity of only 16.13% to that of Beauveria bassiana chrysovirus-1 (BbCV-1). The ORF of dsRNA2 encodes an 805-aa coat protein (CP) (84.7 kDa). The ORFs of dsRNAs 3 and 4 encodes proteins of undetermined function. The virus is a new member of the family Chrysoviridae from B. bassiana.

RevDate: 2021-09-23

Villalobos-Flores LE, Espinosa-Torres SD, Hernández-Quiroz F, et al (2021)

The Bacterial and Fungal Microbiota of the Mexican Rubiaceae Family Medicinal Plant Bouvardia ternifolia.

Microbial ecology [Epub ahead of print].

Bouvardia ternifolia is a medicinal plant considered a source of therapeutic compounds, like the antitumoral cyclohexapeptide bouvardin. It is known that large number of secondary metabolites produced by plants results from the interaction of the host and adjacent or embedded microorganisms. Using high-throughput DNA sequencing of V3-16S and V5-18S ribosomal gene libraries, we characterized the endophytic, endophytic + epiphyte bacterial, and fungal communities associated to flowers, leaves, stems, and roots, as well as the rhizosphere. The Proteobacteria (average 80.7%) and Actinobacteria (average 14.7%) were the most abundant bacterial phyla, while Leotiomycetes (average 54.8%) and Dothideomycetes (average 27.4%) were the most abundant fungal classes. Differential abundance for the bacterial endophyte group showed a predominance of Erwinia, Propionibacterium, and Microbacterium genera, while Sclerotinia, Coccomyces, and Calycina genera predominated for fungi. The predictive metagenome analysis for bacteria showed significative abundance of pathways for secondary metabolite production, while a FUNguild analysis revealed the presence of pathotroph, symbiotroph, and saprotrophs in the fungal community. Intra and inter copresence and mutual exclusion interactions were identified for bacterial and fungal kingdoms in the endophyte communities. This work provides a description of the diversity and composition of bacterial and fungal microorganisms living in flowers, leaves, stems, roots, and the rhizosphere of this medicinal plant; thus, it paves the way towards an integral understanding in the production of therapeutic metabolites.

RevDate: 2021-09-25

Rai N, Kumari Keshri P, Verma A, et al (2021)

Plant associated fungal endophytes as a source of natural bioactive compounds.

Mycology, 12(3):139-159.

Endophytes are a potent source of bioactive compounds that mimic plant-based metabolites. The relationship of host plant and endophyte is significantly associated with alteration in fungal colonisation and the extraction of endophyte-derived bioactive compounds. Screening of fungal endophytes and their relationship with host plants is essential for the isolation of bioactive compounds. Numerous bioactive compounds with antioxidant, antimicrobial, anticancer, and immunomodulatory properties are known to be derived from fungal endophytes. Bioinformatics tools along with the latest techniques such as metabolomics, next-generation sequencing, and metagenomics multilocus sequence typing can potentially fill the gaps in fungal endophyte research. The current review article focuses on bioactive compounds derived from plant-associated fungal endophytes and their pharmacological importance. We conclude with the challenges and opportunities in the research area of fungal endophytes.

RevDate: 2021-09-25

Russo AG, Harding EF, Yan GJH, et al (2021)

Discovery of Novel Viruses Associated With the Invasive Cane Toad (Rhinella marina) in Its Native and Introduced Ranges.

Frontiers in microbiology, 12:733631.

Cane toads (Rhinella marina) are notoriously successful invaders: from 101 individuals brought to Australia in 1935, poisonous toads now cover an area >1.2 million km2 with adverse effects on native fauna. Despite extensive research on the role of macroparasites in cane toad invasion, viral research is lagging. We compared viral prevalence and diversity between toads in their native range (French Guiana, n=25) and two introduced ranges: Australia (n=151) and Hawai'i (n=10) with a metatranscriptomic and metagenomic approach combined with PCR screening. Australian toads almost exclusively harbor one of seven viruses detected globally. Rhimavirus-A (Picornaviridae) exhibited low genetic diversity and likely actively infected 9% of sampled Australian toads extending across ~2,000km of Northern Australia and up to the current invasion front. In native range cane toads, we identified multiple phylogenetically distinct viruses (Iridoviridae, Picornaviridae, Papillomaviridae, and Nackedna-like virus). None of the same viruses was detected in both ranges, suggesting that Australian cane toads have largely escaped the viral infection experienced by their native range counterparts. The novel native range viruses described here are potential biocontrol agents, as Australian toads likely lack prior immunological exposure to these viruses. Overall, our evidence suggests that there may be differences between viruses infecting cane toads in their native vs. introduced ranges, which lays the groundwork for further studies on how these viruses have influenced the toads' invasion history.

RevDate: 2021-09-26

Arroyo Mühr LS, Dillner J, Ure AE, et al (2021)

Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics.

Scientific reports, 11(1):18852.

Although metagenomics and metatranscriptomics are commonly used to identify bacteria and viruses in human samples, few studies directly compare these strategies. We wished to compare DNA and RNA sequencing of bacterial and viral metagenomes and metatranscriptomes in the human cervix. Total nucleic acids from six human cervical samples were subjected to DNA and RNA sequencing. The effect of DNase-treatment before reverse transcription to cDNA were also analyzed. Similarities and differences in the metagenomic findings with the three different sequencing approaches were evaluated. A higher proportion of human sequences were detected by DNA sequencing (93%) compared to RNA sequencing without (76%) and with prior DNase-treatment (11%). On the contrary, bacterial sequences increased 17 and 91 times. However, the number of detected bacterial genera were less by RNA sequencing, suggesting that only a few contribute to most of the bacterial transcripts. The viral sequences were less by RNA sequencing, still twice as many virus genera were detected, including some RNA viruses that were missed by DNA sequencing. Metatranscriptomics of total cDNA provided improved detection of mainly transcribed bacteria and viruses in cervical swabs as well as detection of RNA viruses, compared to metagenomics.

RevDate: 2021-09-25

López-Catalina A, Atxaerandio R, García-Rodríguez A, et al (2021)

Characterisation of the rumen resistome in Spanish dairy cattle.

Animal microbiome, 3(1):63.

BACKGROUND: Rumen microorganisms carry antimicrobial resistance genes which pose a threaten to animals and humans in a One Health context. In order to tackle the emergence of antimicrobial resistance it is vital to understand how they appear, their relationship with the host, how they behave as a whole in the ruminal ecosystem or how they spread to the environment or humans. We sequenced ruminal samples from 416 Holstein dairy cows in 14 Spanish farms using nanopore technology, to uncover the presence of resistance genes and their potential effect on human, animal and environmental health.

RESULTS: We found 998 antimicrobial resistance genes (ARGs) in the cow rumen and studied the 25 most prevalent genes in the 14 dairy cattle farms. The most abundant ARGs were related to the use of antibiotics to treat mastitis, metritis and lameness, the most common diseases in dairy cattle. The relative abundance (RA) of bacteriophages was positively correlated to the ARGs RA. The heritability of the RA of the more abundant ARGs ranged between 0.10 (mupA) and 0.49 (tetW), similar to the heritability of the RA of microbes that carried those ARGs. Even though these genes are carried by the microorganisms, the host is partially controlling their RA by having a more suitable rumen pH, folds, or other physiological traits that promote the growth of those microorganisms.

CONCLUSIONS: We were able to determine the most prevalent ARGs (macB, msbA, parY, rpoB2, tetQ and TaeA) in the ruminal bacteria ecosystem. The rumen is a reservoir of ARGs, and strategies to reduce the ARG load from livestock must be pursued.

RevDate: 2021-09-26

Stražar M, Mourits VP, Koeken VACM, et al (2021)

The influence of the gut microbiome on BCG-induced trained immunity.

Genome biology, 22(1):275.

BACKGROUND: The bacillus Calmette-Guérin (BCG) vaccine protects against tuberculosis and heterologous infections but elicits high inter-individual variation in specific and nonspecific, or trained, immune responses. While the gut microbiome is increasingly recognized as an important modulator of vaccine responses and immunity in general, its potential role in BCG-induced protection is largely unknown.

RESULTS: Stool and blood were collected from 321 healthy adults before BCG vaccination, followed by blood sampling after 2 weeks and 3 months. Metagenomics based on de novo genome assembly reveals 43 immunomodulatory taxa. The nonspecific, trained immune response is detected by altered production of cytokines IL-6, IL-1β, and TNF-α upon ex vivo blood restimulation with Staphylococcus aureus and negatively correlates with abundance of Roseburia. The specific response, measured by IFN-γ production upon Mycobacterium tuberculosis stimulation, is associated positively with Ruminococcus and Eggerthella lenta. The identified immunomodulatory taxa also have the strongest effects on circulating metabolites, with Roseburia affecting phenylalanine metabolism. This is corroborated by abundances of relevant enzymes, suggesting alternate phenylalanine metabolism modules are activated in a Roseburia species-dependent manner.

CONCLUSIONS: Variability in cytokine production after BCG vaccination is associated with the abundance of microbial genomes, which in turn affect or produce metabolites in circulation. Roseburia is found to alter both trained immune responses and phenylalanine metabolism, revealing microbes and microbial products that may alter BCG-induced immunity. Together, our findings contribute to the understanding of specific and trained immune responses after BCG vaccination.

RevDate: 2021-09-26

Bjerre RD, Holm JB, Palleja A, et al (2021)

Skin dysbiosis in the microbiome in atopic dermatitis is site-specific and involves bacteria, fungus and virus.

BMC microbiology, 21(1):256.

BACKGROUND: Microbial dysbiosis with increased Staphylococcus aureus (S. aureus) colonization on the skin is a hallmark of atopic dermatitis (AD), however most microbiome studies focus on bacteria in the flexures and the microbial composition at other body sites have not been studied systematically.

OBJECTIVES: The aim of the study is to characterize the skin microbiome, including bacteria, fungi and virus, at different body sites in relation to AD, lesional state, and S. aureus colonization, and to test whether the nares could be a reservoir for S. aureus strain colonization.

METHODS: Using shotgun metagenomics we characterized microbial compositions from 14 well defined skin sites from 10 patients with AD and 5 healthy controls.

