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Bibliography on: Metagenomics

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ESP: PubMed Auto Bibliography 08 Mar 2021 at 01:30 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: 2021-03-06

Ruiz-Perez CA, Bertagnolli AD, Tsementzi D, et al (2021)

Description of Candidatus Mesopelagibacter carboxydoxydans and Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones.

Systematic and applied microbiology, 44(2):126185 pii:S0723-2020(21)00008-4 [Epub ahead of print].

The diverse and ubiquitous members of the SAR11 lineage (Alphaproteobacteria) represent up to 30-40% of the surface and mesopelagic oceanic microbial communities. However, the molecular and ecological mechanisms that differentiate closely related, yet distinct, SAR11 members that often co-occur under similar environmental conditions remain speculative. Recently, two mesopelagic and oxygen minimum zone (OMZ)-associated subclades of SAR11 (Ic and IIa.A) were described using single-cell amplified genomes (SAGs) linked to nitrate reduction in OMZs. In this current study, the collection of genomes belonging to these two subclades was expanded with thirteen new metagenome-assembled genomes (MAGs), thus providing a more detailed phylogenetic and functional characterization of these subclades. Gene content-based predictions of metabolic functions revealed similarities in central carbon metabolism between subclades Ic and IIa.A and surface SAR11 clades, with small variations in central pathways. These variations included more versatile sulfur assimilation pathways, as well as a previously predicted capacity for nitrate reduction that conferred unique versatility on mesopelagic-adapted clades compared to their surface counterparts. Finally, consistent with previously reported abundances of carbon monoxide (CO) in surface and mesopelagic waters, subclades Ia (surface) and Ic (mesopelagic) have the genetic potential to oxidize carbon monoxide (CO), presumably taking advantage of this abundant compound as an electron donor. Based on genomic analyses, environmental distribution and metabolic reconstruction, we propose two new SAR11 genera, Ca. Mesopelagibacter carboxydoxydans (subclade Ic) and Ca. Anoxipelagibacter denitrificans (subclade IIa.A), which represent members of the mesopelagic and OMZ-adapted SAR11 clades.

RevDate: 2021-03-06

Zheng M, Han H, Shi J, et al (2021)

Metagenomic analysis of aromatic ring-cleavage mechanism in nano-Fe3O4@activated coke enhanced bio-system for coal pyrolysis wastewater treatment.

Journal of hazardous materials, 414:125387 pii:S0304-3894(21)00350-2 [Epub ahead of print].

In current study, nano-Fe3O4@activated coke enhanced bio-system (FEBS) under limited-oxygen condition was applied for efficient treatment of aromatic organics in coal pyrolysis wastewater. Metagenomic analyses revealed functional microbiome linkages and mechanism involved in aromatic ring-cleavage. Based on biodegradation efficiency in different reactors, FEBS supplementation conferred the best organic removal (avg. 92.29%). It also showed a remarkable advantage in biodegradability maintenance (>40%) over control reactors. Metagenomics profiling revealed the degradation processes were driven by Fe3O4 redox reactions and microbial biofilm, while the suspended sludge was the principal force for aromatic mineralization. Based on the analysis of functional species and genes, most bacteria cleaved the benzene ring preferably through the aerobic pathways, mediated by catechol 1, 2-dioxygenase, catechol 2, 3-dioxygenase and protocatechuate 3, 4-dioxygenase (66-84%). Ecological network showed that Comamonas testosterone-centered microbiome and Azotobacter linked to the nitrogen (N)-heterocyclic ring-cleavage. Network linkage further demonstrated that Alicycliphilus and Acidovorax were the key tone taxa involved in benzene ring-cleavage. Finally, combined with analysis of degradation products, bacteria degraded N-heterocyclic ring containing organic aromatic compounds (quinoline) mainly through anaerobic processes, whereas cleavage of benzene ring preferred aerobic pathways. The enriched functional species were the primary reason for the enhanced biodegradation in FEBS.

RevDate: 2021-03-06

Du B, Wang Q, Yang Q, et al (2021)

Responses of bacterial and bacteriophage communities to long-term exposure to antimicrobial agents in wastewater treatment systems.

Journal of hazardous materials, 414:125486 pii:S0304-3894(21)00449-0 [Epub ahead of print].

The occurrence of antibacterial agents has received increasing concern due to their possible threats to human health. However, the effects of antibacterial residues on the evolution and dynamics between bacteria and bacteriophages in wastewater treatment systems have seldom been researched. Especially for phages, little is known about their response to antimicrobial exposure. In this study, two identical anoxic-aerobic wastewater treatment systems were established to evaluate the responses of bacterial and phage communities to long-term exposure to antimicrobial agents. The results indicated simultaneous exposure to combined antimicrobials significantly inhibited (p < 0.05) the abundance of phages and bacteria. Metagenomic sequencing analysis indicated the community of bacteria and phages changed greatly at the genus level due to combined antibacterial exposure. Additionally, long-term exposure to antimicrobial agents promoted the attachment of receptor-binding protein genes to Klebsiella, Escherichia and Salmonella (which were all members of Enterobacteriaceae). Compared to that in the control system, the numbers of receptor-binding protein genes on their possible phages (such as Lambdalikevirus and P2likevirus) were also obviously higher when the microorganisms were exposed to antimicrobials. The results are helpful to understanding the microbial communities and tracking the relationship of phage-bacterial host systems, especially under the pressure of antimicrobial exposure.

RevDate: 2021-03-06

Cheng X, He F, Sun P, et al (2021)

Identification of unknown acid-resistant genes of oral microbiotas in patients with dental caries using metagenomics analysis.

AMB Express, 11(1):39.

Acid resistance is critical for the survival of bacteria in the dental caries oral micro-environment. However, there are few acid-resistant genes of microbiomes obtained through traditional molecular biology experimental techniques. This study aims to try macrogenomics technologies to efficiently identify acid-resistant genes in oral microbes of patients with dental caries. Total DNA was extracted from oral microbiota obtained from thirty dental caries patients and subjected to high-throughput sequencing. This data was used to build a metagenomic library, which was compared to the sequences of two Streptococcus mutant known acid-resistant genes, danK and uvrA, using a BLAST search. A total of 19 and 35 unknown gene sequences showed similarities with S. mutans uvrA and dnaK in the metagenomic library, respectively. Two unknown genes, mo-dnaK and mo-uvrA, were selected for primer design and bioinformatic analysis based on their sequences. Bioinformatics analysis predicted them encoding of a human heat-shock protein (HSP) 70 and an ATP-dependent DNA repair enzyme, respectively, closely related with the acid resistance mechanism. After cloning, these genes were transferred into competent Escherichia coli for acid resistance experiments. E. coli transformed with both genes demonstrated acid resistance, while the survival rate of E. coli transformed with mo-uvrA was significantly higher in an acidic environment (pH = 3). Through this experiment we found that identify unknown acid-resistant genes in oral microbes of patients with caries by establishing a metagenomic library is very efficient. Our results provide an insight into the mechanisms and pathogenesis of dental caries for their treatment without affecting oral probiotics.

RevDate: 2021-03-06

Arumugam M, Sundararaju S, Jagadesan S, et al (2021)

Metagenomic Analysis of Microbial Community Affiliated with Termitarium Reveals High Lignocellulolytic Potential.

Current microbiology [Epub ahead of print].

Termitarium (nest of termites) is a rich source of microbial populations whose resources remain untapped to date. Using the metagenomic sequencing approach, we generated 38 GB sequences comprising 808,386 contigs (896 MB) with a maximum contig size of 470 kb. The taxonomic profile obtained by BLAST against the NCBI NR database and annotation by MEGAN showed that the termitarium microbial community was dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Functional annotation using the CAZY database revealed a huge diversity of glycosyl hydrolase genes from 104 families, some of which appeared to be part of polysaccharide utilization systems (PUL). Strikingly, Actinobacteria was the main contributor of the cellulolytic and hemicellulolytic GHs. Genes involving in lignin degradation were also abundantly identified in this metagenome. Comparative analysis of COG profiles of termitarium with those of other lignocellulolytic microbial communities showed a distant clustering pattern resulting from the dietary differences in carbohydrate compositions. Altogether, this study revealed that termitarium hosts a unique microbial community, which can efficiently degrade lignocelluloses.

RevDate: 2021-03-06

Collins JH, Keating KW, Jones TR, et al (2021)

Engineered yeast genomes accurately assembled from pure and mixed samples.

Nature communications, 12(1):1485.

Yeast whole genome sequencing (WGS) lacks end-to-end workflows that identify genetic engineering. Here we present Prymetime, a tool that assembles yeast plasmids and chromosomes and annotates genetic engineering sequences. It is a hybrid workflow-it uses short and long reads as inputs to perform separate linear and circular assembly steps. This structure is necessary to accurately resolve genetic engineering sequences in plasmids and the genome. We show this by assembling diverse engineered yeasts, in some cases revealing unintended deletions and integrations. Furthermore, the resulting whole genomes are high quality, although the underlying assembly software does not consistently resolve highly repetitive genome features. Finally, we assemble plasmids and genome integrations from metagenomic sequencing, even with 1 engineered cell in 1000. This work is a blueprint for building WGS workflows and establishes WGS-based identification of yeast genetic engineering.

RevDate: 2021-03-06

Madoroba E, Magwedere K, Chaora NS, et al (2021)

Microbial Communities of Meat and Meat Products: An Exploratory Analysis of the Product Quality and Safety at Selected Enterprises in South Africa.

Microorganisms, 9(3): pii:microorganisms9030507.

Consumption of food that is contaminated by microorganisms, chemicals, and toxins may lead to significant morbidity and mortality, which has negative socioeconomic and public health implications. Monitoring and surveillance of microbial diversity along the food value chain is a key component for hazard identification and evaluation of potential pathogen risks from farm to the consumer. The aim of this study was to determine the microbial diversity in meat and meat products from different enterprises and meat types in South Africa. Samples (n = 2017) were analyzed for Yersinia enterocolitica, Salmonella species, Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Staphylococcus aureus, Clostridium perfringens, Bacillus cereus, and Clostridium botulinum using culture-based methods. PCR was used for confirmation of selected pathogens. Of the 2017 samples analyzed, microbial ecology was assessed for selected subsamples where next generation sequencing had been conducted, followed by the application of computational methods to reconstruct individual genomes from the respective sample (metagenomics). With the exception of Clostridium botulinum, selective culture-dependent methods revealed that samples were contaminated with at least one of the tested foodborne pathogens. The data from metagenomics analysis revealed the presence of diverse bacteria, viruses, and fungi. The analyses provide evidence of diverse and highly variable microbial communities in products of animal origin, which is important for food safety, food labeling, biosecurity, and shelf life limiting spoilage by microorganisms.

RevDate: 2021-03-06

Marzano M, Fosso B, Piancone E, et al (2021)

Stem Cell Impairment at the Host-Microbiota Interface in Colorectal Cancer.

Cancers, 13(5): pii:cancers13050996.