RESULTS: We found clear differences in microbial composition between AD and controls at multiple skin sites, most pronounced on the flexures and neck. The flexures exhibited lower alpha-diversity and were colonized by S. aureus, accompanied by S. epidermidis in lesions. Malassezia species were absent on the neck in AD. Virus mostly constituted Propionibacterium and Staphylococcus phages, with increased abundance of Propionibacterium phages PHL041 and PHL092 and Staphylococcus epidermidis phages CNPH82 and PH15 in AD. In lesional samples, both the genus Staphylococcus and Staphylococcus phages were more abundant. S. aureus abundance was higher across all skin sites except from the feet. In samples where S. aureus was highly abundant, lower abundances of S. hominis and Cutibacterium acnes were observed. M. osloensis and M. luteus were more abundant in AD. By single nucleotide variant analysis of S. aureus we found strains to be subject specific. On skin sites some S. aureus strains were similar and some dissimilar to the ones in the nares.

CONCLUSIONS: Our data indicate a global and site-specific dysbiosis in AD, involving both bacteria, fungus and virus. When defining targeted treatment clinicians should both consider the individual and skin site and future research into potential crosstalk between microbiota in AD yields high potential.

RevDate: 2021-09-22

Piscotta FJ, Whitfield ST, Nakashige TG, et al (2021)

Multiplexed functional metagenomic analysis of the infant microbiome identifies effectors of NF-κB, autophagy, and cellular redox state.

Cell reports, 36(12):109746.

The human microbiota plays a critical role in host health. Proper development of the infant microbiome is particularly important. Its dysbiosis leads to both short-term health issues and long-term disorders lasting into adulthood. A central way in which the microbiome interacts with the host is through the production of effector molecules, such as proteins and small molecules. Here, a metagenomic library constructed from 14 infant stool microbiomes is analyzed for the production of effectors that modulate three distinct host pathways: immune response (nuclear factor κB [NF-κB] activation), autophagy (LC3-B puncta formation), and redox potential (NADH:NAD ratio). We identify microbiome-encoded bioactive metabolites, including commendamide and hydrogen sulfide and their associated biosynthetic genes, as well as a previously uncharacterized autophagy-inducing operon from Klebsiella spp. This work extends our understanding of microbial effector molecules that are known to influence host pathways. Parallel functional screening of metagenomic libraries can be easily expanded to investigate additional host processes.

RevDate: 2021-09-22

Cremonesi P, Severgnini M, Romanò A, et al (2021)

Bovine Milk Microbiota: Comparison among Three Different DNA Extraction Protocols To Identify a Better Approach for Bacterial Analysis.

Microbiology spectrum [Epub ahead of print].

The bovine udder is colonized by a huge quantity of microorganisms that constitute the intramammary ecosystem, with a specific role in modulating not only udder homeostasis and mastitis susceptibility, but also the quality of the dairy products. However, generating high-quality bacterial DNA can be critical, especially starting from a complex biological matrix like milk, characterized by high fat, protein, and calcium contents. Here, bacterial DNA was recovered from a commercial ultra-high-temperature (UHT) milk sample artificially spiked with a predetermined mock community composition and from three bulk tank milk (raw milk) samples. The DNA was isolated using three different protocols to evaluate the effect of the extraction procedures on the milk microbiota composition. In the mock community experiment, the bacterial profiles generated by the three DNA extraction protocols were profoundly different, with the genera Staphylococcus, Lactobacillus, Listeria, and Salmonella underestimated by all the protocols. Only one protocol revealed values close to the expected abundances for Escherichia/Shigella spp., Bacillus spp., Enterococcus spp., and Pseudomonas spp. On the other hand, the nonspiked UHT milk sample exhibited a similar microbiota composition, revealing the prevalence of Acinetobacter spp., for all the DNA extraction protocols. For the raw milk samples, the three DNA extraction kits performed differently, revealing significant separations in both the microbial richness (alpha diversity) and composition (beta diversity). Our study highlights the presence of significant differences among these procedures, probably due to the different DNA extracting capacities and to the different properties of the milk samples, revealing that the selection of DNA extraction protocol is a critical point. IMPORTANCE The advance of high-throughput technologies has increased our knowledge of the world of microorganisms, especially of microbial populations inhabiting living animals. This study provides evidence that milk, as other complex sources, could be critical for generating high-quality DNA for microbiota analysis. In addition, it demonstrates that the microbial population highlighted by metagenomic studies changes in relation to different DNA extraction procedures, revealing that attention should be paid especially when comparing different studies.

RevDate: 2021-09-23

Virtanen J, Zalewski A, Kołodziej-Sobocińska M, et al (2021)

Diversity and transmission of Aleutian mink disease virus in feral and farmed American mink and native mustelids.

Virus evolution, 7(2):veab075.

Aleutian mink disease virus (AMDV), which causes Aleutian disease, is widely spread both in farmed mink and wild mustelids. However, only limited data are available on the role of wild animals in AMDV transmission and spread. Our aim was to shed light on AMDV transmission among wild mustelids and estimate the effect of intense farming practices on the virus circulation by studying AMDV prevalence and genetic diversity among wild mustelids in Poland. We compared AMDV seroprevalence and proportion of PCR-positive individuals in American mink, polecats, otters, stone martens, and pine martens and used the phylogenetic analysis of the NS1 region to study transmission. In addition, we used a metagenomic approach to sequence complete AMDV genomes from tissue samples. In eastern Poland, AMDV seroprevalence in wild mustelids varied from 22 per cent in otters to 62 per cent and 64 per cent in stone martens and feral mink, respectively. All studied antibody-positive mink were also PCR positive, whereas only 10, 15, and 18 per cent of antibody-positive polecats, pine martens, and stone martens, respectively, were PCR positive, suggesting lower virus persistence among these animal species as compared to feral mink. In phylogenetic analysis, most sequences from feral mink formed region-specific clusters that have most likely emerged through multiple introductions of AMDV to feral mink population over decades. However, virus spread between regions was also observed. Virus sequences derived from farmed and wild animals formed separate subclusters in the phylogenetic tree, and no signs of recent virus transmission between farmed and wild animals were observed despite the frequent inflow of farmed mink escapees to wild populations. These results provide new information about the role of different mustelid species in AMDV transmission and about virus circulation among the wild mustelids. In addition, we pinpoint gaps of knowledge, where more studies are needed to achieve a comprehensive picture of AMDV transmission.

RevDate: 2021-09-25

Wang L, Huang G, Hou R, et al (2021)

Multi-omics reveals the positive leverage of plant secondary metabolites on the gut microbiota in a non-model mammal.

Microbiome, 9(1):192.

BACKGROUND: Flavonoids are important plant secondary metabolites (PSMs) that have been widely used for their health-promoting effects. However, little is known about overall flavonoid metabolism and the interactive effects between flavonoids and the gut microbiota. The flavonoid-rich bamboo and the giant panda provide an ideal system to bridge this gap.

RESULTS: Here, integrating metabolomic and metagenomic approaches, and in vitro culture experiment, we identified 97 flavonoids in bamboo and most of them have not been identified previously; the utilization of more than 70% flavonoid monomers was attributed to gut microbiota; the variation of flavonoid in bamboo leaves and shoots shaped the seasonal microbial fluctuation. The greater the flavonoid content in the diet was, the lower microbial diversity and virulence factor, but the more cellulose-degrading species.

CONCLUSIONS: Our study shows an unprecedented landscape of beneficial PSMs in a non-model mammal and reveals that PSMs remodel the gut microbiota conferring host adaptation to diet transition in an ecological context, providing a novel insight into host-microbe interaction. Video abstract.

RevDate: 2021-09-23

Li X, Liu X, Cao N, et al (2021)

Adaptation mechanisms of arsenic metabolism genes and their host microorganisms in soils with different arsenic contamination levels around abandoned gold tailings.

Environmental pollution (Barking, Essex : 1987), 291:117994 pii:S0269-7491(21)01576-1 [Epub ahead of print].

Soil around the gold tailing due to the smelting process of wastewater and solid waste can lead to metal (loids) contamination, especially arsenic (As). Soil microorganisms have gradually evolved adaptive mechanisms in the process of long-term adaptation to As contamination. However, comprehensive investigations on As metabolism genes and their host microbial communities in soil profiles with different levels under long-term As contamination are lacking. There are selected three typical soil profiles (0-100 cm) with different metal (loids) contamination levels (L-low, M-moderate and H-high) around tailings in this research. It uses a Metagenomic approach to explore the adaptation mechanisms of arsenic metabolism genes and arsenic metabolism gene host microorganisms in both horizontal and vertical dimensions. The results showed that four categories of As metabolism genes were prevalent in soil profiles at different As contamination, with As reduction genes being the most abundant, followed by As oxidation genes, then respiration genes and methylation genes. The As metabolism genes arsBCR, aioE, arsPH, arrAB increased with the increase of metal (loid) contaminants concentration. Longitudinal arsA, arrA, aioA, arsM and acr3 increased in abundance in deep soil. Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi were the dominant phylum of As metabolism gene host microorganisms. Different concentrations of metal (loid) contamination significantly affected the distribution of host As metabolism genes. Random forest prediction identified As as the most critical driver of As metabolism genes and their host microorganisms. Overall, this study provides a reference for a comprehensive investigation of the detoxification mechanisms of As metabolism microorganisms in soil profiles with different As contamination conditions, and is important for the development of As metabolism gene host microbial strains and engineering applications of microbial technologies to manage As contamination.

RevDate: 2021-09-25

Tan L, Zhang C, Liu F, et al (2021)

Three-compartment septic tanks as sustainable on-site treatment facilities? Watch out for the potential dissemination of human-associated pathogens and antibiotic resistance.

Journal of environmental management, 300:113709 pii:S0301-4797(21)01771-0 [Epub ahead of print].