Colorectal cancer (CRC) initiation is believed to result from the conversion of normal intestinal stem cells (ISCs) into cancer stem cells (CSCs), also known as tumor-initiating cells (TICs). Hence, CRC evolves through the multiple acquisition of well-established genetic and epigenetic alterations with an adenoma-carcinoma sequence progression. Unlike other stem cells elsewhere in the body, ISCs cohabit with the intestinal microbiota, which consists of a diverse community of microorganisms, including bacteria, fungi, and viruses. The gut microbiota communicates closely with ISCs and mounting evidence suggests that there is significant crosstalk between host and microbiota at the ISC niche level. Metagenomic analyses have demonstrated that the host-microbiota mutually beneficial symbiosis existing under physiologic conditions is lost during a state of pathological microbial imbalance due to the alteration of microbiota composition (dysbiosis) and/or the genetic susceptibility of the host. The complex interaction between CRC and microbiota is at the forefront of the current CRC research, and there is growing attention on a possible role of the gut microbiome in the pathogenesis of CRC through ISC niche impairment. Here we primarily review the most recent findings on the molecular mechanism underlying the complex interplay between gut microbiota and ISCs, revealing a possible key role of microbiota in the aberrant reprogramming of CSCs in the initiation of CRC. We also discuss recent advances in OMICS approaches and single-cell analyses to explore the relationship between gut microbiota and ISC/CSC niche biology leading to a desirable implementation of the current precision medicine approaches.

RevDate: 2021-03-06

Park H, Yeo S, Kang S, et al (2021)

Longitudinal Microbiome Analysis in a Dextran Sulfate Sodium-Induced Colitis Mouse Model.

Microorganisms, 9(2): pii:microorganisms9020370.

The role of the gut microbiota in the pathogenesis of inflammatory bowel disease (IBD) has been in focus for decades. Although metagenomic observations in patients/animal colitis models have been attempted, the microbiome results were still indefinite and broad taxonomic presumptions were made due to the cross-sectional studies. Herein, we conducted a longitudinal microbiome analysis in a dextran sulfate sodium (DSS)-induced colitis mouse model with a two-factor design based on serial DSS dose (0, 1, 2, and 3%) and duration for 12 days, and four mice from each group were sacrificed at two-day intervals. During the colitis development, a transition of the cecal microbial diversity from the normal state to dysbiosis and dynamic changes of the populations were observed. We identified genera that significantly induced or depleted depending on DSS exposure, and confirmed the correlations of the individual taxa to the colitis severity indicated by inflammatory biomarkers (intestinal bleeding and neutrophil-derived indicators). Of note, each taxonomic population showed its own susceptibility to the changing colitis status. Our findings suggest that an understanding of the individual susceptibility to colitis conditions may contribute to identifying the role of the gut microbes in the pathogenesis of IBD.

RevDate: 2021-03-06

Turanli B, Yildirim E, Gulfidan G, et al (2021)

Current State of "Omics" Biomarkers in Pancreatic Cancer.

Journal of personalized medicine, 11(2): pii:jpm11020127.

Pancreatic cancer is one of the most fatal malignancies and the seventh leading cause of cancer-related deaths related to late diagnosis, poor survival rates, and high incidence of metastasis. Unfortunately, pancreatic cancer is predicted to become the third leading cause of cancer deaths in the future. Therefore, diagnosis at the early stages of pancreatic cancer for initial diagnosis or postoperative recurrence is a great challenge, as well as predicting prognosis precisely in the context of biomarker discovery. From the personalized medicine perspective, the lack of molecular biomarkers for patient selection confines tailored therapy options, including selecting drugs and their doses or even diet. Currently, there is no standardized pancreatic cancer screening strategy using molecular biomarkers, but CA19-9 is the most well known marker for the detection of pancreatic cancer. In contrast, recent innovations in high-throughput techniques have enabled the discovery of specific biomarkers of cancers using genomics, transcriptomics, proteomics, metabolomics, glycomics, and metagenomics. Panels combining CA19-9 with other novel biomarkers from different "omics" levels might represent an ideal strategy for the early detection of pancreatic cancer. The systems biology approach may shed a light on biomarker identification of pancreatic cancer by integrating multi-omics approaches. In this review, we provide background information on the current state of pancreatic cancer biomarkers from multi-omics stages. Furthermore, we conclude this review on how multi-omics data may reveal new biomarkers to be used for personalized medicine in the future.

RevDate: 2021-03-06

Gao B, Zhang X, B Schnabl (2021)

Fungi-Bacteria Correlation in Alcoholic Hepatitis Patients.

Toxins, 13(2): pii:toxins13020143.

Alcohol-related liver disease is one of the most prevalent types of chronic liver diseases globally. Alcohol-related liver disease begins with fatty liver, which further develops into hepatic inflammation, hepatocyte injury, and progresses to fibrosis and cirrhosis. Compositional changes of gut bacteria and fungi were found in patients with alcohol-related liver disease. However, the functional changes of fungi and correlations between fungi and bacteria have not been investigated. In this study, we first examined the functional capacity of fungi in patients with alcohol-related liver disease using shotgun metagenomics. Among 24 MetaCyc pathways contributed by fungi, superpathway of allantoin degradation in yeast was enriched in patients with alcoholic hepatitis. Furthermore, we compared the predictive power of bacteria versus fungi and found that bacteria performed better than fungi to separate patients with alcoholic hepatitis from non-alcoholic controls and patients with alcohol use disorder. Finally, we investigated the associations between the intestinal fungi and bacteria in alcoholic hepatitis patients. Positive association between fungi and bacteria was found between Cladosporium and Gemmiger, meanwhile negative association was found between Cryptococcus and Pseudomonas in alcoholic hepatitis patients.

RevDate: 2021-03-06

Beyi AF, Hassall A, Phillips GJ, et al (2021)

Tracking Reservoirs of Antimicrobial Resistance Genes in a Complex Microbial Community Using Metagenomic Hi-C: The Case of Bovine Digital Dermatitis.

Antibiotics (Basel, Switzerland), 10(2): pii:antibiotics10020221.

Bovine digital dermatitis (DD) is a contagious infectious cause of lameness in cattle with unknown definitive etiologies. Many of the bacterial species detected in metagenomic analyses of DD lesions are difficult to culture, and their antimicrobial resistance status is largely unknown. Recently, a novel proximity ligation-guided metagenomic approach (Hi-C ProxiMeta) has been used to identify bacterial reservoirs of antimicrobial resistance genes (ARGs) directly from microbial communities, without the need to culture individual bacteria. The objective of this study was to track tetracycline resistance determinants in bacteria involved in DD pathogenesis using Hi-C. A pooled sample of macerated tissues from clinical DD lesions was used for this purpose. Metagenome deconvolution using ProxiMeta resulted in the creation of 40 metagenome-assembled genomes with ≥80% complete genomes, classified into five phyla. Further, 1959 tetracycline resistance genes and ARGs conferring resistance to aminoglycoside, beta-lactams, sulfonamide, phenicol, lincosamide, and erythromycin were identified along with their bacterial hosts. In conclusion, the widespread distribution of genes conferring resistance against tetracycline and other antimicrobials in bacteria of DD lesions is reported for the first time. Use of proximity ligation to identify microorganisms hosting specific ARGs holds promise for tracking ARGs transmission in complex microbial communities.

RevDate: 2021-03-06

Sanchez-Cid C, Guironnet A, Wiest L, et al (2021)

Gentamicin Adsorption onto Soil Particles Prevents Overall Short-Term Effects on the Soil Microbiome and Resistome.

Antibiotics (Basel, Switzerland), 10(2): pii:antibiotics10020191.

Antibiotics used in agriculture may reach the environment and stimulate the development and dissemination of antibiotic resistance in the soil microbiome. However, the scope of this phenomenon and the link to soil properties needs to be elucidated. This study compared the short-term effects of a range of gentamicin concentrations on the microbiome and resistome of bacterial enrichments and microcosms of an agricultural soil using a metagenomic approach. Gentamicin impact on bacterial biomass was roughly estimated by the number of 16SrRNA gene copies. In addition, the soil microbiome and resistome response to gentamicin pollution was evaluated by 16SrRNA gene and metagenomic sequencing, respectively. Finally, gentamicin bioavailability in soil was determined. While gentamicin pollution at the scale of µg/g strongly influenced the bacterial communities in soil enrichments, concentrations up to 1 mg/g were strongly adsorbed onto soil particles and did not cause significant changes in the microbiome and resistome of soil microcosms. This study demonstrates the differences between the response of bacterial communities to antibiotic pollution in enriched media and in their environmental matrix, and exposes the limitations of culture-based studies in antibiotic-resistance surveillance. Furthermore, establishing links between the effects of antibiotic pollution and soil properties is needed.

RevDate: 2021-03-06

Yoo K, G Lee (2021)

Investigation of the Prevalence of Antibiotic Resistance Genes According to the Wastewater Treatment Scale Using Metagenomic Analysis.

Antibiotics (Basel, Switzerland), 10(2): pii:antibiotics10020188.

Although extensive efforts have been made to investigate the dynamics of the occurrence and abundance of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), understanding the acquisition of antibiotic resistance based on the WWTP scale and the potential effects on WWTPs is of relatively less interest. In this study, metagenomic analysis was carried out to investigate whether the WWTP scale could be affected by the prevalence and persistence of ARGs and mobile genetic elements (MGEs). As a result, 152 ARG subtypes were identified in small-scale WWTP samples, while 234 ARG subtypes were identified in large-scale WWTP samples. Among the detectable ARGs, multidrug, MLS (macrolide-lincosamide-streptogramin), sulfonamide, and tetracycline resistance genes had the highest abundance, and large and small WWTPs had similar composition characteristics of ARGs. In MGE analysis, plasmids and integrons were 1.5-2.0-fold more abundant in large-scale WWTPs than in small-scale WWTPs. The profile of bacteria at the phylum level showed that Proteobacteria and Actinobacteria were the most dominant bacteria, representing approximately 70% across large- and small-scale WWTPs. Overall, the results of this study elucidate the different abundances and dissemination of ARGs between large- and small-scale WWTPs, which facilitates the development of next-generation engineered wastewater treatment systems.

RevDate: 2021-03-06

Kazarina A, Petersone-Gordina E, Kimsis J, et al (2021)

The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles.

Genes, 12(2): pii:genes12020309.

Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16-17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.

RevDate: 2021-03-06

Nakatani H, K Hori (2021)

Establishing a Percutaneous Infection Model Using Zebrafish and a Salmon Pathogen.

Biology, 10(2): pii:biology10020166.

To uncover the relationship between skin bacterial flora and pathogen infection, we developed a percutaneous infection model using zebrafish and Yersinia ruckeri, a pathogen causing enteric redmouth disease in salmon and in trout. Pathogen challenge, either alone or together with pricking by a small needle, did not cause infection of the fish. However, cold stress given by water temperature shift from the optimum 28 °C for zebrafish to 20 °C caused fatal infection of injured fish following pathogen challenge. We investigated the effects of cold stress, injury, and pathogen challenge, alone and in combination, on fish skin bacterial flora using 16S rDNA metagenomics. We found that cold stress drastically altered the skin bacterial flora, which was dominated by Y. ruckeri on infected fish. In addition, fish whose intrinsic skin bacterial flora was disrupted by antibiotics had their skin occupied by Y. ruckeri following a challenge with this pathogen, although the fish survived without injury to create a route for invasion into the fish body. Our results suggest that the intrinsic skin bacterial flora of fish protects them from pathogen colonization, and that its disruption by stress allows pathogens to colonize and dominate their skin.

RevDate: 2021-03-06

Zakaria NN, Convey P, Gomez-Fuentes C, et al (2021)

Oil Bioremediation in the Marine Environment of Antarctica: A Review and Bibliometric Keyword Cluster Analysis.

Microorganisms, 9(2): pii:microorganisms9020419.