Improved sanitation is critical important to reduce the spread of human deposited pathogens and antibiotic resistance genes (ARGs). In the China's rural "Toilet Revolution", three-compartment septic tanks (SPTs) are widely used as household domestic sewage treatment facilities. The effluents of SPTs are encouraged to be used as fertilizer in agriculture. However, whether SPT could eliminate fecal pathogens and ARGs is still unrevealed which is crucial in risk assessment of SPT effluent utilization. Herein, we employed metagenomic sequencing to investigate the pathogens and ARGs in rural household SPTs from Tianjin, China. We found that rural household SPT effluents conserved pathogens comparable to that of the influents. A total of 441 ARGs conferring resistance to 26 antibiotic classes were observed in rural household SPTs, with the relative abundance ranging from 709 to 1800 ppm. Results of metagenomic assembly indicated that some ARG-MGE-carrying contigs were carried by pathogens, which may pose risk to human and animal health after being introduced to the environment. This study raises the question of SPTs as sustainable on-site treatment facilities for rural domestic sewage and underscores the need for more attention to the propagation and dissemination of antibiotic-resistant pathogens from SPT to the environments, animals, and humans.

RevDate: 2021-09-22

He D, Quan M, Zhong H, et al (2021)

Emergomyces orientalis Emergomycosis Diagnosed by Metagenomic Next-Generation Sequencing.

Emerging infectious diseases, 27(10):2740-2742.

Emergomyces is a newly described dimorphic fungus genus; it may cause fatal infections in immunocompromised patients, but diagnosis is often delayed. We report a case of disseminated emergomycosis caused by the novel species Emergomyces orientalis in a kidney transplant recipient from Tibet. Infection was diagnosed early by metagenomic next-generation sequencing.

RevDate: 2021-09-21

Flores Ramos S, Brugger SD, Escapa IF, et al (2021)

Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome.

mSystems [Epub ahead of print].

Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum's chromosomal structure, pangenome, and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites, including one RM system hot spot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. IMPORTANCE Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the United States across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation, and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.

RevDate: 2021-09-21

Dery KJ, Kupiec-Weglinski JW, TS Dong (2021)

The human microbiome in transplantation: the past, present, and future.

Current opinion in organ transplantation pii:00075200-900000000-98811 [Epub ahead of print].

PURPOSE OF REVIEW: Over the past 20 years, DNA sequencing technology has transformed human microbiome research from identity characterizations to metagenomics approaches that reveal how microbials correlate with human health and disease. New studies are showing unprecedented opportunity for deep characterization of the human microbial ecosystem, with benefits to the field of organ transplantation.

RECENT FINDINGS: In the present review, we focus on past milestones of human-associated microbiota research, paying homage to microbiota pioneers. We highlight the role of sequencing efforts to provide insights beyond taxonomic identification. Recent advances in microbiome technology is now integrating high-throughput datasets, giving rise to multi'omics - a comprehensive assessment modeling dynamic biologic networks. Studies that show benefits and mechanisms in peritransplant antibiotic (Abx)-conditioned recipients are reviewed. We describe how next-generation microbial sequencing has the potential to combine with new technologies like phage therapy (PT) to translate into life-saving therapeutics.

SUMMARY: The study of the microbiome is advancing the field of transplantation by enhancing our knowledge of precision medicine. Sequencing technology has allowed the use of the microbiome as a biomarker to risk stratify patients. Further research is needed to better understand how microbiomes shape transplantation outcomes while informing immune cell - tissue crosstalk platforms.

RevDate: 2021-09-21

Jurelevicius D, Pereira RDS, da Mota FF, et al (2021)

Metagenomic analysis of microbial communities across a transect from low to highly hydrocarbon-contaminated soils in King George Island, Maritime Antarctica.

Geobiology [Epub ahead of print].

Soil samples from a transect from low to highly hydrocarbon-contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p-value = <.05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative-PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon-contaminated soils in polar environments.

RevDate: 2021-09-21

Basit A, Shah ST, Ullah I, et al (2021)

Microbe-assisted phytoremediation of environmental pollutants and energy recycling in sustainable agriculture.

Archives of microbiology [Epub ahead of print].

The perception of phytoremediation is efficiently utilized as an eco-friendly practice of green plants combating and cleaning up the stressed environment without harming it. The industrial revolution was followed by the green revolution which fulfilled the food demands of the growing population caused an increase in yield per unit area in crop production, but it also increased the use of synthetic fertilizers in agriculture. Globally, the intensive use of inorganic fertilizers in agriculture has led to serious health problems and irreversible environmental damage. Biofertilizers improve the growth of the plant and can be applied as an alternative to chemical/synthetic fertilizers. Cyanobacteria, bacteria, and fungi are known as some of the principal microbe groups used to produce biofertilizers that form symbiotic associations with plants. Microorganisms perform a key role in phosphate solubilization and mobilization, nitrogen fixation, nutrient management, biotic elicitors and probiotics, and pollution management (biodegradation agents), specifically bacteria which also help in atmospheric nitrogen fixation and are thus available for the growth of the plant. Management or biodegradation of hazardous chemical residues and heavy metals produced by a huge number of large-scale industries should be given primary importance to be transformed by various bacterial strains, fungi, algae. Currently, modern omics technologies such as metagenomic, transcriptomic, and proteomic are being used to develop strategies for studying the ecology of microorganisms, as well as their use in environmental monitoring and bioremediation. This review briefly discusses some of the major groups of microorganisms that can perform different functions responsible for plant health, crop production, phytoremediation and also focus on the omics techniques reportedly used in environmental monitoring to tackle the pollution load.

RevDate: 2021-09-23

Karr AF, Hauzel J, Menon P, et al (2021)

Specified Certainty Classification, with Application to Read Classification for Reference-Guided Metagenomic Assembly.


Specified Certainty Classification (SCC) is a new paradigm for employing classifiers whose outputs carry uncertainties, typically in the form of Bayesian posterior probabilities. By allowing the classifier output to be less precise than one of a set of atomic decisions, SCC allows all decisions to achieve a specified level of certainty, as well as provides insights into classifier behavior by examining all decisions that are possible. Our primary illustration is read classification for reference-guided genome assembly, but we demonstrate the breadth of SCC by also analyzing COVID-19 vaccination data.

RevDate: 2021-09-21

Oh JH, B Rehermann (2021)

Natural versus Laboratory World: Incorporating Wild-Derived Microbiota into Preclinical Rodent Models.

Journal of immunology (Baltimore, Md. : 1950), 207(7):1703-1709.

Advances in data collection (high-throughput shotgun metagenomics, transcriptomics, and metabolomics) and analysis (bioinformatics and multiomics) led to the realization that all mammals are metaorganisms, shaped not only by their own genome but also by the genomes of the microbes that colonize them. To date, most studies have focused on the bacterial microbiome, whereas curated databases for viruses, fungi, and protozoa are still evolving. Studies on the interdependency of microbial kingdoms and their combined effects on host physiology are just starting. Although it is clear that past and present exposure to commensals and pathogens profoundly affect human physiology, such exposure is lacking in standard preclinical models such as laboratory mice. Laboratory mouse colonies are repeatedly rederived in germ-free status and subjected to restrictive, pathogen-free housing conditions. This review summarizes efforts to bring the wild microbiome into the laboratory setting to improve preclinical models and their translational research value.

RevDate: 2021-09-24

Katz KS, Shutov O, Lapoint R, et al (2021)

STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions.

Genome biology, 22(1):270.

Sequence Read Archive submissions to the National Center for Biotechnology Information often lack useful metadata, which limits the utility of these submissions. We describe the Sequence Taxonomic Analysis Tool (STAT), a scalable k-mer-based tool for fast assessment of taxonomic diversity intrinsic to submissions, independent of metadata. We show that our MinHash-based k-mer tool is accurate and scalable, offering reliable criteria for efficient selection of data for further analysis by the scientific community, at once validating submissions while also augmenting sample metadata with reliable, searchable, taxonomic terms.

RevDate: 2021-09-24
CmpDate: 2021-09-22

Zhang W, Liang Y, Zheng K, et al (2021)

Characterization and genomic analysis of the first Oceanospirillum phage, vB_OliS_GJ44, representing a novel siphoviral cluster.

BMC genomics, 22(1):675.

BACKGROUND: Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. Oceanospirillum, within the order Oceanospirillales, are important symbiotic marine bacteria associated with hydrocarbon degradation and algal blooms, especially in polar regions. However, until now there has been no isolate of an Oceanospirillum bacteriophage, and so details of their metagenome has remained unknown.

RESULTS: Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786 bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. The recombinant module was highly adapted to the host, according to the tetranucleotides correlations. Genomic and morphological analyses identified vB_OliS_GJ44 as a siphovirus, however, due to the distant evolutionary relationship with any other known siphovirus, it is proposed that this virus could be classified as the type phage of a new Oceanospirivirus genus within the Siphoviridae family. vB_OliS_GJ44 showed synteny with six uncultured phages, which supports its representation in uncultured environmental viral contigs from metagenomics. Homologs of several vB_OliS_GJ44 genes have mostly been found in marine metagenomes, suggesting the prevalence of this phage genus in the oceans.

CONCLUSIONS: These results describe the first Oceanospirillum phage, vB_OliS_GJ44, that represents a novel viral cluster and exhibits interesting genetic features related to phage-host interactions and evolution. Thus, we propose a new viral genus Oceanospirivirus within the Siphoviridae family to reconcile this cluster, with vB_OliS_GJ44 as a representative member.

RevDate: 2021-09-24

Koo H, CD Morrow (2021)

Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy.

BMC microbiology, 21(1):251.

BACKGROUND: To understand inter-individual variability of fecal microbe transplantation (FMT) to enhance anti-PD-1 immunotherapy (IT) for melanoma, we analyzed the data sets from two recent publications with a microbial strain-tracking tool to determine if donor strains were dominant in the recipient feces following FMT.

RESULTS: Analysis of the Baruch et al. data set found that the presence of commensal donor microbes in recipient feces post-FMT did not correlate with the patient response to IT. From the Davar et al., data set, we found 4 patients that responded to IT had donor's related strain post-FMT, while 2 patients that did not respond to the IT also had donor's strain post-FMT. Importantly, we identified no donor microbes in the feces in one recipient post-FMT that responded to IT. Furthermore, in depth analysis from two patients who responded to IT revealed both donor and recipient strains at different times post-FMT. Colonization of the gastrointestinal tract niches is important for the interaction with the host immune system. Using a separate data set, we show that mucosa from the cecum, transverse colon, and sigmoid colon share strains, providing a large reservoir of niches containing recipient microbes.