Bioremediation of hydrocarbons has received much attention in recent decades, particularly relating to fuel and other oils. While of great relevance globally, there has recently been increasing interest in hydrocarbon bioremediation in the marine environments of Antarctica. To provide an objective assessment of the research interest in this field we used VOSviewer software to analyze publication data obtained from the ScienceDirect database covering the period 1970 to the present, but with a primary focus on the years 2000-2020. A bibliometric analysis of the database allowed identification of the co-occurrence of keywords. There was an increasing trend over time for publications relating to oil bioremediation in maritime Antarctica, including both studies on marine bioremediation and of the metabolic pathways of hydrocarbon degradation. Studies of marine anaerobic degradation remain under-represented compared to those of aerobic degradation. Emerging keywords in recent years included bioprospecting, metagenomic, bioindicator, and giving insight into changing research foci, such as increasing attention to microbial diversity. The study of microbial genomes using metagenomic approaches or whole genome studies is increasing rapidly and is likely to drive emerging fields in future, including rapid expansion of bioprospecting in diverse fields of biotechnology.

RevDate: 2021-03-06

Daliri EB, Ofosu FK, Chelliah R, et al (2021)

Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies.

Biomolecules, 11(2): pii:biom11020300.

The advent of omic technology has made it possible to identify viable but unculturable micro-organisms in the gut. Therefore, application of multi-omic technologies in gut microbiome studies has become invaluable for unveiling a comprehensive interaction between these commensals in health and disease. Meanwhile, despite the successful identification of many microbial and host-microbial cometabolites that have been reported so far, it remains difficult to clearly identify the origin and function of some proteins and metabolites that are detected in gut samples. However, the application of single omic techniques for studying the gut microbiome comes with its own challenges which may be overcome if a number of different omics techniques are combined. In this review, we discuss our current knowledge about multi-omic techniques, their challenges and future perspective in this field of gut microbiome studies.

RevDate: 2021-03-06

Hernandez-Baixauli J, Puigbò P, Torrell H, et al (2021)

A Pilot Study for Metabolic Profiling of Obesity-Associated Microbial Gut Dysbiosis in Male Wistar Rats.

Biomolecules, 11(2): pii:biom11020303.

Obesity is one of the most incident and concerning disease worldwide. Definite strategies to prevent obesity and related complications remain elusive. Among the risk factors of the onset of obesity, gut microbiota might play an important role in the pathogenesis of the disease, and it has received extensive attention because it affects the host metabolism. In this study, we aimed to define a metabolic profile of the segregated obesity-associated gut dysbiosis risk factor. The study of the metabolome, in an obesity-associated gut dysbiosis model, provides a relevant way for the discrimination on the different biomarkers in the obesity onset. Thus, we developed a model of this obesity risk factors through the transference of gut microbiota from obese to non-obese male Wistar rats and performed a subsequent metabolic analysis in the receptor rats. Our results showed alterations in the lipid metabolism in plasma and in the phenylalanine metabolism in urine. In consequence, we have identified metabolic changes characterized by: (1) an increase in DG:34:2 in plasma, a decrease in hippurate, (2) an increase in 3-HPPA, and (3) an increase in o-coumaric acid. Hereby, we propose these metabolites as a metabolic profile associated to a segregated dysbiosis state related to obesity disease.

RevDate: 2021-03-06

Vigneron A, Cruaud P, Ducellier F, et al (2021)

Syntrophic Hydrocarbon Degradation in a Decommissioned Off-Shore Subsea Oil Storage Structure.

Microorganisms, 9(2): pii:microorganisms9020356.

Over the last decade, metagenomic studies have revealed the impact of oil production on the microbial ecology of petroleum reservoirs. However, despite their fundamental roles in bioremediation of hydrocarbons, biocorrosion, biofouling and hydrogen sulfide production, oil field and oil production infrastructure microbiomes are poorly explored. Understanding of microbial activities within oil production facilities is therefore crucial for environmental risk mitigation, most notably during decommissioning. The analysis of the planktonic microbial community from the aqueous phase of a subsea oil-storage structure was conducted. This concrete structure was part of the production platform of the Brent oil field (North Sea), which is currently undergoing decommissioning. Quantification and sequencing of microbial 16S rRNA genes, metagenomic analysis and reconstruction of metagenome assembled genomes (MAGs) revealed a unique microbiome, strongly dominated by organisms related to Dethiosulfatibacter and Cloacimonadetes. Consistent with the hydrocarbon content in the aqueous phase of the structure, a strong potential for degradation of low molecular weight aromatic hydrocarbons was apparent in the microbial community. These degradation pathways were associated with taxonomically diverse microorganisms, including the predominant Dethiosulfatibacter and Cloacimonadetes lineages, expanding the list of potential hydrocarbon degraders. Genes associated with direct and indirect interspecies exchanges (multiheme type-C cytochromes, hydrogenases and formate/acetate metabolism) were widespread in the community, suggesting potential syntrophic hydrocarbon degradation processes in the system. Our results illustrate the importance of genomic data for informing decommissioning strategies in marine environments and reveal that hydrocarbon-degrading community composition and metabolisms in man-made marine structures might differ markedly from natural hydrocarbon-rich marine environments.

RevDate: 2021-03-06

Pane S, Sacco A, Iorio A, et al (2021)

Strongyloides stercoralis Infestation in a Child: How a Nematode Can Affect Gut Microbiota.

International journal of molecular sciences, 22(4): pii:ijms22042131.

Background: Strongyloidiasis is a neglected tropical disease caused by the intestinal nematode Strongyloides stercoralis and characterized by gastrointestinal and pulmonary involvement. We report a pediatric case of strongyloidiasis to underline the response of the host microbiota to the perturbation induced by the nematode. Methods: We performed a 16S rRNA-metagenomic analysis of the gut microbiota of a 7-year-old female during and after S. stercolaris infection, investigating three time-point of stool samples' ecology: T0- during parasite infection, T1- a month after parasite infection, and T2- two months after parasite infection. Targeted-metagenomics were used to investigate ecology and to predict the functional pathways of the gut microbiota. Results: an increase in the alpha-diversity indices in T0-T1 samples was observed compared to T2 and healthy controls (CTRLs). Beta-diversity analysis showed a shift in the relative abundance of specific gut bacterial species from T0 to T2 samples. Moreover, the functional prediction of the targeted-metagenomics profiles suggested an enrichment of microbial glycan and carbohydrate metabolisms in the T0 sample compared with CTRLs. Conclusions: The herein report reinforces the literature suggestion of a putative direct or immune-mediated ability of S. stercolaris to promote the increase in bacterial diversity.

RevDate: 2021-03-06

Tabacchioni S, Passato S, Ambrosino P, et al (2021)

Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture.

Microorganisms, 9(2): pii:microorganisms9020426.

A growing body of evidence demonstrates the potential of various microbes to enhance plant productivity in cropping systems although their successful field application may be impaired by several biotic and abiotic constraints. In the present work, we aimed at developing multifunctional synthetic microbial consortia to be used in combination with suitable bioactive compounds for improving crop yield and quality. Plant growth-promoting microorganisms (PGPMs) with different functional attributes were identified by a bottom-up approach. A comprehensive literature survey on PGPMs associated with maize, wheat, potato and tomato, and on commercial formulations, was conducted by examining peer-reviewed scientific publications and results from relevant European projects. Metagenome fragment recruitments on genomes of potential PGPMs represented in databases were also performed to help identify plant growth-promoting (PGP) strains. Following evidence of their ability to coexist, isolated PGPMs were synthetically assembled into three different microbial consortia. Additionally, the effects of bioactive compounds on the growth of individually PGPMs were tested in starvation conditions. The different combination products based on microbial and non-microbial biostimulants (BS) appear worth considering for greenhouse and open field trials to select those potentially adoptable in sustainable agriculture.

RevDate: 2021-03-06

McCauley M, Chiarello M, Atkinson CL, et al (2021)

Gut Microbiomes of Freshwater Mussels (Unionidae) Are Taxonomically and Phylogenetically Variable across Years but Remain Functionally Stable.

Microorganisms, 9(2): pii:microorganisms9020411.

Freshwater mussels perform essential ecosystem functions, yet we have no information on how their microbiomes fluctuate over time. In this study, we examined temporal variation in the microbiome of six mussel species (Lampsilis ornata, Obovaria unicolor, Elliptio arca, Fusconaia cerina, Cyclonaias asperata, and Tritogonia verrucosa) sampled from the same river in 2016 and 2019. We examined the taxonomic, phylogenetic, and inferred functional (from 16S rRNA sequences) facets of their microbiome diversity. Significant differences between the two years were identified in five of the six species sampled. However, not all species that exhibited a temporally variable microbiome were functionally distinct across years, indicating functional redundancy within the mussel gut microbiome. Inferred biosynthesis pathways showed temporal variation in pathways involved in degradation, while pathways involved in cellular metabolism were stable. There was no evidence for phylosymbiosis across any facet of microbiome biodiversity. These results indicate that temporal variation is an important factor in the assembly of the gut microbiomes of freshwater mussels and provides further support that the mussel gut microbiome is involved in host development and activity.

RevDate: 2021-03-06

de Miranda JR, Granberg F, Onorati P, et al (2021)

Virus Prospecting in Crickets-Discovery and Strain Divergence of a Novel Iflavirus in Wild and Cultivated Acheta domesticus.

Viruses, 13(3): pii:v13030364.

Orthopteran insects have high reproductive rates leading to boom-bust population dynamics with high local densities that are ideal for short, episodic disease epidemics. Viruses are particularly well suited for such host population dynamics, due to their supreme ability to adapt to changing transmission criteria. However, very little is known about the viruses of Orthopteran insects. Since Orthopterans are increasingly reared commercially, for animal feed and human consumption, there is a risk that viruses naturally associated with these insects can adapt to commercial rearing conditions, and cause disease. We therefore explored the virome of the house cricket Acheta domesticus, which is both part of the natural Swedish landscape and reared commercially for the pet feed market. Only 1% of the faecal RNA and DNA from wild-caught A. domesticus consisted of viruses. These included both known and novel viruses associated with crickets/insects, their bacterial-fungal microbiome, or their plant food. Relatively abundant among these viral Operational Taxonomic Units (OTUs) was a novel Iflavirus, tentatively named Acheta domesticus Iflavirus (AdIV). Quantitative analyses showed that AdIV was also abundant in frass and insect samples from commercially reared crickets. Interestingly, the wild and commercial AdIV strains had short, extremely divergent variation hotspots throughout the genome, which may indicate specific adaptation to their hosts' distinct rearing environments.

RevDate: 2021-03-06

Wang YJ, Li SC, Lin WC, et al (2021)

Intracellular Microbiome Profiling of the Acanthamoeba Clinical Isolates from Lens Associated Keratitis.

Pathogens (Basel, Switzerland), 10(3): pii:pathogens10030266.

Acanthamoeba act as hosts for various microorganisms and pathogens, causing Acanthamoeba Keratitis (AK). To investigate the association between endosymbionts and AK progression, we performed a metagenomics study to characterize the intracellular microbiome from five lenses associated with AK isolates and standard strains to characterize the role of ocular flora in AK progression. The used clinical isolates were axenic cultured from lenses associated with AK patients. AK isolates and standard controls such as 16S ribosomal RNA sequencing techniques were used for analysis. The microbiome compositions and relative abundance values were compared. The orders of Clostridiales and Bacteroidales presented major populations of intracellular microbes belonging to all isolates. Comparison of the different source isolates showed that most of the abundance in keratitis isolates came from Ruminococcus gnavus (121.0 folds), Eubacterium dolichum (54.15 folds), Roseburia faecis (24.51 folds), and Blautia producta (3.15 folds). Further analysis of the relative abundance data from keratitis isolates showed that Blautia producta was positively correlated with the disease course. In contrast, Bacteroides ovatus was found to be abundant in early-stage keratitis isolates. This study reveals the abundant anaerobic Gram-positive rods present in severe keratitis isolate and characterize the association between Acanthamoeba and ocular flora in AK progression.

RevDate: 2021-03-06

Sadeghi M, Tomaru Y, T Ahola (2021)

RNA Viruses in Aquatic Unicellular Eukaryotes.

Viruses, 13(3): pii:v13030362.

Increasing sequence information indicates that RNA viruses constitute a major fraction of marine virus assemblages. However, only 12 RNA virus species have been described, infecting known host species of marine single-celled eukaryotes. Eight of these use diatoms as hosts, while four are resident in dinoflagellate, raphidophyte, thraustochytrid, or prasinophyte species. Most of these belong to the order Picornavirales, while two are divergent and fall into the families Alvernaviridae and Reoviridae. However, a very recent study has suggested that there is extraordinary diversity in aquatic RNA viromes, describing thousands of viruses, many of which likely use protist hosts. Thus, RNA viruses are expected to play a major ecological role for marine unicellular eukaryotic hosts. In this review, we describe in detail what has to date been discovered concerning viruses with RNA genomes that infect aquatic unicellular eukaryotes.

RevDate: 2021-03-06

Raethong N, Nakphaichit M, Suratannon N, et al (2021)

Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults.

Genes, 12(3): pii:genes12030331.

The gut microbiome plays a major role in the maintenance of human health. Characterizing the taxonomy and metabolic functions of the human gut microbiome is necessary for enhancing health. Here, we analyzed the metagenomic sequencing, assembly and construction of a meta-gene catalogue of the human gut microbiome with the overall aim of investigating the taxonomy and metabolic functions of the gut microbiome in Thai adults. As a result, the integrative analysis of 16S rRNA gene and whole metagenome shotgun (WMGS) sequencing data revealed that the dominant gut bacterial families were Lachnospiraceae and Ruminococcaceae of the Firmicutes phylum. Consistently, across 3.8 million (M) genes annotated from 163.5 gigabases (Gb) of WMGS sequencing data, a significant number of genes associated with carbohydrate metabolism of the dominant bacterial families were identified. Further identification of bacterial community-wide metabolic functions promisingly highlighted the importance of Roseburia and Faecalibacterium involvement in central carbon metabolism, sugar utilization and metabolism towards butyrate biosynthesis. This work presents an initial study of shotgun metagenomics in a Thai population-based cohort in a developing Southeast Asian country.

RevDate: 2021-03-05

Broman E, Zilius M, Samuiloviene A, et al (2021)

Active DNRA and denitrification in oxic hypereutrophic waters.

Water research, 194:116954 pii:S0043-1354(21)00152-4 [Epub ahead of print].

Since the start of synthetic fertilizer production more than a hundred years ago, the coastal ocean has been exposed to increasing nutrient loading, which has led to eutrophication and extensive algal blooms. Such hypereutrophic waters might harbor anaerobic nitrogen (N) cycling processes due to low-oxygen microniches associated with abundant organic particles, but studies on nitrate reduction in coastal pelagic environments are scarce. Here, we report on 15N isotope-labeling experiments, metagenome, and RT-qPCR data from a large hypereutrophic lagoon indicating that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were active processes, even though the bulk water was fully oxygenated (> 224 µM O2). DNRA in the bottom water corresponded to 83% of whole-ecosystem DNRA (water + sediment), while denitrification was predominant in the sediment. Microbial taxa important for DNRA according to the metagenomic data were dominated by Bacteroidetes (genus Parabacteroides) and Proteobacteria (genus Wolinella), while denitrification was mainly associated with proteobacterial genera Pseudomonas, Achromobacter, and Brucella. The metagenomic and microscopy data suggest that these anaerobic processes were likely occurring in low-oxygen microniches related to extensive growth of filamentous cyanobacteria, including diazotrophic Dolichospermum and non-diazotrophic Planktothrix. By summing the total nitrate fluxes through DNRA and denitrification, it results that DNRA retains approximately one fifth (19%) of the fixed N that goes through the nitrate pool. This is noteworthy as DNRA represents thus a very important recycling mechanism for fixed N, which sustains algal proliferation and leads to further enhancement of eutrophication in these endangered ecosystems.

RevDate: 2021-03-05

Huang Y, Lv H, Song Y, et al (2021)

Community composition of cecal microbiota in commercial yellow broilers with high and low feed efficiencies.

Poultry science, 100(4):100996 pii:S0032-5791(21)00030-4 [Epub ahead of print].

The cecal microbiota plays important roles in host food digestion and nutrient absorption, which may in part affect feed efficiency (FE). To investigate the composition and functional differences of cecal microbiota between high (n = 30) and low (n = 29) feed conversion ratio (FCR; metric for FE) groups, we performed 16S rRNA gene sequencing and predicted the metagenome function using Phylogenetic Investigation of Communities by Reconstruction of Unobserved Species in yellow broilers. The results showed that the 2 groups had the same prominent microbes but with differing abundance. Firmicutes, Bacteroidetes, and Actinobacteria were 3 prominent bacterial phyla in the cecal microbial community. Although there were no differences in microbial diversity, compositional differences related to FCR were found via linear discriminant analysis (LDA) effect size; the genus Bacteroides had a significantly higher abundance (LDA >2) in the high FE (HFE) group than in the low FE group. Furthermore, genus Bacteroides had a negative FCR-associated correlation (P < 0.05). Oscillospira was positively correlated with Bacteroides in both groups, whereas Dorea was negatively correlated with Bacteroides in the HFE group. Predictive functional analysis revealed that metabolic pathways such as "starch and sucrose metabolism," "phenylalanine, tyrosine and tryptophan biosynthesis," and "carbohydrate metabolism" were significantly enriched in the HFE group. The relatively subtle differences in FE-associated cecal microbiota composition suggest a possible link between cecal microbiota and FE. Moreover, Bacteroides may potentially be used as biomarkers for FE to improve growth performance in yellow broilers.

RevDate: 2021-03-05

Xiong D, Zhang X, Xiong J, et al (2021)

Rapid genome-wide sequence typing of African swine fever virus based on alleles.

Virus research pii:S0168-1702(21)00064-2 [Epub ahead of print].

Rapid and accurate molecular typing of African swine fever virus (ASFV) during outbreaks is important to reveal diversity and sourcing of ASFV. Here we present a new way to perform rapid genome-wide multi-locus sequence typing of ASFV using an allele calling based on gene by gene approach. Using open-accessed chewBBACA software, 41 publicly available ASFV genomes were analyzed to optimize the parameters to find the alleles. Alleles as many as 127 were found for building the phylogenetic trees, which covered more than 60% of the whole genome. Then the method was used to analyze two ASFV genomes assembled from two metagenomic sequences of a swine whole blood and a swine spleen tissue collected in Wuhan, China. It reveals that the two ASFV genomes are the closest to that of Pig/HLJ/2018 strain and DB/LN/2018 strain, which were isolated earlier in China. This proved that the ASFV in Wuhan originated from the same source causing the earlier outbreaks in Heilongjiang and Liaoning province of China. This method could identify more informative genome regions that could be used for accurate typing than other genome-wide analysis, and with less demand on computing resources. It also showed tolerance to analyze ASFV draft genomes assembled directly from metagenomic sequences. Furthermore, the ASFV-specific genetic markers found by the allele calling could be translated into clinical diagnostics or can be used broadly to identify conserved putative therapeutic candidates.

RevDate: 2021-03-05

Fadiji AE, Kanu JO, OO Babalola (2021)

Metagenomic profiling of rhizosphere microbial community structure and diversity associated with maize plant as affected by cropping systems.

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

Soil microbial diversity is believed to be vital in maintaining soil quality and health. Limited knowledge exists on the impact of cropping systems (mono-cropping and crop rotation) on the diversity of the whole soil microbiome. In this study, we investigated the effects of two cropping systems, namely crop rotation and mono-cropping, on the community structure and diversity of rhizosphere microbiome in the rhizosphere and bulk soil associated with maize plant using shotgun metagenomics. Whole DNA was extracted from bulk, and rhizosphere soils associated with maize plant from the mono-cropping (LT and LTc) and crop rotation (VD and VDc) sites, respectively, and sequenced employing shotgun metagenomics. The results obtained via the Subsystem database showed 23 bacteria, 2 fungi, and 3 archaea most abundant phyla. The major bacterial phyla are Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Cyanobacteria, Spirochaetes, Aquificae, Verrucomicrobia, Chloroflexi, Planctomycetes, and Chlorobi. The major fungi phyla observed were Ascomycota and Basidiomycota, while the dominant archaea phyla are Euryarchaeota, Thaumarchaeota, and Crenarchaeota. Our diversity assessment showed that the rhizosphere microbial community was more abundant in the samples from the rotational crop site following VD>VDc>LT>LTc. Alpha diversity showed that there was no significant difference (P>0.05) in the soil microbial communities (P>0.05), while better diversity indicated that a significant difference (P = 0.01) occurred. Taken together, crop rotational practice was found to positively influence the rhizosphere microbial community associated with the maize plant.

RevDate: 2021-03-05

Yao J, Gui L, S Yin (2021)

A novel esterase from a soil metagenomic library displaying a broad substrate range.

AMB Express, 11(1):38.

A novel esterase gene was isolated from a soil metagenomic library. The gene encoded a protein of 520 amino acids which contained a 21 aa signal peptide. Primary structure analysis of the protein sequence revealed that it contained a conserved active site motif (SxSxG) and a structural motif (CS-D-HC). Then the esterase gene was cloned and expressed in Escherichia coli BL21(DE3). SDS-PAGE analysis of the purified esterase showed that it was expressed in a highly soluble form and its molecular mass was estimated to be 55 kDa. Characterization of the esterase revealed that it exhibited high activity toward p-nitrophenyl esters with short acyl chains and especially p-nitrophenyl acetate, suggesting that it was a typical carboxylesterase rather than a lipase. With p-nitrophenyl acetate as substrate, the enzyme showed its optimal activity at pH 7.0 and 30 °C, and it was stable at a broad pH range from 4.5 to 10.0 and temperature not higher than 50 °C. Furthermore, the enzyme showed different substrate specificity from known esterase, it was not only hydrolyzing against p-nitrophenyl esters, but also hydrolyzing all hydroxybenzoic esters and hydroxycinnamic ester assayed. As it was an enzyme active on a broad range of phenolic esters, simultaneously possessing feruloyl esterase, chlorogenate esterase and tannase activities, it could serve as a valuable candidate for applications in biotechnology.

RevDate: 2021-03-05

Ruiz ON, Radwan O, RC Striebich (2021)

GC-MS hydrocarbon degradation profile data of Pseudomonas frederiksbergensis SI8, a bacterium capable of degrading aromatics at low temperatures.

Data in brief, 35:106864 pii:S2352-3409(21)00148-7.