CONCLUSIONS: We demonstrated using strain-tracking analysis individual variation with the respect to the presence of fecal dominant donor microbes in the recipient following FMT that did not correlate with the response to anti-PD-1 immunotherapy. The inter-individual differences of FMT to enhance IT might be explained by the variability of the donor microbes to occupy and outcompete recipient microbes for the gastrointestinal niches. The result from our study supports the use of new approaches to clear the niches in the gastrointestinal tract to promote donor colonization to reduce inter-individual variability of IT for melanoma and potentially other cancers.

RevDate: 2021-09-20

Dell'Anno F, van Zyl LJ, Trindade M, et al (2021)

Metagenome-assembled genome (MAG) of Oceancaulis alexandrii NP7 isolated from Mediterranean Sea polluted marine sediments and its bioremediation potential.

G3 (Bethesda, Md.), 11(9):.

Oceanicaulis alexandrii strain NP7 is a marine bacterium which belongs to the Hyphomonadaceae family and was isolated from sediments highly contaminated with metals and polycyclic aromatic hydrocarbons released for decades by industrial activities in the Gulf of Naples (Mediterranean Sea). Here, we report the partial genome sequence and annotation of O. alexandrii strain NP7 that contains a chromosome of 2,954,327 bp and encodes for 2914 predicted coding sequences (CDSs) and 44 RNA-encoding genes. Although the presence of some CDSs for genes involved in hydrocarbon degradation processes (e.g., alkB) have already been described in the literature associated with the Oceanicaulis, this is the first time that more than 100 genes involved in metal detoxification processes and hydrocarbon degradation are reported belonging to this genus. The presence of a heterogeneous set of genes involved in stress response, hydrocarbon degradation, heavy metal resistance, and detoxification suggests a possible role for O. alexandrii NP7 in the bioremediation of these highly contaminated marine sediments.

RevDate: 2021-09-25

Sun F, Xu Z, L Fan (2021)

Response of heavy metal and antibiotic resistance genes and related microorganisms to different heavy metals in activated sludge.

Journal of environmental management, 300:113754 pii:S0301-4797(21)01816-8 [Epub ahead of print].

With the recent growing interest of antibiotic resistance genes (ARGs) and their co-selection with heavy metal resistance genes (HMRGs), their relationship to heavy metals needs further analysis. This study examined the response of heavy metal resistant microorganisms (HMRMs) and antibiotic resistant microorganisms (ARMs) and their resistance genes (HMRGs and ARGs) to Cu and Cr stresses using metagenome. Results showed that Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Nitrospirae are the dominant HMRMs and ARMs, with majority of HMRMs taxa presenting changes similar to ARMs under heavy metal stresses. Types of HMRGs and ARGs changed (increased or decreased) under Cu and Cr stresses, and a significant relationship was noted between HMRGs and ARGs and their related microbe (p < 0.05). Network analysis revealed synergistic relationships between majority of HMRGs and ARGs; however, negative correlations were also noted between them. Co-occurrence of HMRGs and ARGs was mainly observed in chromosomes, and plasmids were found to provide limited opportunities for heavy metals to promote antibiotic resistance through co-selection. These findings imply that the response of HMRMs and ARMs is induced by heavy metals, and that the changes in these microbial communities are the main factor driving the diversity and abundance of HMRGs and ARGs.

RevDate: 2021-09-24

Liu S, Lang D, Meng G, et al (2021)

Tracing the origin of honey products based on metagenomics and machine learning.

Food chemistry, 371:131066 pii:S0308-8146(21)02072-0 [Epub ahead of print].

The adulteration of honey is common. Recently, High Throughput Sequencing (HTS)-based metabarcoding method has been applied successfully to pollen/honey identification to determine floral composition that, in turn, can be used to identify the geographical origins of honeys. However, the lack of local references materials posed a serious challenge for HTS-based pollen identification methods. Here, we sampled 28 honey samples from various geographic origins without prior knowledge of local floral information and applied a machine learning method to determine geographical origins. The machine learning method uses a resilient backpropagation algorithm to train a neural network. The results showed that biological components in honey provided characteristic traits that enabled accurate geographic tracing for nearly all honey samples, confidently discriminating honeys to their geographic origin with >99% success rates, including those separated by as little as 39 km.

RevDate: 2021-09-20

Pilloni G, Cao F, Ruhmel M, et al (2021)

Proteins identified through predictive metagenomics as potential biomarkers for the detection of microbiologically influenced corrosion.

Journal of industrial microbiology & biotechnology pii:6372907 [Epub ahead of print].

The unpredictability of microbial growth and subsequent localized corrosion of steel can cause significant cost for the oil and gas industry, due to production downtime, repair and replacement. Despite a long tradition of academic research and industrial experience, microbial corrosion is not yet fully understood and thus not effectively controlled. In particular, biomarkers suitable for diagnosing microbial corrosion which abstain from the detection of the classic signatures of sulfate reducing bacteria are urgently required. In this study, a natural microbial community was enriched anaerobically with carbon steel coupons and in the presence of a variety of physical and chemical conditions. With the characterization of the microbiome and of its functional properties inferred through predictive metagenomics, a series of proteins were identified as biomarkers in the water phase that could be correlated directly to corrosion. This study provides an opportunity for the further development of a protein-based biomarker approach for effective and reliable microbial corrosion detection and monitoring in the field.

RevDate: 2021-09-21

Liu H, Tang Y, Zhang S, et al (2022)

Anti-infection mechanism of a novel dental implant made of titanium-copper (TiCu) alloy and its mechanism associated with oral microbiology.

Bioactive materials, 8:381-395.

This work was focused on study of anti-infection ability and its underlying mechanism of a novel dental implant made of titanium-copper (TiCu) alloy. In general, most studies on antibacterial implants have used a single pathogen to test their anti-infection ability using infectious animal models. However, dental implant-associated infections are polymicrobial diseases. We innovatively combine the classic ligature model in dogs with sucrose-rich diets to induce oral infections via the canine native oral bacteria. The anti-infection ability, biocompatibility and underlying mechanism of TiCu implant were systematically investigated in comparison with pure Ti implant via general inspection, hematology, imageology (micro-CT), microbiology (16S rDNA and metagenome), histology, and Cu ion detections. Compared with Ti implant, TiCu implant demonstrated remarkable anti-infection potentials with excellent biocompatibility. Additionally, the underlying anti-infection mechanism of TiCu implant was considered to involve maintaining the oral microbiota homeostasis. It was found that the carbohydrates in the plaques formed on the surface of TiCu implant were metabolized through the tricarboxylic acid cycle (TCA) cycles, which prevented the formation of an acidic microenvironment and inhibited the accumulation of acidogens and pathogens, thereby maintaining the microflora balance between aerobic and anaerobic bacteria.

RevDate: 2021-09-21

Tudela H, Claus SP, M Saleh (2021)

Next Generation Microbiome Research: Identification of Keystone Species in the Metabolic Regulation of Host-Gut Microbiota Interplay.

Frontiers in cell and developmental biology, 9:719072.

The community of the diverse microorganisms residing in the gastrointestinal tract, known as the gut microbiota, is exceedingly being studied for its impact on health and disease. This community plays a major role in nutrient metabolism, maintenance of the intestinal epithelial barrier but also in local and systemic immunomodulation. A dysbiosis of the gut microbiota, characterized by an unbalanced microbial ecology, often leads to a loss of essential functions that may be associated with proinflammatory conditions. Specifically, some key microbes that are depleted in dysbiotic ecosystems, called keystone species, carry unique functions that are essential for the balance of the microbiota. In this review, we discuss current understanding of reported keystone species and their proposed functions in health. We also elaborate on current and future bioinformatics tools needed to identify missing functions in the gut carried by keystone species. We propose that the identification of such keystone species functions is a major step for the understanding of microbiome dynamics in disease and toward the development of microbiome-based therapeutics.

RevDate: 2021-09-21

Rajeoni AH, Ghalyanchilangeroudi A, Khalesi B, et al (2021)

The tracheal virome of broiler chickens with respiratory disease complex in Iran: the metagenomics study.

Iranian journal of microbiology, 13(3):337-344.

Background and Objectives: Avian respiratory disease complex (RDC) is one of the most detrimental economic diseases that affected different parts of the world. Various pathogens cause the disease, but the most significant viral pathogens include avian influenza virus (AIV), infectious bronchitis virus (IBV), and Newcastle disease virus (NDV) are the most prevalent. To detect these pathogens, various methods have been discovered in the last decades. Detection and characterization of viruses by metagenomics methods have improved our knowledge about the role of virome in the avian complex respiratory disease.

Materials and Methods: This research investigates the viral pathogen populations that mostly participate in emerging these diseases using the NGS method RNA-sequencing. In surveillance of ten broiler farms from different cities with respiratory symptoms, trachea samples were collected to determine the pathogenic virome causing the disease.

Results: In this metagenomics analysis, nine viral families were identified, comprising 72.82% of RNA viruses, 24.32% of RT viruses, and 2.86% of DNA viruses. RNA viruses had the highest contribution to the respiratory disease complex instead of disease, including paramyxoviridae, orthomyxoviridae, coronaviridae, and picornaviridae viruses. Other viruses from the RNA viruses and DNA virus families were also identified in addition to these results.

Conclusion: This research suggests that studies of pathogenic viromes in different diseases can help monitor different diseases and predict their future occurrence.

RevDate: 2021-09-21

Rahalkar MC, Khatri K, Pandit P, et al (2021)

Cultivation of Important Methanotrophs From Indian Rice Fields.

Frontiers in microbiology, 12:669244.