The ability of the psychrotrophic bacterium Pseudomonas frederiksbergensis SI8 to grow and degrade aromatic hydrocarbons efficiently at low temperature is shown in this study. The robust growth of P. frederiksbergensis SI8 was demonstrated in jet fuel and an aromatic blend. The bacterium showed 2.5 to 3-fold faster growth in the aromatic blend than in jet fuel. The hydrocarbons degradation profile of P. frederiksbergensis SI8 at ambient temperature (i.e., 28 °C) and low temperature (i.e., 4 °C) was characterized by Gas Chromatography-Mass Spectrometry (GC-MS) analysis. GC-MS data demonstrated that P. frederiksbergensis SI8 is a novel psychrotrophic bacterium with the ability to degrade aromatic hydrocarbons at temperatures as low as 4 °C. Specifically, P. frederiksbergensis SI8 consumed toluene, ethylbenzene, n-propylbenzene and methyl ethyl benzene efficiently. The data presented here serves to characterize the hydrocarbon degradation profile of P. frederiksbergensis SI8 and corroborates the capacity of this bacterium to degrade aromatic hydrocarbons at low temperatures. The raw GC-MS data for the degradation of hydrocarbons by P. frederiksbergensis SI8 grown at 4 °C and 28 °C for 14 days have been deposited in Mendeley Data and can be retrieved from and The datasets and raw data presented here were associated with the main research work "Metagenomic characterization reveals complex association of soil hydrocarbon-degrading bacteria" [1].

RevDate: 2021-03-05

Nguyen M, Holdbrooks H, Mishra P, et al (2021)

Impact of Probiotic B. infantis EVC001 Feeding in Premature Infants on the Gut Microbiome, Nosocomially Acquired Antibiotic Resistance, and Enteric Inflammation.

Frontiers in pediatrics, 9:618009.

Background: Preterm birth is a major determinant of neonatal survival and morbidity, but the gut microbiome and associated enteric inflammation are also key factors in neonatal development and the risk of associated morbidities. We prospectively and longitudinally followed two cohorts of preterm infants, one of which was fed activated Bifidobacterium longum subsp. infantis (B. infantis) EVC001 8 × 109 CFU daily, and the other was not fed a probiotic. Hospital feeding protocol assigned all infants born at <1500 g and/or < 32 weeks corrected gestational age to the probiotic feeding protocol, whereas infants born at >1500 g and/or >32 weeks corrected gestational age were not fed a probiotic. Fecal samples were opportunistically collected from 77 infants throughout the hospital stay, and subjected to shotgun metagenomic sequencing and quantification of enteric inflammation. De-identified metadata was collected from patient medical records. Results: The gut microbiome of preterm infants was typified by a high abundance of Enterobacteriaceae and/or Staphylococcaceae, and multivariate modeling identified the probiotic intervention, rather than degree of prematurity, day of life, or other clinical interventions, as the primary source of change in the gut microbiome. Among infants fed B. infantis EVC001, a high abundance of total Bifidobacteriaceae developed rapidly, the majority of which was B. infantis confirmed via subspecies-specific qPCR. Associated with this higher abundance of Bifidobacteriaceae, we found increased functional capacity for utilization of human milk oligosaccharides (HMOs), as well as reduced abundance of antibiotic resistance genes (ARGs) and the taxa that harbored them. Importantly, we found that infants fed B. infantis EVC001 exhibited diminished enteric inflammation, even when other clinical variables were accounted for using multivariate modeling. Conclusion: These results provide an important observational background for probiotic use in a NICU setting, and describe the clinical, physiological, and microbiome-associated improvements in preterm infants associated with B. infantis EVC001 feeding.

RevDate: 2021-03-05

Verce M, Schoonejans J, Hernandez Aguirre C, et al (2021)

A Combined Metagenomics and Metatranscriptomics Approach to Unravel Costa Rican Cocoa Box Fermentation Processes Reveals Yet Unreported Microbial Species and Functionalities.

Frontiers in microbiology, 12:641185.

Cocoa fermentation is the first step in the post-harvest processing chain of cocoa and is important for the removal of the cocoa pulp surrounding the beans and the development of flavor and color precursors. In the present study, metagenomic and metatranscriptomic sequencing were applied to Costa Rican cocoa fermentation processes to unravel the microbial diversity and assess the function and transcription of their genes, thereby increasing the knowledge of this spontaneous fermentation process. Among 97 genera found in these fermentation processes, the major ones were Acetobacter, Komagataeibacter, Limosilactobacillus, Liquorilactobacillus, Lactiplantibacillus, Leuconostoc, Paucilactobacillus, Hanseniaspora, and Saccharomyces. The most prominent species were Limosilactobacillus fermentum, Liquorilactobacillus cacaonum, and Lactiplantibacillus plantarum among the LAB, Acetobacter pasteurianus and Acetobacter ghanensis among the AAB, and Hanseniaspora opuntiae and Saccharomyces cerevisiae among the yeasts. Consumption of glucose, fructose, and citric acid, and the production of ethanol, lactic acid, acetic acid, and mannitol were linked to the major species through metagenomic binning and the application of metatranscriptomic sequencing. By using this approach, it was also found that Lacp. plantarum consumed mannitol and oxidized lactic acid, that A. pasteurianus degraded oxalate, and that species such as Cellvibrio sp., Pectobacterium spp., and Paucilactobacillus vaccinostercus could contribute to pectin degradation. The data generated and results presented in this study could enhance the ability to select and develop appropriate starter cultures to steer the cocoa fermentation process toward a desired course.

RevDate: 2021-03-05

Liu J, Mu W, Shi M, et al (2021)

The Species Identification in Traditional Herbal Patent Medicine, Wuhu San, Based on Shotgun Metabarcoding.

Frontiers in pharmacology, 12:607200 pii:607200.

Traditional herbal patent medicine typically consists of multiple ingredients, making it challenging to supervise contamination by impurities and the improper use of raw materials. This study employed shotgun metabarcoding for the species identification of biological ingredients in traditional herbal patent medicine, Wuhu San. The five prescribed herbal materials found in Wuhu San were collected, and their reference sequences were obtained by traditional DNA barcoding using Sanger sequencing. Two lab-made and three commercial Wuhu San samples were collected, and a total of 37.14 Gb of shotgun sequencing data was obtained for these five samples using the Illumina sequencing platform. A total of 1,421,013 paired-end reads were enriched for the Internal Transcribed Spacer 2 (ITS2), psbA and trnH intergenic spacer region (psbA-trnH), maturase k (matK), and ribulose-1, 5-bisphosphate carboxylase (rbcL) regions. Furthermore, 80, 11, 9, and 8 operational taxonomic units were obtained for the ITS2, psbA-trnH, matK, and rbcL regions, respectively, after metagenomic assembly, annotation, and chimeric detection. In the two lab-made mock samples, all labeled ingredients in the Wuhu San prescription were successfully detected, and the positive control, Panax quinquefolius L., was detected in the HSZY172 mock sample. Three species, namely Angelica sinensis (Oliv.) Diels, Saposhnikovia divaricata (Turcz. ex Ledeb.) Schischk., and Carthamus tinctorius L., belonging to three labeled ingredients, Angelicae Sinensis Radix (Danggui), Saposhnikoviae Radix (Fangfeng), and Carthami Flos (Honghua), were detected in the three commercial samples. Angelica dahurica (Hoffm.) Benth. & Hook. f. ex Franch. & Sav., the original Angelicae Dahuricae Radix (Baizhi) species, was only detected in WHS003. Arisaema erubescens (Wall.) Schott, Arisaema heterophyllum Blume, or Arisaema amurense Maxim., the original Arisaematis Rhizoma (Tiannanxing) species, were not detected in any of the commercial samples, which could be attributed to the fact that this medicinal material underwent extensive processing. In addition, the Saposhnikovia divaricata adulterant was detected in all the commercial samples, while 24 fungal genera, including Aspergillus, were identified in both the lab-made and commercial samples. This study showed that shotgun metabarcoding provided alternative strategy and technical means for identifying prescribed ingredients in traditional herbal patent medicine and displayed the potential to effectively complement traditional methods.

RevDate: 2021-03-05

Wylie TN, KM Wylie (2021)

ViroMatch: A Computational Pipeline for the Detection of Viral Sequences from Complex Metagenomic Data.

Microbiology resource announcements, 10(9):.

ViroMatch is an automated pipeline that takes metagenomic sequencing reads as input and performs iterative nucleotide and translated nucleotide mapping to identify viral sequences. We provide a Docker image for ViroMatch, so that users will not have to install dependencies.

RevDate: 2021-03-05

Muwonge A, Karuppannan AK, T Opriessnig (2021)

Probiotics mediated gut microbiota diversity shifts are associated with reduction in histopathology and shedding of Lawsonia intracellularis.

Animal microbiome, 3(1):22.

BACKGROUND: Clinical intervention during bacterial infections in farm animals such as pigs commonly includes the use of antimicrobials. With the rise of antimicrobial resistance and the attempts to reduce the use of antibiotics in food animals, effective alternatives are urgently needed to reduce or even remove pathogens and disease risks. Improving clinical outcomes and overall pig health by using probiotics appears attractive. However, reliable data sets on the efficacy of probiotics are scarce. The obligate intracellular bacterium Lawsonia intracellularis is widespread in pigs and associated with severe enteropathy, mainly in the ileum, commonly resulting in substantial reduction in weight gain. The impact of three in-feed probiotics and a commercial live L. intracellularis vaccine was compared in a pig challenge model. Probiotic treatment was associated with reduced L. intracellularis fecal shedding and reduced gut lesions. Here, the bacterial microbiota of the ileum of these pigs was characterized with 16S rRNA gene sequencing and was subsequently analyzed with bioinformatics tools.

RESULTS: The greatest microbial richness was observed in the probiotic treated group T03-LAW, which accounted for 87% of richness observed in the study. Treatment had a significant impact on both the microbiota structure and taxonomic profile in the ileum, explaining between 26 and 36% of the structural variation, with the strongest association in the T03-LAW group. Overall, the largest changes were observed for the pigs treated with in-feed Bacillus pumilus; the microbiota of these pigs had the greatest diversity and highest richness. We also observed depleted and enriched core microbiota amongst the groups; however, there was no correlation with clinical characteristics. The results suggest that an increased diversity of the ileal microbiota is associated with a reduction in shedding, i.e. a unit increase in Shannon diversity index resulted in 2.8 log reduction in shedding.

CONCLUSIONS: Probiotic supplementation of a base feed ration increased ileum microbiota diversity leading to a mitigation of the effects of a pathogenic L. intracellularis challenge. An even and diverse microbiota community benefits pigs infected with L. intracellularis, however, investigations are needed to determine if this is also true for other pathogens. The study unambiguously demonstrates the usefulness of probiotic supplementation in reducing the impact of enteric pathogens and pathogen shedding rates in food animals without the use of antimicrobials.

RevDate: 2021-03-05

Ji HY, Wang GP, Guo Q, et al (2021)

[A case report of Q-fever endocarditis diagnosed by metagenomic next generation sequencing].

Zhonghua nei ke za zhi, 60(3):247-248.

RevDate: 2021-03-05

Zhao CZ, Chen Z, MY Li (2021)

[Research progress of polymicrobial synergy and dysbiosis in periodontitis].

Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology, 56(3):301-305.

Human oral cavity is colonized by various microbial communities which play an important role in the initiation and progression of periodontitis. However, it is still not clear how these microbial communities mediate the disease. With the rise of metagenomics research, polymicrobial synergy and dysbiosis (PSD) model, a new periodontitis pathogenesis mechanism, was proposed. The importance of the microbial communities acting as a whole system in the development of periodontitis is gradually recognized. Host susceptibility, as another key factor in the initiation of the disease, is vital in PSD model. This article reviews the mechanisms of the PSD model and its research progress in periodontitis as well as some other diseases and briefly highlights the positive significance in terms of prevention and treatment of periodontitis in order to provide insights and perspectives for the future periodontal researches.

RevDate: 2021-03-03
CmpDate: 2021-03-03

Martínez-Núñez MA, Z Rodríguez-Escamilla (2020)

Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes.

Toxins, 12(6):.