Methanotrophs are aerobic to micro-aerophilic bacteria, which oxidize and utilize methane, the second most important greenhouse gas. The community structure of the methanotrophs in rice fields worldwide has been studied mainly using culture-independent methods. Very few studies have focused on culturing methanotrophs from rice fields. We developed a unique method for the cultivation of methanotrophs from rice field samples. Here, we used a modified dilute nitrate mineral salts (dNMS) medium, with two cycles of dilution till extinction series cultivation with prolonged incubation time, and used agarose in the solid medium. The cultivation approach resulted in the isolation of methanotrophs from seven genera from the three major groups: Type Ia (Methylomonas, Methylomicrobium, and Methylocucumis), Type Ib (Methylocaldum and Methylomagnum), and Type II (Methylocystis and Methylosinus). Growth was obtained till 10-6-10-8 dilutions in the first dilution series, indicating the culturing of dominant methanotrophs. Our study was supported by 16S rRNA gene-based next-generation sequencing (NGS) of three of the rice samples. Our analyses and comparison with the global scenario suggested that the cultured members represented the major detected taxa. Strain RS1, representing a putative novel species of Methylomicrobium, was cultured; and the draft genome sequence was obtained. Genome analysis indicated that RS1 represented a new putative Methylomicrobium species. Methylomicrobium has been detected globally in rice fields as a dominant genus, although no Methylomicrobium strains have been isolated from rice fields worldwide. Ours is one of the first extensive studies on cultured methanotrophs from Indian rice fields focusing on the tropical region, and a unique method was developed. A total of 29 strains were obtained, which could be used as models for studying methane mitigation from rice fields and for environmental and biotechnological applications.

RevDate: 2021-09-21

Garber AI, Cohen AB, Nealson KH, et al (2021)

Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats.

Frontiers in microbiology, 12:667944.

Microbial iron cycling influences the flux of major nutrients in the environment (e.g., through the adsorptive capacity of iron oxides) and includes biotically induced iron oxidation and reduction processes. The ecological extent of microbial iron cycling is not well understood, even with increased sequencing efforts, in part due to limitations in gene annotation pipelines and limitations in experimental studies linking phenotype to genotype. This is particularly true for the marine subseafloor, which remains undersampled, but represents the largest contiguous habitat on Earth. To address this limitation, we used FeGenie, a database and bioinformatics tool that identifies microbial iron cycling genes and enables the development of testable hypotheses on the biogeochemical cycling of iron. Herein, we survey the microbial iron cycle in diverse subseafloor habitats, including sediment-buried crustal aquifers, as well as surficial and deep sediments. We inferred the genetic potential for iron redox cycling in 32 of the 46 metagenomes included in our analysis, demonstrating the prevalence of these activities across underexplored subseafloor ecosystems. We show that while some processes (e.g., iron uptake and storage, siderophore transport potential, and iron gene regulation) are near-universal, others (e.g., iron reduction/oxidation, siderophore synthesis, and magnetosome formation) are dependent on local redox and nutrient status. Additionally, we detected niche-specific differences in strategies used for dissimilatory iron reduction, suggesting that geochemical constraints likely play an important role in dictating the dominant mechanisms for iron cycling. Overall, our survey advances the known distribution, magnitude, and potential ecological impact of microbe-mediated iron cycling and utilization in sub-benthic ecosystems.

RevDate: 2021-09-20

Vitko D, McQuaid JW, Gheinani AH, et al (2021)

Urinary Tract Infections in Children with Vesicoureteral Reflux Are Accompanied by Alterations in Urinary Microbiota and Metabolome Profiles.

European urology pii:S0302-2838(21)01990-4 [Epub ahead of print].

Children with vesicoureteral reflux (VUR) are at an increased risk of recurrent urinary tract infections (UTIs) and renal scarring. Gut microbiota are associated with disease phenotypes, but there has been no study that associates urinary microbiota (uMB) and metabolic profiles with VUR pathology. To identify dominant uMB genera and metabolites associated with UTIs in VUR, urine samples collected under sterile conditions underwent 16S ribosomal RNA sequencing (n = 49) and metabolomic analysis by mass spectrometry (n = 96). Alterations in uMB and metabolomic profiles in VUR patients suggest remodeling of urinary bacterial communities after UTIs: Dorea- and Escherichia-dominant uMB profiles were more frequently identified in participants with VUR. Prevotella- and Lactobacillus-dominant uMB profiles were more prevalent in controls (p < 0.001). Microbial composition varied based on recurrent febrile UTI status (p = 0.001). A total of 243 urinary metabolites involved in energy, amino acid, nucleotide, and lipid metabolism were altered in VUR patients with UTIs (p < 0.05). Importantly, VUR specimens revealed changes in the bacteria-associated metabolic pathways such as glutamate degradation, methyl-citrate cycle, and bile acid metabolism. PATIENT SUMMARY: Differences in urinary commensal bacteria and metabolites exist between children with and without vesicoureteral reflux (VUR). These changes may be utilized to identify patients at risk of VUR-associated kidney damage.

RevDate: 2021-09-24

Zhang Z, Zhang Q, Lu T, et al (2021)

Residual chlorine disrupts the microbial communities and spreads antibiotic resistance in freshwater.

Journal of hazardous materials, 423(Pt B):127152 pii:S0304-3894(21)02120-8 [Epub ahead of print].

Chlorine disinfection is a key global public health strategy for the prevention and control of diseases, such as COVID-19. However, little is known about effects of low levels of residual chlorine on freshwater microbial communities and antibiotic resistomes. Here, we treated freshwater microcosms with continuous low concentrations of chlorine and quantified the effects on aquatic and zebrafish intestinal microbial communities and antibiotic resistomes, using shotgun metagenome and 16S rRNA gene sequencing. Although chlorine rapidly degraded, it altered the aquatic microbial community composition over time and disrupted interactions among microbes, leading to decreases in community complexity and stability. However, community diversity was unaffected. The majority of ecological functions, particularly metabolic capacities, recovered after treatment with chlorine for 14 d, due to microbial community redundancy. There were also increased levels of antibiotic-resistance gene dissemination by horizontal and vertical gene transfer under chlorine treatment. Although the zebrafish intestinal microbial community recovered from temporary dysbiosis, growth and behavior of zebrafish adults were negatively affected by chlorine. Overall, our findings demonstrate the negative effects of residual chlorine on freshwater ecosystems and highlight a possible long-term risk to public health.

RevDate: 2021-09-23

Di Cesare A, Pinnell LJ, Brambilla D, et al (2021)

Bioplastic accumulates antibiotic and metal resistance genes in coastal marine sediments.

Environmental pollution (Barking, Essex : 1987), 291:118161 pii:S0269-7491(21)01743-7 [Epub ahead of print].

The oceans are increasingly polluted with plastic debris, and several studies have implicated plastic as a reservoir for antibiotic resistance genes and a potential vector for antibiotic-resistant bacteria. Bioplastic is widely regarded as an environmentally friendly replacement to conventional petroleum-based plastic, but the effects of bioplastic pollution on marine environments remain largely unknown. Here, we present the first evidence that bioplastic accumulates antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in marine sediments. Biofilms fouling ceramic, polyethylene terephthalate (PET), and polyhydroxyalkanoate (PHA) were investigated by shotgun metagenomic sequencing. Four ARG groups were more abundant in PHA: trimethoprim resistance (TMP), multidrug resistance (MDR), macrolide-lincosamide-streptogramin resistance (MLS), and polymyxin resistance (PMR). One MRG group was more abundant in PHA: multimetal resistance (MMR). The relative abundance of ARGs and MRGs were strongly correlated based on a Mantel test between the Bray-Curtis dissimilarity matrices (R = 0.97, p < 0.05) and a Pearson's analysis (R = 0.96, p < 0.05). ARGs were detected in more than 40% of the 57 metagenome-assembled genomes (MAGs) while MRGs were detected in more than 90% of the MAGs. Further investigation (e.g., culturing, genome sequencing, antibiotic susceptibility testing) revealed that PHA biofilms were colonized by hemolytic Bacillus cereus group bacteria that were resistant to beta-lactams, vancomycin, and bacitracin. Taken together, our findings indicate that bioplastic, like conventional petroleum-based plastic, is a reservoir for resistance genes and a potential vector for antibiotic-resistant bacteria in coastal marine sediments.

RevDate: 2021-09-19

Jia J, Liang C, Wu X, et al (2021)

Effect of high proportion concentrate dietary on Ashdan Yak jejunal barrier and microbial function in cold season.

Research in veterinary science, 140:259-267 pii:S0034-5288(21)00281-2 [Epub ahead of print].

The intestinal health of ruminants plays a vital role in absorbing and metabolizing nutrients. In order to explore the jejunal barrier and microbiota dysfunction of Ashdan yaks, animals were fed with a high proportion of concentrated feeds in cold season. In present study, twelve Ashdan male yaks were arbitrarily separated into two categories, namely FF and CF. Compositional and functional differences in their jejunum barrier and microbiota between the FF and CF yaks were compared using metagenomics and proteomics methods. The results showed that the activity of jejunum digestive protease and microbe metabolite of forage-fed yaks were more conducive to healthy cultivation than the concentrate-fed yaks. 57 differentially expressed proteins (DEPs) were recognized using label-free MS, those could conclude to 2 principal classes: structural proteins and inflammatory factors, and 14 proteins were relatively active in those principal classes. Firmicutes were the dominant bacterial phylum in the jejunum microbiota of both the forage-fed group (24.33%) and concentrate-fed group (23.16%). As compared to forage-fed group, the concentrate-fed group showed enhanced alpha diversity and reduced beta diversity of the jejunal microbiota. The long-term high-proportion concentrate feeding inhibited the growth of Actinobacteria, Proteo-bacteria, Ascomycota, Bacteroidetes and stimulated the growth of Streptophyta, Cyanobacteria, Fusobacteria and Chlamydiae. The concentrate-fed group showed increase in the abundance of immune system process, along with decrease in the metabolic process, especially the binding process. Interestingly, the proteomics and metagenomics results were both inclined to the enrichment of jejunum mechanical barrier and inflammatory response. Overall, the study suggested that the long-term high-proportion concentrate feeding affected the expressions of specific jejunum proteins and composition of microbiota, which damaged the jejunum barrier and the function of microbiota in yaks.