Prokaryotes represent a source of both biotechnological and pharmaceutical molecules of importance, such as nonribosomal peptides (NRPs). NRPs are secondary metabolites which their synthesis is independent of ribosomes. Traditionally, obtaining NRPs had focused on organisms from terrestrial environments, but in recent years marine and coastal environments have emerged as an important source for the search and obtaining of nonribosomal compounds. In this study, we carried out a metataxonomic analysis of sediment of the coast of Yucatan in order to evaluate the potential of the microbial communities to contain bacteria involved in the synthesis of NRPs in two sites: one contaminated and the other conserved. As well as a metatranscriptomic analysis to discover nonribosomal peptide synthetases (NRPSs) genes. We found that the phyla with the highest representation of NRPs producing organisms were the Proteobacteria and Firmicutes present in the sediments of the conserved site. Similarly, the metatranscriptomic analysis showed that 52% of the sequences identified as catalytic domains of NRPSs were found in the conserved site sample, mostly (82%) belonging to Proteobacteria and Firmicutes; while the representation of Actinobacteria traditionally described as the major producers of secondary metabolites was low. It is important to highlight the prediction of metabolic pathways for siderophores production, as well as the identification of NRPS's condensation domain in organisms of the Archaea domain. Because this opens the possibility to the search for new nonribosomal structures in these organisms. This is the first mining study using high throughput sequencing technologies conducted in the sediments of the Yucatan coast to search for bacteria producing NRPs, and genes that encode NRPSs enzymes.

RevDate: 2021-03-04

Zhai Y, IM Pérez-Díaz (2021)

Identification of potential causative agents of the CO2-mediated bloater defect in low salt cucumber fermentation.

International journal of food microbiology, 344:109115 pii:S0168-1605(21)00074-X [Epub ahead of print].

Development of bloater defect in cucumber fermentations is the result of carbon dioxide (CO2) production by the indigenous microbiota. The amounts of CO2 needed to cause bloater defect in cucumber fermentations brined with low salt and potential microbial contributors of the gas were identified. The carbonation of acidified cucumbers showed that 28.68 ± 6.04 mM (12%) or higher dissolved CO2 induces bloater defect. The microbiome and biochemistry of cucumber fermentations (n = 9) brined with 25 mM calcium chloride (CaCl2) and 345 mM sodium chloride (NaCl) or 1.06 M NaCl were monitored on day 0, 2, 3, 5, 8, 15 and 21 using culture dependent and independent microbiological techniques and High-Performance Liquid Chromatography. Changes in pH, CO2 concentrations and the incidence of bloater defect were also followed. The enumeration of Enterobacteriaceae on Violet Red Bile Glucose agar plates detected a cell density of 5.2 ± 0.7 log CFU/g on day 2, which declined to undetectable levels by day 8. A metagenomic analysis identified Leuconostocaceae in all fermentations at 10 to 62%. The presence of both bacterial families in fermentations brined with CaCl2 and NaCl coincided with a bloater index of 24.0 ± 10.3 to 58.8 ± 23.9. The prevalence of Lactobacillaceae in a cucumber fermentation brined with NaCl with a bloater index of 41.7 on day 5 suggests a contribution to bloater defect. This study identifies the utilization of sugars and malic acid by the cucumber indigenous Lactobacillaceae, Leuconostocaceae and Enterobacteriaceae as potential contributors to CO2 production during cucumber fermentation and the consequent bloater defect.

RevDate: 2021-03-04

Zhao X, Jiang J, Zhou Z, et al (2021)

Responses of microbial structures, functions and metabolic pathways for nitrogen removal to different hydraulic retention times in anaerobic side-stream reactor coupled membrane bioreactors.

Bioresource technology, 329:124903 pii:S0960-8524(21)00242-X [Epub ahead of print].

Synchronous sludge reduction and nitrogen removal have attracted increasing attention, while the underlying mechanisms of diverse nitrogen metabolism within the complicated processes remain unclear. Four anoxic/oxic membrane bioreactors, three of which were upgraded by anaerobic side-stream reactors (ASSR) and carriers (APSSR-MBRs), were operated to determine effects of hydraulic retention time of ASSRs. APSSR-MBRs achieved more significant nitrogen removal and higher nitrate uptake rate because of more denitrifying bacteria and the supernumerary release of secondary substrates. Ammonia uptake rate showed the diverse Nitrospira preceded over anaerobic decay and sulfide inhibition in the ASSR, and made the reactor exhibit higher nitrification capacity. Metagenomic analysis indicated that APSSR-MBRs showed higher abundances of genes related to nitrogen consumption processes, and higher abundances on the carriers, confirming their pivotal roles in nitrogen metabolism. This study provided novel perspectives to build a bridge between process model and nitrogen metabolism in the sludge reduction system..

RevDate: 2021-03-04

Domanska-Blicharz K, J Sajewicz-Krukowska (2021)

Recombinant turkey coronavirus: are some S gene structures of gammacoronaviruses especially prone to exchange?.

Poultry science, 100(4):101018 pii:S0032-5791(21)00052-3 [Epub ahead of print].

The objective of the present study was to characterize the atypical turkey coronavirus strain detected in a commercial meat turkey farm in Poland. Using the viral metagenomics approach, we obtained a complete genome sequence of coronavirus, isolated from duodenum samples of animals suffering from acute enteritis. The nearly full-length genome consisted of 27,614 nucleotides and presented a typical genetic organization similar to that of Polish infectious bronchitis virus (IBV) or French turkey coronavirus/guinea fowl coronavirus strains. Phylogenetic analysis based on both the full-length genome and the whole S gene suggested that gCoV/Tk/Poland/G160/2016 is related to turkey and guinea fowl coronavirus and not IBV strains. Sequence analysis of the genome revealed unique genetic characteristics of the present strain, demonstrating that the virus emerged as a result of the exchange of the S gene of IBV GI-19 lineage with the S gene related to the North American turkey coronaviruses and French guinea fowl coronaviruses. Analysis of earlier, similar recombinations suggests that both the S gene structures may be particularly mobile, willingly switching between different gammacoronavirus genomic backbones. The identified recombinant caused a severe course of the disease, which may imply that it is in the first phase of breaking the barriers between different bird species.

RevDate: 2021-03-04

Moll JM, Myers PN, Zhang C, et al (2021)

Gut microbiota perturbation in IgA deficiency is influenced by IgA-autoantibody status.

Gastroenterology pii:S0016-5085(21)00458-3 [Epub ahead of print].

BACKGROUND AND AIMS: Immunoglobulin A (IgA) exerts its primary function at mucosal surfaces where it binds microbial antigens to regulate bacterial growth and epithelial attachment. One-third of individuals with IgA deficiency (IgAD) suffer from recurrent mucosal infections, possibly related to an altered microbiota. We here aimed to delineate the impact of IgA deficiency and the IgA-autoantibody status on the composition and functional capacity of the gut microbiota.

METHODS: We performed a paired, lifestyle-balanced analysis of the effect of IgA on the gut microbiota composition and functionality based on fecal samples from IgAD subjects and IgA sufficient household members (n = 100), involving quantitative shotgun metagenomics, species-centric functional annotation of gut bacteria and strain level analyses. We supplemented the dataset with 32 IgAD subjects and examined the influence of IgA-autoantibody status on the composition and functionality of the gut microbiota.

RESULTS: The IgAD gut microbiota exhibited decreased richness and diversity and was enriched for bacterial species encoding pathogen-related functions including multi-drug and antimicrobial peptide resistance, virulence factors, and Type III and VI secretion systems. These functional changes are largely attributed to E. coli, but were independent of E. coli strain variations and most prominent in IgAD subjects with IgA-specific autoreactive antibodies.

CONCLUSION: The microbiota of individuals with IgAD is enriched for species holding increased proinflammatory potential, thereby potentially decreasing the resistance to gut barrier-perturbing events. This phenotype is especially pronounced in IgAD subjects with IgA-specific autoreactive antibodies, thus warranting a screening for IgA-specific autoreactive antibodies in IgAD to identify IgAD subjects with increased risk for gastrointestinal implications.

RevDate: 2021-03-04

El Alam MB, Sims TT, Kouzy R, et al (2021)

A prospective study of the adaptive changes in the gut microbiome during standard-of-care chemoradiotherapy for gynecologic cancers.

PloS one, 16(3):e0247905 pii:PONE-D-20-16939.

BACKGROUND: A diverse and abundant gut microbiome can improve cancer patients' treatment response; however, the effect of pelvic chemoradiotherapy (CRT) on gut diversity and composition is unclear. The purpose of this prospective study was to identify changes in the diversity and composition of the gut microbiome during and after pelvic CRT.

MATERIALS AND METHODS: Rectal swabs from 58 women with cervical, vaginal, or vulvar cancer from two institutions were prospectively analyzed before CRT (baseline), during CRT (weeks 1, 3, and 5), and at first follow-up (week 12) using 16Sv4 rRNA gene sequencing of the V4 hypervariable region of the bacterial 16S rRNA marker gene. 42 of these patients received antibiotics during the study period. Observed operational taxonomic units (OTUs; representative of richness) and Shannon, Simpson, Inverse Simpson, and Fisher diversity indices were used to characterize alpha (within-sample) diversity. Changes over time were assessed using a paired t-test, repeated measures ANOVA, and linear mixed modeling. Compositional changes in specific bacteria over time were evaluated using linear discriminant analysis effect size.

RESULTS: Gut microbiome richness and diversity levels continually decreased throughout CRT (mean Shannon diversity index, 2.52 vs. 2.91; all P <0.01), but were at or near baseline levels in 60% of patients by week 12. Patients with higher gut diversity at baseline had the steepest decline in gut microbiome diversity. Gut microbiome composition was significantly altered during CRT, with increases in Proteobacteria and decreases in Clostridiales, but adapted after CRT, with increases in Bacteroides species.

CONCLUSION: After CRT, the diversity of the gut microbiomes in this population tended to return to baseline levels by the 12 week follow-up period, but structure and composition remained significantly altered. These changes should be considered when designing studies to analyze the gut microbiome in patients who receive pelvic CRT for gynecologic cancers.

RevDate: 2021-03-04

Verschaffelt P, Den Bossche TV, Gabriel W, et al (2021)

MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets.

Journal of proteome research [Epub ahead of print].

The study of microbiomes has gained in importance over the past few years and has led to the emergence of the fields of metagenomics, metatranscriptomics, and metaproteomics. While initially focused on the study of biodiversity within these communities, the emphasis has increasingly shifted to the study of (changes in) the complete set of functions available in these communities. A key tool to study this functional complement of a microbiome is Gene Ontology (GO) term analysis. However, comparing large sets of GO terms is not an easy task due to the deeply branched nature of GO, which limits the utility of exact term matching. To solve this problem, we here present MegaGO, a user-friendly tool that relies on semantic similarity between GO terms to compute the functional similarity between multiple data sets. MegaGO is high performing: Each set can contain thousands of GO terms, and results are calculated in a matter of seconds. MegaGO is available as a web application at and is installable via pip as a standalone command line tool and reusable software library. All code is open source under the MIT license and is available at

RevDate: 2021-03-04

Gonzales JA, Takhar JS, Joye A, et al (2021)

Peripheral Blood Transcriptome in Patients with Sarcoidosis-Associated Uveitis.

Ocular immunology and inflammation [Epub ahead of print].