RevDate: 2021-09-19

Kallscheuer N, C Jogler (2021)

The bacterial phylum Planctomycetes as novel source for bioactive small molecules.

Biotechnology advances pii:S0734-9750(21)00124-5 [Epub ahead of print].

Extensive knowledge and methodological expertise on the bacterial cell biology has been accumulated over the last decades and bacterial cells have now become an integral part of several (bio-)technical processes. While it appears reasonable to focus on a relatively small number of fast-growing and genetically easily manipulable model bacteria as biotechnological workhorses, the for the most part untapped diversity of bacteria needs to be explored when it comes to bioprospecting for natural product discovery. Members of the underexplored and evolutionarily deep-branching phylum Planctomycetes have only recently gained increased attention with respect to the production of small molecules with biomedical activities, e.g. as a natural source of novel antibiotics. Next-generation sequencing and metagenomics can provide access to the genomes of uncultivated bacteria from sparsely studied phyla, this, however, should be regarded as an addition rather than a substitute for classical strain isolation approaches. Ten years ago, a large sampling campaign was initiated to isolate planctomycetes from their varied natural habitats and protocols were developed to address complications during cultivation of representative species in the laboratory. The chracterisation of approximately 90 novel strains by several research groups in the recent years opened a detailed in silico look into the coding potential of individual members of this phylum. Here, we review the current state on planctomycetal research, focusing on diversity, small molecule production and potential future applications. Although the field developed promising, the time frame of 10 years illustrates that the study other additional promising bacterial phyla as sources for novel small molecules needs to start rather today than tomorrow.

RevDate: 2021-09-22
CmpDate: 2021-09-21

Castillo-Álvarez F, Pérez-Matute P, Oteo JA, et al (2021)

The influence of interferon β-1b on gut microbiota composition in patients with multiple sclerosis.

Neurologia (Barcelona, Spain), 36(7):495-503.

INTRODUCTION: The association between gut microbiota and animal models of multiple sclerosis has been well established; however, studies in humans are scarce.

METHODS: We performed a descriptive, cross-sectional study comparing the relative composition of gut microbiota in 30 patients with multiple sclerosis (15 treated with interferon β-1b, 15 not receiving this treatment) and 14 healthy controls using next generation sequencing.

RESULTS: Patients with multiple sclerosis and controls showed differences in the proportion of Euryarchaeota, Firmicutes, Proteobacteria, Actinobacteria, and Lentisphaerae phyla and in 17 bacterial species. More specifically, we found significant differences in the proportion of Firmicutes, Actinobacteria, and Lentisphaerae and 6 bacteria species between controls and untreated patients; however, these differences disappeared when compared with treated patients. Untreated patients showed a significant reduction in the proportion of Prevotella copri compared to controls, while the bacteria was significantly more abundant in patients treated with interferon β-1b than in untreated patients, with levels resembling those observed in the healthy control group.

CONCLUSION: We observed differences in gut microbiota composition between patients with multiple sclerosis and controls, and between patients treated and not treated with interferon β-1b. In most cases, no differences were observed between treated patients and healthy controls, particularly for P. copri levels. This suggests that the clinical improvements observed in patients with multiple sclerosis receiving interferon β-1b may result from the effect of the drug on gut microbiota. Longitudinal and functional studies are necessary to establish a causal relationship.

RevDate: 2021-09-24

Li N, Chen J, Liu C, et al (2021)

Cu and Zn exert a greater influence on antibiotic resistance and its transfer than doxycycline in agricultural soils.

Journal of hazardous materials, 423(Pt B):127042 pii:S0304-3894(21)02010-0 [Epub ahead of print].

Livestock manure is a main source of heavy metals, antibiotics and antibiotic resistance genes (ARGs) in agricultural soils. The co-existence of heavy metals and ARGs needs to be systematically studied, since manure application is greatly encouraged. In this study, we examined soils for alterations in antibiotic resistance where doxycycline, Cu, and Zn were added equivalent to those found in typical pig manure applications. The results indicated that high levels of Cu inhibited soil respiration and urease for the first 10 days. Metagenomic analysis demonstrated that Cu and Zn additions caused profound alterations in bacterial community, metal resistance genes (MRGs) and mobile genetic elements. Among the differential ARGs, efflux pump genes took a significantly high ratio compared with control for the first 5 days, emphasizing their important roles in the profile of antibiotic resistance. Moreover, the number of differential MRGs was < 30 for doxycycline treatment, but 66-87 for Cu and Zn treatments. The number of differential integrative and conjugative elements was 3 for doxycycline treatment, and 6-13 for Cu and Zn treatments. Overall, high Cu and Zn levels caused a greater influence than did doxycycline on bacterial communities and transfer of antibiotic resistance in soil.

RevDate: 2021-09-24

Zhou J, Wang D, Ju F, et al (2021)

Profiling microbial removal of micropollutants in sand filters: Biotransformation pathways and associated bacteria.

Journal of hazardous materials, 423(Pt B):127167 pii:S0304-3894(21)02135-X [Epub ahead of print].

Although there is growing evidence that micropollutants can be microbially converted in rapid sand filters of drinking water treatment plants (DWTPs), little is known about the biotransformation pathways and associated microbial strains in this process. Here, we constructed sand filter columns filled with manganese or quartz sand obtained from full-scale DWTPs to explore the biotransformation of eight micropollutants. Under seven different empty bed contact times (EBCTs), the column experiments showed that caffeine and atenolol were easily removed (up to 92.1% and 97.6%, respectively) with adsorption and microbial biotransformation of the filters. In contrast, the removal of other six micropollutants (i.e., naproxen, carbamazepine, atrazine, trimethoprim, sulfamethoxazole, and sulfadiazine) in the filters were less than 27.1% at shorter EBCTs, but significantly increased at EBCT = 4 h, indicating the dominant role of microbial biotransformation in these micropollutants removal. Integrated analysis of metagenomic reads and transformation products of micropollutants showed a shift in caffeine oxidation and demethylation pathways at different EBCTs, simultaneous occurrence of atrazine hydrolysis and oxidation pathways, and sulfadiazine and sulfamethoxazole oxidation in the filters. Furthermore, using genome-centric analysis, we observed previously unidentified degrading strains, e.g., Piscinibacter, Hydrogenophaga, and Rubrivivax for caffeine transformation, and Methylophilus and Methyloversatilis for atenolol transformation.

RevDate: 2021-09-20

Nathani NM, Dave KJ, Vatsa PP, et al (2021)

Author Correction: 309 metagenome assembled microbial genomes from deep sediment samples in the Gulfs of Kathiawar Peninsula.

Scientific data, 8(1):246 pii:10.1038/s41597-021-01027-1.

RevDate: 2021-09-24
CmpDate: 2021-09-24

Mao Y, Li X, Lou H, et al (2021)

Detection of Coccidioides posadasii in a patient with meningitis using metagenomic next-generation sequencing: a case report.

BMC infectious diseases, 21(1):968.

BACKGROUND: Coccidioidomycosis is a systemic infection caused by dimorphic fungi Coccidioides spp. endemic to Southwestern United States and Central and South America. A history of residence and travel in these areas is essential for the diagnostic of coccidioidomycosis, which has highly variable symptoms ranging from asymptomatic to severe, disseminated infection, and even death. Immunocompromised patients of coccidioidomycosis experience a high risk of dissemination, chronic infection, and mortality. Meningitis is one of the most deleterious coccidioidomycosis and can cause various life-threatening complications.

CASE PRESENTATION: Here we report a case of Coccidioides posadasii meningitis in a 49-year-old female who returned to China after one and a half years residence in Los Angeles, USA. The repeated routine cultures using CSF for bacteria or fungi were all negative. To hunt for an infectious etiology, the state-of-the-art technology metagenomic next-generation sequencing (mNGS) was then utilized, suggesting Coccidioides posadasii. Organizational pathological examination and polymerase-chain-reaction (PCR) results subsequently confirmed the mNGS detection.

CONCLUSION: To our knowledge, cases for coccidioidal meningitis have been rarely reported in China. While global travelling may spread this disease across continents and make the diagnosis more difficult. mNGS can detect almost all known pathogens with high sensitivity and specificity, especially for uncommon pathogen, such as Coccidioides posadasii in China.

RevDate: 2021-09-17

Pellitier PT, DR Zak (2021)

Ectomycorrhizal fungal decay traits along a soil nitrogen gradient.

The New phytologist [Epub ahead of print].

The extent to which ectomycorrhizal fungi decay soil organic matter SOM has implications for accurate predictions of forest ecosystem response to climate change. The distribution of gene-traits associated with SOM decay remains poorly understood among ectomycorrhizal fungal communities. We hypothesized that soil inorganic N availability acts as an environmental filter that structures the distribution of genes associated with SOM decay and specifically, that ectomycorrhizal fungal communities occurring in inorganic N poor soils have greater SOM decay potential. To test this hypothesis, we paired amplicon and shotgun metagenomic sequencing of 60 ectomycorrhizal fungal communities associating with Quercus rubra L. along a natural soil inorganic N gradient. Ectomycorrhizal fungal communities occurring in low inorganic N soils were enriched in gene families involved in the decay of lignin, cellulose, and chitin. Ectomycorrhizal fungal community composition were the strongest driver of shifts in metagenomic estimates of fungal decay potential. Our study illuminates the identity of key ectomycorrhizal fungal taxa and gene families potentially involved in the decay of SOM, and we link rhizomorphic and medium-distance hyphal morphologies with enhanced SOM decay potential. Coupled shifts in ectomycorrhizal fungal community composition and community level decay gene frequencies are consistent with outcomes of trait-mediated community assembly processes.

RevDate: 2021-09-18

Vanmechelen B, Merino M, Vergote V, et al (2021)

Exploration of the Ixodes ricinus virosphere unveils an extensive virus diversity including novel coltiviruses and other reoviruses.

Virus evolution, 7(2):veab066.

Recent metagenomics studies have revealed several tick species to host a variety of previously undiscovered RNA viruses. Ixodes ricinus, which is known to be a vector for many viral, bacterial, and protozoan pathogens, is the most prevalent tick species in Europe. For this study, we decided to investigate the virosphere of Belgian I. ricinus ticks. High-throughput sequencing of tick pools collected from six different sampling sites revealed the presence of viruses belonging to many different viral orders and families, including Mononegavirales, Bunyavirales, Partitiviridae, and Reoviridae. Of particular interest was the detection of several new reoviruses, two of which cluster together with members of the genus Coltivirus. This includes a new strain of Eyach virus, a known causative agent of tick-borne encephalitis. All genome segments of this new strain are highly similar to those of previously published Eyach virus genomes, except for the fourth segment, encoding VP4, which is markedly more dissimilar, potentially indicating the occurrence of a genetic reassortment. Further polymerase chain reaction-based screening of over 230 tick pools for 14 selected viruses showed that most viruses could be found in all six sampling sites, indicating the wide spread of these viruses throughout the Belgian tick population. Taken together, these results illustrate the role of ticks as important virus reservoirs, highlighting the need for adequate tick control measures.

RevDate: 2021-09-18

Islam SMS, Ryu HM, Sayeed HM, et al (2021)

Eubacterium rectale Attenuates HSV-1 Induced Systemic Inflammation in Mice by Inhibiting CD83.

Frontiers in immunology, 12:712312.

The purpose of this study was to determine whether administration of the microorganism Eubacterium rectale (E. rectale) could regulate dendritic cell (DC) activation and systemic inflammation in herpes simplex virus type 1-induced Behçet's disease (BD). E. rectale, butyrate-producing bacteria, was administered to BD mice. Peripheral blood leukocytes (PBL) and lymph node cells were isolated and analyzed by flow cytometry. 16S rRNA metagenomic analysis was performed in the feces of mice to determine the differences in the composition of the microbial population between normal and BD mice. Serum cytokine levels were measured by enzyme-linked immunosorbent assay. The frequency of DC activation marker CD83 positive cells was significantly increased in PBL of BD mice. Frequencies of CD83+ cells were also significantly increased in patients with active BD. 16S rRNA metagenomic analysis revealed different gut microbiota composition between normal and BD mice. The administration of E. rectale to BD mice reduced the frequency of CD83+ cells and significantly increased the frequency of NK1.1+ cells with the improvement of symptoms. The co-administration of colchicine and E. rectale also significantly reduced the frequency of CD83+ cells. Differences in gut microbiota were observed between normal mice and BD mice, and the administration of E. rectale downregulated the frequency of CD83, which was associated with BD deterioration. These data indicate that E. rectale could be a new therapeutic adjuvant for BD management.

RevDate: 2021-09-24
CmpDate: 2021-09-24

Xie Z, Lai J, Ning C, et al (2021)

A case of paraplegia due to asymptomatic varicella-zoster virus infection in AIDS patient unexpectedly diagnosed by CSF metagenomic next-generation sequencing.

BMC infectious diseases, 21(1):963.

BACKGROUND: Varicella-zoster virus (VZV) infection may induce central nervous system complications in HIV/AIDS patients. However, it is rare to have paraplegia caused by VZV infection but no herpes zoster clinically. Asymptomatic VZV infection in HIV/AIDS patient increased the difficulty of diagnosis.

CASE PRESENTATION: We reported a 41-year-old male AIDS patient with rare asymptomatic VZV infection-induced paraplegia after his anti-retroviral therapy initiation. MRI of the spinal cord showed the morphology of the thoracic spinal cord was irregular and locally inflated. The patient was confirmed as VZV induced thoracic myelomyelitis by using the cerebrospinal fluid for metagenomic next-generation sequencing (mNGS).

CONCLUSIONS: mNGS may contribute to disease diagnosis for asymptomatic VZV infection-induced myelitis.

RevDate: 2021-09-17

Xu S, Lyu L, Zhu H, et al (2021)

Serum Metabolome Mediates the Antiobesity Effect of Celastrol-Induced Gut Microbial Alterations.

Journal of proteome research [Epub ahead of print].

The antiobesity effect of celastrol has been reported in numerous studies, but the underlying mechanism remains unclear. It is widely accepted that gut dysbiosis is closely related to obesity. The potential effect of celastrol on microbiota is worth exploring. In this study, the celastrol-induced weight loss was validated in high-fat diet (HFD)-induced obese mice, with the detection of reported phenotypes including a reduction in food intake, augments in dyslipidemia and glucose metabolism, and adipose thermogenesis. The anti-inflammatory effect of celastrol was also proved based on the alterations in serum cytokines. Antibiotic interference showed that gut microbiota contributes to celastrol-induced weight loss. Several key bacteria were identified using shotgun metagenomic sequencing to display the alterations of the intestinal microbiome in obese mice treated with celastrol. Meanwhile, the fecal and serum metabolic profiles were generated by pseudotargeted metabolomics, and changes in some critical metabolites related to appetite and metabolism were detected. Importantly, we applied in silico bidirectional mediation analysis to identify the precise connections among the alterations in gut microbes, serum metabolome, and host phenotypes induced by celastrol treatment for the first time. Therefore, we concluded that the celastrol-induced microbial changes partially contribute to the antiobesity effect via the serum metabolome. The mass spectrometry data are deposited on MetaboLights (ID: MTBLS3278).

RevDate: 2021-09-23

Zhang Q, Xu J, Wang X, et al (2021)

Performance of full-scale aerobic composting and anaerobic digestion on the changes of antibiotic resistance genes in dairy manure.

Bioresource technology, 342:125898 pii:S0960-8524(21)01240-2 [Epub ahead of print].

Understanding the different performances of full-scale active composting (AC) and anaerobic digestion (AD) on the changes of antibiotic resistance genes (ARGs) in dairy manure is crucial to uncover the dissemination risks of ARGs in post-biotreated manure. In this regard, metagenomic sequencing was deployed to reveal the variations of ARGs in dairy manure in an intensive dairy farm. Results showed that the total abundance of ARGs increased from 150.64 reads/ng DNA to 204.06 reads/ng DNA in dairy manure, and it is mainly attributed to the contributions of AC (85.49%) rather than AD (14.51%). In AC, more ARG subtypes were induced and the dominant ARG subtypes were shifted completely, probably due to the enrichment of Proteobacteria and Actinobacteria which could be the hosts of multiple ARGs. These results inspire us to further evaluate the dissemination risks of ARGs along the route from composted manure to soil and to plants.

RevDate: 2021-09-23

Liu C, Yan H, Sun Y, et al (2021)

Contribution of enrofloxacin and Cu2+ to the antibiotic resistance of bacterial community in a river biofilm.

Environmental pollution (Barking, Essex : 1987), 291:118156 pii:S0269-7491(21)01738-3 [Epub ahead of print].

Pollutants discharged from wastewater are the main cause of the spread of antibiotic resistance in river biofilms. There is controversy regarding the primary contribution of environmental selectors such as antibiotics and heavy metals to the development of antibiotic resistance in bacterial communities. Here, this study compared the effect of environmental safety concentration Cu2+ and enrofloxacin (ENR) on the evolution of antibiotic resistance by examining phenotypic characteristics and genotypic profiles of bacterial communities in a river biofilm, and then distinguished the major determinants from a comprehensive perspective. The pollution induced community tolerance in ENR-treated group was significantly higher than that in Cu2+-treated group (at concentration levels of 100 and 1000 μg/L). Metagenomic sequencing results showed that ENR significantly increased the number and total abundance of antibiotic resistance genes (ARGs), but there was no significant change in the Cu2+- treated group. Compared with Cu2+, ENR was the major selective agent in driving the change of taxonomic composition because the taxonomic composition in ENR was the most different from the original biofilm. Comparing and analyzing the prokaryotic composition, the phylum of Proteobacteria was enriched in both ENR and Cu2+ treated groups. Among them, Acidovorax and Bosea showed resistance to both pollutants. Linking taxonomic composition to ARGs revealed that the main potential hosts of fluoroquinolone resistance genes were Comamonas, Sphingopyxis, Bradyrhizobium, Afipia, Rhodopseudomonas, Luteimonas and Hoeflea. The co-occurrence of ARGs and metal resistance genes (MRGs) showed that the multidrug efflux pump was the key mechanism connecting MRGs and ARGs. Network analysis also revealed that the reason of Cu2+ selected for fluoroquinolones resistant bacterial communities was the coexistence of multidrug efflux gene and MRGs. Our research emphasizes the importance of antibiotics in promoting the development of antibiotic resistant bacterial communities from the perspective of changes in community structure and resistome in river biofilms.

RevDate: 2021-09-24

Quispe-Cardenas E, S Rogers (2021)

Microbial adaptation and response to high ammonia concentrations and precipitates during anaerobic digestion under psychrophilic and mesophilic conditions.

Water research, 204:117596 pii:S0043-1354(21)00791-0 [Epub ahead of print].

This study explored microbial adaptation to high ammonia concentrations (<1000 mg/L to 4000 mg/L) during anaerobic digestion (AD) under psychrophilic and mesophilic conditions, the latter of which yielded precipitates facilitating investigation of microbial response. The experimental setup was performed at bench-scale using microbial consortia from four different operating anaerobic digesters treating different organic wastes (WW-wastewater sludge, MN-manure, FW- food waste and CO-co-digestion (FW & MN)). Adaptation experiments were conducted with semi-continuous flow mode to resemble large-scale operation. Metagenome and 16S RNA analysis were performed for the first time in a psychrophilic reactor during an ammonia acclimation process. These analyses were also performed in mesophilic reactor exposed to precipitates and high ammonia levels. Diversity reduced when adaptation occurred successfully from 1.1 to 4 g/L of total ammonia nitrogen (TAN) under psychrophilic conditions, while the microbial community became more diverse under mesophilic conditions with ammonia inhibition. We report for the first time Methanocorposculum as a robust hydrogenotrophic methanogen at high ammoniacal concentrations under psychrophilic conditions. Additionally, Methanosarcina was present in low and high ammoniacal concentrations in mesophilic conditions, but there was a shift in species dominance. Methanosarcina barkeri stands out as a more resilient methanogen compared to Methanosarcina mazei, which initially dominated at <1.1 g/L TAN. We also explored the effects of sudden precipitates on methanogenic communities and methane production when they occurred under mesophilic conditions in two reactors. Methane production declined by more than 50% when precipitates occurred and was accompanied by pH reduction and VFA accumulation. Diversity data corroborated that methanogens were severely reduced. These two reactors were not able to recover with 50 days of added operation, demonstrating potential for long-term negative impacts of precipitate formation on AD performance stemming from negative impact to methanogenic communities.