Purpose: To identify peripheral blood transcriptome differences in uveitis patients with sarcoidosis compared to those with Vogt-Koyanagi-Harada (VKH) syndrome and controls.Methods: Ten patients with uveitis compatible with sarcoidosis (eight with pulmonary sarcoidosis, one with central nervous system sarcoidosis, and one with conjunctival sarcoidosis), nine patients with VKH, and nine healthy controls were prospectively enrolled.Results: Ten genes exhibited a four-fold difference in expression in sarcoidosis patients compared to controls, many being involved in regulating inflammatory processes or cellular responses to microbes.Conclusions: This research suggests that the transcriptome in sarcoidosis is robust enough to be detected in the peripheral blood and that sarcoidosis can be distinguished from healthy controls. Differentially expressed genes may serve as candidates warranting further investigation with respect to disease pathophysiology and may provide additional information, such as ability to stratify patients based on associated disease severity and anatomical location of inflammation within the eye.

RevDate: 2021-03-04

Krishnamoorthy A, Gupta A, Sar P, et al (2021)

Metagenomics of two gnotobiotically grown aromatic rice cultivars reveals genotype-dependent and tissue-specific colonization of endophytic bacterial communities attributing multiple plant growth promoting traits.

World journal of microbiology & biotechnology, 37(4):59.

Exploration of community structures, habitations, and potential plant growth promoting (PGP) attributes of endophytic bacteria through next generation sequencing (NGS) is a prerequisite to culturing PGP endophytic bacteria for their application in sustainable agriculture. The present study unravels the taxonomic abundance and diversity of endophytic bacteria inhabiting in vitro grown root, shoot and callus tissues of two aromatic rice cultivars through 16S rRNA gene-based Illumina NGS. Wide variability in the number of bacterial operational taxonomic units (OTUs) and genera was observed between the two samples of the root (55, 14 vs. 310, 76) and shoot (26, 12 vs. 276, 73) but not between the two callus samples (251, 61 vs. 259, 51), indicating tissue-specific and genotype-dependent bacterial community distribution in rice plant, even under similar gnotobiotic growth conditions. Sizes of core bacteriomes of the selected two rice genotypes varied from 1 to 15 genera, with Sphingomonas being the only genus detected in all six samples. Functional annotation, based upon the abundance of bacterial OTUs, revealed the presence of several PGP trait-related genes having variable relative abundance in tissue-specific and genotype-dependent manners. In silico study also documented a higher abundance of certain genes in the same biochemical pathway, such as nitrogen fixation, phosphate solubilization and indole acetic acid production; implying their crucial roles in the biosynthesis of metabolites leading to PGP. New insights on utilizing callus cultures for isolation of PGP endophytes aiming to improve rice crop productivity are presented, owing to constancy in bacterial OTUs and genera in callus tissues of both the rice genotypes.

RevDate: 2021-03-04

Lee MD, O'Rourke A, Lorenzi H, et al (2021)

Reference-guided metagenomics reveals genome-level evidence of potential microbial transmission from the ISS environment to an astronaut's microbiome.

iScience, 24(2):102114 pii:S2589-0042(21)00082-1.

Monitoring microbial communities aboard the International Space Station (ISS) is essential to maintaining astronaut health and the integrity of life-support systems. Using assembled genomes of ISS-derived microbial isolates as references, recruiting metagenomic reads from an astronaut's nasal microbiome revealed no recruitment to a Staphylococcus aureus isolate from samples before launch, yet systematic recruitment across the genome when sampled after 3 months aboard the ISS, with a median percent identity of 100%. This suggests that either a highly similar S. aureus population colonized the astronaut's nasal microbiome while the astronaut was aboard the ISS or that it may have been below detection before spaceflight, instead supporting a shift in community composition. This work highlights the value in generating genomic libraries of microbes from built-environments such as the ISS and demonstrates one way such data can be integrated with metagenomics to facilitate the tracking and monitoring of astronaut microbiomes and health.

RevDate: 2021-03-04

Kashnikov AY, Epifanova NV, NA Novikova (2020)

Picobirnaviruses: prevalence, genetic diversity, detection methods.

Vavilovskii zhurnal genetiki i selektsii, 24(6):661-672.

This article presents a general overview of the prevalence, genetic diversity and detection methods of picobirnaviruses (PBVs), which are small, non-enveloped icosahedral viruses with a segmented double-stranded RNA genome consisting of two segments taxonomically related to the genus Picobirnavirus of the family Picobirnaviridae. This review of scientific papers published in 1988-2019 provides data on the PBV distribution in the nature and a broad host range. PBV infection is characterized as opportunistic, the lack of understanding of the etiological role of PBVs in diarrhea is emphasized, since these viruses are detected both in symptomatic and asymptomatic cases. The concept of PBV infection as a chronic disease caused by a long-lasting persistence of the virus in the host is considered. Such factors as stress syndrome, physiological conditions, immune status and host age at the time of primary PBV infection influence the virus detection rate in humans and animals. The possible zoonotic nature of human PBV infection is noted due to the capacity for interspecies PBV transmission acquired during evolution as a result of the reassortment of the genome segments of different viruses infecting the same host. Data providing evidence that PBVs belong to eukaryotes and a challenging hypothesis stating that PBVs are bacterial viruses are presented. The need to intensify work on PBV detection because of their wide distribution, despite the complexity due to the lack of the cultivation system, is emphasized. Two strategies of RT-PCR as main PBV detection methods are considered. The genomes of individual representatives of the genus isolated from different hosts are characterized. Emphasis is placed on the feasibility of developing primers with broader specificity for expanding the range of identifiable representatives of the genus PBV due to a huge variety of their genotypes. The importance of effective monitoring of PBV prevalence for studying the zoonotic and anthroponotic potential using metagenomic analysis is highlighted, and so is the possibility of using PBV as a marker for environmental monitoring.

RevDate: 2021-03-04

Rozadilla G, Clemente JM, CB McCarthy (2020)

HoSeIn: A Workflow for Integrating Various Homology Search Results from Metagenomic and Metatranscriptomic Sequence Datasets.

Bio-protocol, 10(14):e3679 pii:3679.

Data generated by metagenomic and metatranscriptomic experiments is both enormous and inherently noisy. When using taxonomy-dependent alignment-based methods to classify and label reads, the first step consists in performing homology searches against sequence databases. To obtain the most information from the samples, nucleotide sequences are usually compared to various databases (nucleotide and protein) using local sequence aligners such as BLASTN and BLASTX. Nevertheless, the analysis and integration of these results can be problematic because the outputs from these searches usually show inconsistencies, which can be notorious when working with RNA-seq. Moreover, and to the best of our knowledge, existing tools do not criss-cross and integrate information from the different homology searches, but provide the results of each analysis separately. We developed the HoSeIn workflow to intersect the information from these homology searches, and then determine the taxonomic and functional profile of the sample using this integrated information. The workflow is based on the assumption that the sequences that correspond to a certain taxon are composed of: sequences that were assigned to the same taxon by both homology searches; sequences that were assigned to that taxon by one of the homology searches but returned no hits in the other one.

RevDate: 2021-03-04

da Silva Maciel FC, Machado SL, de Souza Queiroz AF, et al (2021)

Analysis of column reactor results with organic decay by native organic microbiota and varying permeability.

Scientific reports, 11(1):5069.

Field bio-remediation techniques (FBRT) can be a low cost method to avoid the removal of top layers of soil which are rich in organic matter and bio diversity. The use of native microorganisms in FBRT is preferable because non-indigenous species can transfer their genetic material to the environment with negative impacts on the local ecological equilibrium. Petroleum Produced Water (PPW) is an important pollutant source in onshore production areas. However, due to high sodium concentrations in PPW and the occurrence of organic matter in dissolved and dispersed forms, obtaining pollutant transport parameters may be a difficult task. Results of column tests performed using a natural soil permeated by PPW are presented. All the samples presented a permeability decrease over time and the total hydrocarbon petroleum (TPH) breakthrough curves presented evidence of biological decay. Soil samples underwent biological characterization after tests (Metagenomic analyses and cultural media tests). Curves were modelled in an incremental way using a non-constant decay rate to better simulate the growing process of the microorganisms and consider the occurrence of varying velocity/permeability. Biological characterization results indicate the native organisms that are potentially more able to degrade PPW, including four bacteria (Bacillus and Lysinibacillus genus) and two fungi species (Malassezia and Talaromyces genus) that have not previously been mentioned in the consulted literature. The obtained results contribute to the development of more sustainable FBRTs focusing on native microorganisms, already adapted to the local environmental conditions.

RevDate: 2021-03-04

Yeoman CJ, Fields CJ, Lepercq P, et al (2021)

In Vivo Competitions between Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminoccus albus in a Gnotobiotic Sheep Model Revealed by Multi-Omic Analyses.

mBio, 12(2):.

Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens are the three predominant cellulolytic bacterial species found in the rumen. In vitro studies have shown that these species compete for adherence to, and growth upon, cellulosic biomass. Yet their molecular interactions in vivo have not heretofore been examined. Gnotobiotically raised lambs harboring a 17-h-old immature microbiota devoid of culturable cellulolytic bacteria and methanogens were inoculated first with F. succinogenes S85 and Methanobrevibacter sp. strain 87.7, and 5 months later, the lambs were inoculated with R. albus 8 and R. flavefaciens FD-1. Longitudinal samples were collected and profiled for population dynamics, gene expression, fibrolytic enzyme activity, in sacco fibrolysis, and metabolite profiling. Quantitative PCR, metagenome and metatranscriptome data show that F. succinogenes establishes at high levels initially but is gradually outcompeted following the introduction of the ruminococci. This shift resulted in an increase in carboxymethyl cellulase (CMCase) and xylanase activities but not in greater fibrolysis, suggesting that F. succinogenes and ruminococci deploy different but equally effective means to degrade plant cell walls. Expression profiles showed that F. succinogenes relied upon outer membrane vesicles and a diverse repertoire of CAZymes, while R. albus and R. flavefaciens preferred type IV pili and either CBM37-harboring or cellulosomal carbohydrate-active enzymes (CAZymes), respectively. The changes in cellulolytics also affected the rumen metabolome, including an increase in acetate and butyrate at the expense of propionate. In conclusion, this study provides the first demonstration of in vivo competition between the three predominant cellulolytic bacteria and provides insight on the influence of these ecological interactions on rumen fibrolytic function and metabolomic response.IMPORTANCE Ruminant animals, including cattle and sheep, depend on their rumen microbiota to digest plant biomass and convert it into absorbable energy. Considering that the extent of meat and milk production depends on the efficiency of the microbiota to deconstruct plant cell walls, the functionality of predominant rumen cellulolytic bacteria, Fibrobacter succinogenes, Ruminococcus albus, and Ruminococcus flavefaciens, has been extensively studied in vitro to obtain a better knowledge of how they operate to hydrolyze polysaccharides and ultimately find ways to enhance animal production. This study provides the first evidence of in vivo competitions between F. succinogenes and the two Ruminococcus species. It shows that a simple disequilibrium within the cellulolytic community has repercussions on the rumen metabolome and fermentation end products. This finding will have to be considered in the future when determining strategies aiming at directing rumen fermentations for animal production.

RevDate: 2021-03-04

Young C, Wood HM, Fuentes Balaguer A, et al (2021)

Microbiome Analysis of More Than 2,000 NHS Bowel Cancer Screening Programme Samples Shows the Potential to Improve Screening Accuracy.

Clinical cancer research : an official journal of the American Association for Cancer Research pii:1078-0432.CCR-20-3807 [Epub ahead of print].

PURPOSE: There is potential for fecal microbiome profiling to improve colorectal cancer screening. This has been demonstrated by research studies, but it has not been quantified at scale using samples collected and processed routinely by a national screening program.