RevDate: 2021-09-24

Kim DD, Wan L, Cao X, et al (2021)

Metagenomic insights into co-proliferation of Vibrio spp. and dinoflagellates Prorocentrum during a spring algal bloom in the coastal East China Sea.

Water research, 204:117625 pii:S0043-1354(21)00820-4 [Epub ahead of print].

Coastal harmful algal blooms (HABs), commonly termed 'red tides', have severe undesirable consequences to the marine ecosystems and local fishery and tourism industries. Increase in nitrogen and/or phosphorus loading is often regarded as the major culprits of increasing frequency and intensity of the coastal HAB; however, fundamental understanding is lacking as to the causes and mechanism of bloom formation despite decades of intensive investigation. In this study, we interrogated the prokaryotic microbiomes of surface water samples collected at two neighboring segments of East China Sea that contrast greatly in terms of the intensity and frequency of Prorocentrum-dominated HAB. Mantel tests identified significant correlations between the structural and functional composition of the microbiomes and the physicochemical state and the algal biomass density of the surface seawater, implying the possibility that prokaryotic microbiota may play key roles in the coastal HAB. A conspicuous feature of the microbiomes at the sites characterized with high trophic state index and eukaryotic algal cell counts was disproportionate proliferation of Vibrio spp., and their complete domination of the functional genes attributable to the dissimilatory nitrate reduction to ammonia (DNRA) pathway substantially enriched at these sites. The genes attributed to phosphorus uptake function were significantly enriched at these sites, presumably due to the Pi-deficiency induced by algal growth; however, the profiles of the phosphorus mineralization genes lacked consistency, barring any conclusive evidence with regard to contribution of prokaryotic microbiota to phosphorus bioavailability. The results of the co-occurrence network analysis performed with the core prokaryotic microbiome supported that the observed proliferation of Vibrio and HAB may be causally associated. The findings of this study suggest a previously unidentified association between Vibrio proliferation and the Prorocentrum-dominated HAB in the subtropical East China Sea, and opens a discussion regarding a theoretically unlikely, but still possible, involvement of Vibrio-mediated DNRA in Vibrio-Prorocentrum symbiosis. Further experimental substantiation of this supposed symbiotic mechanism may prove crucial in understanding the dynamics of explosive local algal growth in the region during spring algal blooms.

RevDate: 2021-09-26

Zhang Q, Guo X, Xie C, et al (2021)

Unraveling the metabolic pathway of choline-TMA-TMAO: Effects of gypenosides and implications for the therapy of TMAO related diseases.

Pharmacological research, 173:105884 pii:S1043-6618(21)00468-0 [Epub ahead of print].

Trimethylamine-N-oxide (TMAO) has emerged as a promising new therapeutic target for the treatment of central nervous system diseases, atherosclerosis and other diseases. However, its origin in the brain is unclear. Gynostemma pentaphyllum (Thunb.) Makino can reduce the increase of TMAO level caused by a high fat diet. But its effective chemical composition and specific mechanism have not been reported. The study confirmed that TMA was more easily to penetrate blood brain barrier than TMAO, the MAO enzyme was partly involved in the transformation of the TMA in brain, which further supplemented the choline-TMA-TMAO pathway. Based on the above metabolic pathway, using multi-omics approaches, such as microbiodiversity, metagenomics and lipidomics, it was demonstrated that the reduction of plasma TMAO levels by gypenosides did not act on FMO3 and MAO in the pathway, but remodeled the microbiota and affected the trimethylamine lyase needed in the conversion of choline to TMA in intestinal flora. At the same time, gypenosides interfered with enzymes associated with TCA and lipid metabolism, thus affecting TMAO and lipid metabolism. Considering the bidirectional transformation of phosphatidycholine and choline, lipid metabolism and TMAO metabolism could affected each other to some extent. In conclusion, our study revealed the intrinsic correlation between long-term application of gypenosides to lipid reduction and nervous system protection, and explained why gypenosides were used to treat brain diseases, even though they had a poor ability to enter the brain. Besides, it provided a theoretical basis for clinical application of gypenosides and the development of new drugs.

RevDate: 2021-09-16

Lanko K, Shi C, Patil S, et al (2021)

Assessing In Vitro Resistance Development in Enterovirus A71 in the Context of Combination Antiviral Treatment.

ACS infectious diseases [Epub ahead of print].

There are currently no antivirals available to treat infection with enterovirus A71 (EV-A71) or any other enterovirus. The extensively studied capsid binders rapidly select for drug-resistant variants. We here explore whether the combination of two direct-acting enterovirus inhibitors with a different mechanism of action may delay or prevent resistance development to the capsid binders. To that end, the in vitro dynamics of resistance development to the capsid binder pirodavir was studied either alone or in combination with a viral 2C-targeting compound (SMSK_0213), a viral 3C-protease inhibitor (rupintrivir) or a viral RNA-dependent RNA polymerase inhibitor (7DMA). We demonstrate that combining pirodavir with either rupintrivir or 7DMA delays the development of resistance to pirodavir and that no resistance to the protease or polymerase inhibitor develops. The combination of pirodavir with the 2C inhibitor results in a double-resistant virus population, where only the minority carries the resistant mutation.

RevDate: 2021-09-16

Gorovtsov A, Demin K, Sushkova S, et al (2021)

The effect of combined pollution by PAHs and heavy metals on the topsoil microbial communities of Spolic Technosols of the lake Atamanskoe, Southern Russia.

Environmental geochemistry and health [Epub ahead of print].

The contamination with organic and inorganic pollutants changes significantly soil microbial community structure. These shifts indicate anthropogenic pressure and help to discover new possibilities for soil remediation. In this study, the microbial community structure of Spolic Technosols formed at the territory of a former industrial sludge reservoir near the Kamensk-Shakhtinsky (Southern Russia) was studied using a metagenomics approach. The studied soils contain high concentrations of heavy metals (HM) (up to 72,900 mg kg-1) and 16 priority polycyclic aromatic hydrocarbons (PAHs) (up to 6670 mg kg-1). Its microbial communities demonstrate an excellent adaptability level reflected in their complexity and diversity. As shown by the high values of alpha diversity indices (Shannon values up to 10.1, Chao1 values from 1430 to 4273), instead of decreasing quantitatively and qualitatively on the systemic level, microbial communities tend to undergo complex redistribution. Regardless of contamination level, the share of Actinobacteria and Proteobacteria was consistently high and varied from 20 to 50%. Following the results of the Mann-Whitney U test, there were significant changes of less abundant phyla. The abundance of oligotrophic bacteria from Gemmatimonadetes and Verrucomicrobia phyla and autotrophic bacteria (e.g., Nitrospira) decreased due to the high PAH's level. And abundance of Firmicutes and amoebae-associated bacteria such as TM6 and soil Chlamydia increased in highly contaminated plots. In the Spolic Technosols studied, the influence of factors on the microbial community composition decreased from PAHs concentration to soil characteristics (organic carbon content) and phylum-phylum interactions. The high concentrations of HMs influenced weakly on the microbial community composition.

RevDate: 2021-09-19

Hause BM, Nelson E, J Christopher-Hennings (2021)

Identification of boosepivirus B in U.S. calves.

Archives of virology [Epub ahead of print].

Bovine enteric disease has a complex etiology that can include viral, bacterial, and parasitic pathogens and is a significant source of losses due to morbidity and mortality. Boosepivirus was identified in calves with enteric disease with unclear etiology in Japan in 2009 and has not been reported elsewhere. Metagenomic sequencing and PCR here identified boosepivirus in bovine enteric disease diagnostic submissions from six states in the USA with 98% sequence identity to members of the species Boosepivirus B. In all cases, boosepivirus was identified as a coinfection with the established pathogens bovine coronavirus, bovine rotavirus, and cryptosporidia. Further research is needed to determine the clinical significance of boosepivirus infection.

RevDate: 2021-09-22
CmpDate: 2021-09-22

Zhu N, Zhou D, S Li (2021)

Diagnostic Accuracy of Metagenomic Next-Generation Sequencing in Sputum-Scarce or Smear-Negative Cases with Suspected Pulmonary Tuberculosis.

BioMed research international, 2021:9970817.

Objective: To investigate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) samples or lung biopsy specimens from which suspected pulmonary tuberculosis (PTB) patients have no sputum or negative smear.

Materials and Methods: Sputum-scarce or smear-negative cases with suspected PTB (n = 107) were analyzed from January 2018 to June 2020. We collected BALF or lung tissue biopsy samples with these cases of suspected TB during hospitalization. The diagnostic accuracy of mNGS for these samples was compared with those of conventional tests or the T-SPOT.TB assay.

Results: 46 cases of PTB patients and 61 cases of non-PTB patients were finally enrolled and analyzed. mNGS exhibited a sensitivity of 89.13%, which was higher than conventional tests (67.39%) but equivalent to those of the T-SPOT.TB assay alone (76.09%) or T-SPOT.TB assay in combination with conventional tests (91.30%). The specificity of mNGS was 98.36%, similar to conventional tests (95.08%) but significantly higher than those of the T-SPOT.TB assay alone (65.57%) or the T-SPOT.TB assay in combination with conventional tests (63.93%). There was no significant difference in the diagnostic accuracy of mNGS in BALF samples and lung biopsy tissue specimens.

Conclusion: Our findings demonstrate that mNGS could offer improved detection of Mycobacterium tuberculosis in BALF or lung tissue biopsy samples in sputum-scarce or smear-negative cases with suspected PTB.


RJR Experience and Expertise


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.


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.


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.


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.


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.


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.


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.


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.

963 Red Tail Lane
Bellingham, WA 98226


E-mail: RJR8222@gmail.com

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

short personal version

Curriculum Vitae for R J Robbins

long standard version

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