EXPERIMENTAL DESIGN: Between 2016 and 2019, the largest of the NHS Bowel Cancer Screening Programme hubs prospectively collected processed guaiac fecal occult blood test (gFOBT) samples with subsequent colonoscopy outcomes: blood-negative [n = 491 (22%)]; colorectal cancer [n = 430 (19%)]; adenoma [n = 665 (30%)]; colonoscopy-normal [n = 300 (13%)]; nonneoplastic [n = 366 (16%)]. Samples were transported and stored at room temperature. DNA underwent 16S rRNA gene V4 amplicon sequencing. Taxonomic profiling was performed to provide features for classification via random forests (RF).

RESULTS: Samples provided 16S amplicon-based microbial profiles, which confirmed previously described colorectal cancer-microbiome associations. Microbiome-based RF models showed potential as a first-tier screen, distinguishing colorectal cancer or neoplasm (colorectal cancer or adenoma) from blood-negative with AUC 0.86 (0.82-0.89) and AUC 0.78 (0.74-0.82), respectively. Microbiome-based models also showed potential as a second-tier screen, distinguishing from among gFOBT blood-positive samples, colorectal cancer or neoplasm from colonoscopy-normal with AUC 0.79 (0.74-0.83) and AUC 0.73 (0.68-0.77), respectively. Models remained robust when restricted to 15 taxa, and performed similarly during external validation with metagenomic datasets.

CONCLUSIONS: Microbiome features can be assessed using gFOBT samples collected and processed routinely by a national colorectal cancer screening program to improve accuracy as a first- or second-tier screen. The models required as few as 15 taxa, raising the potential of an inexpensive qPCR test. This could reduce the number of colonoscopies in countries that use fecal occult blood test screening.

RevDate: 2021-03-04

Lind AL, KS Pollard (2021)

Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing.

Microbiome, 9(1):58.

BACKGROUND: Microbial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. While microbial eukaryotes are critical to these communities, they are challenging to study with shotgun sequencing techniques and are therefore often excluded.

RESULTS: Here, we present EukDetect, a bioinformatics method to identify eukaryotes in shotgun metagenomic sequencing data. Our approach uses a database of 521,824 universal marker genes from 241 conserved gene families, which we curated from 3713 fungal, protist, non-vertebrate metazoan, and non-streptophyte archaeplastida genomes and transcriptomes. EukDetect has a broad taxonomic coverage of microbial eukaryotes, performs well on low-abundance and closely related species, and is resilient against bacterial contamination in eukaryotic genomes. Using EukDetect, we describe the spatial distribution of eukaryotes along the human gastrointestinal tract, showing that fungi and protists are present in the lumen and mucosa throughout the large intestine. We discover that there is a succession of eukaryotes that colonize the human gut during the first years of life, mirroring patterns of developmental succession observed in gut bacteria. By comparing DNA and RNA sequencing of paired samples from human stool, we find that many eukaryotes continue active transcription after passage through the gut, though some do not, suggesting they are dormant or nonviable. We analyze metagenomic data from the Baltic Sea and find that eukaryotes differ across locations and salinity gradients. Finally, we observe eukaryotes in Arabidopsis leaf samples, many of which are not identifiable from public protein databases.

CONCLUSIONS: EukDetect provides an automated and reliable way to characterize eukaryotes in shotgun sequencing datasets from diverse microbiomes. We demonstrate that it enables discoveries that would be missed or clouded by false positives with standard shotgun sequence analysis. EukDetect will greatly advance our understanding of how microbial eukaryotes contribute to microbiomes. Video abstract.

RevDate: 2021-03-03

Wu S, Jiang P, Zhao XM, et al (2021)

Treatment regimens may compromise gut-microbiome-derived signatures for liver cirrhosis.

Cell metabolism, 33(3):455-456.

Many of the gut-microbiome-derived signatures for liver cirrhosis, especially the important ones, were likely under the influence of proton pump inhibitors (PPIs). Wu et al. suggest that drug usage is a confounding factor in metagenomics analysis that should be controlled for.

RevDate: 2021-03-03

Rosario D, Bidkhori G, Lee S, et al (2021)

Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson's disease.

Cell reports, 34(9):108807.

Parkinson's disease (PD) is the most common progressive neurological disorder compromising motor functions. However, nonmotor symptoms, such as gastrointestinal (GI) dysfunction, precede those affecting movement. Evidence of an early involvement of the GI tract and enteric nervous system highlights the need for better understanding of the role of gut microbiota in GI complications in PD. Here, we investigate the gut microbiome of patients with PD using metagenomics and serum metabolomics. We integrate these data using metabolic modeling and construct an integrative correlation network giving insight into key microbial species linked with disease severity, GI dysfunction, and age of patients with PD. Functional analysis reveals an increased microbial capability to degrade mucin and host glycans in PD. Personalized community-level metabolic modeling reveals the microbial contribution to folate deficiency and hyperhomocysteinemia observed in patients with PD. The metabolic modeling approach could be applied to uncover gut microbial metabolic contributions to PD pathophysiology.

RevDate: 2021-03-03

Li B, Song Y, Liu C, et al (2021)

Rapid cultivation of anammox bacteria by forming free cells in a membrane bioreactor.

Water environment research : a research publication of the Water Environment Federation [Epub ahead of print].

The low growth rate of anammox bacteria is one of the main obstacles to its broad use in removing biological nitrogen in sewage treatment. Free cells show the characteristics of relatively rapid growth. To increase the growth rate, this study cultivated free-living anammox bacteria using a membrane bioreactor. The particle size distributions showed that more than 95.48% of biomass was less than 50 μm in size, and the growth rate of free-living anammox bacteria was shortened to 5.68 d after cultivation. Candidatus Brocadia was the most important anammox genus, with a relative abundance of 8.83%. The key functional genes, including hzs, hdh, and hao, were identified and expressed using metagenomic and metaproteomic analyses. After the rapid cultivation of the free-living anammox bacteria, a potential method shortening the start-up time was proposed to rapidly form anammox biofilm by attaching to carriers.

RevDate: 2021-03-03

Xie J, Tong P, Zhang L, et al (2021)

First detection and genetic characterization of equid herpesvirus 2, 4, and 5 in China.

Archives of virology [Epub ahead of print].

In November 2018, an outbreak of respiratory disease occurred in foals at an equestrian club in Changji, northern Xinjiang, China. We applied viral metagenomics to investigate this outbreak and identify potential pathogens involved in this equine respiratory syndrome. The metagenomics data revealed the presence of sequences matching those of equid herpesvirus (EHV) 2, 4, and 5. PCR with specific primers targeting ORF33 of EHV-4 and ORF8 of EHV-2 and EHV-5 revealed coinfection with these viruses in this respiratory syndrome. To investigate the prevalence of these viruses in China, 453 nasal swabs from clinically healthy thoroughbred foals (36/453, 7.9%) and horses (417/453, 92.1%) were collected from several equestrian clubs. Forty-five (9.9%) of the samples tested positive for EHV-5 DNA, and seven (1.5%) tested positive for EHV-2, but all were negative for EHV-4 DNA. Forty-nine (10.8%) samples tested positive for both EHV-5 and EHV-2 DNA. Using these samples, one complete EHV-4 ORF33, 10 partial EHV-2 ORF8, and 50 partial EHV-5 ORF8 sequences from the 10 diseased foals and 50 thoroughbred horses were then determined. Sequence analysis indicated that EHV-4 ORF33 and EHV-5 ORF8, in contrast to EHV-2 ORF8, had high sequence similarity to those of published sequences. Our data provide the first evidence that EHV-2, -4, and -5 co-circulate in China and that EHV-4 is potentially involved in this respiratory disease in foals.

RevDate: 2021-03-03

Tortelli BA, Lewis AL, JC Fay (2021)

The structure and diversity of strain-level variation in vaginal bacteria.

Microbial genomics [Epub ahead of print].

The vaginal microbiome plays an important role in human health and species of vaginal bacteria have been associated with reproductive disease. Strain-level variation is also thought to be important, but the diversity, structure and evolutionary history of vaginal strains is not as well characterized. We developed and validated an approach to measure strain variation from metagenomic data based on SNPs within the core genomes for six species of vaginal bacteria: Gardnerella vaginalis, Lactobacillus crispatus, Lactobacillus iners, Lactobacillus jensenii, Lactobacillus gasseri and Atopobium vaginae. Despite inhabiting the same environment, strain diversity and structure varies across species. All species except L. iners are characterized by multiple distinct groups of strains. Even so, strain diversity is lower in the Lactobacillus species, consistent with a more recent colonization of the human vaginal microbiome. Both strain diversity and the frequency of multi-strain samples is related to species-level diversity of the microbiome in which they occur, suggesting similar ecological factors influencing diversity within the vaginal niche. We conclude that the structure of strain-level variation provides both the motivation and means of testing whether strain-level differences contribute to the function and health consequences of the vaginal microbiome.

RevDate: 2021-03-03

Bağcı C, Patz S, DH Huson (2021)

DIAMOND+MEGAN: Fast and Easy Taxonomic and Functional Analysis of Short and Long Microbiome Sequences.

Current protocols, 1(3):e59.

One main approach to computational analysis of microbiome sequences is to first align against a reference database of annotated protein sequences (NCBI-nr) and then perform taxonomic and functional binning of the sequences based on the resulting alignments. For both short and long reads (or assembled contigs), alignment is performed using DIAMOND, whereas taxonomic and functional binning, followed by inter- active exploration and analysis, is performed using MEGAN. We provide two step-by-step descriptions of this approach: © 2021 The Authors. Basic Protocol 1: Taxonomic and functional analysis of short read microbiome sequences Support Protocol 1: Preprocessing Basic Protocol 2: taxonomic and functional analysis of assembled long read microbiome sequences Support Protocol 2: Taxonomic binning and CheckM.

RevDate: 2021-03-03

Sulaiman I, Chung M, Angel L, et al (2021)

Microbial signatures in the lower airways of mechanically ventilated COVID19 patients associated with poor clinical outcome.

medRxiv : the preprint server for health sciences.

Mortality among patients with COVID-19 and respiratory failure is high and there are no known lower airway biomarkers that predict clinical outcome. We investigated whether bacterial respiratory infections and viral load were associated with poor clinical outcome and host immune tone. We obtained bacterial and fungal culture data from 589 critically ill subjects with COVID-19 requiring mechanical ventilation. On a subset of the subjects that underwent bronchoscopy, we also quantified SARS-CoV-2 viral load, analyzed the microbiome of the lower airways by metagenome and metatranscriptome analyses and profiled the host immune response. We found that isolation of a hospital-acquired respiratory pathogen was not associated with fatal outcome. However, poor clinical outcome was associated with enrichment of the lower airway microbiota with an oral commensal (Mycoplasma salivarium), while high SARS-CoV-2 viral burden, poor anti-SARS-CoV-2 antibody response, together with a unique host transcriptome profile of the lower airways were most predictive of mortality. Collectively, these data support the hypothesis that 1) the extent of viral infectivity drives mortality in severe COVID-19, and therefore 2) clinical management strategies targeting viral replication and host responses to SARS-CoV-2 should be prioritized.

RevDate: 2021-03-03

Puentes LA, Ramos YL, Inojosa YA, et al (2019)

Isolation of PCR-quality Genomic DNA from Soils Impacted with Extra Heavy Crude Oil.

Bio-protocol, 9(12):e3265 pii:3265.

For the study of microbial communities in samples of soils impacted with extra heavy crude oil, it is necessary to perform molecular analyses. Due to the difficulty of oil matrix handling, there are very few protocols reported in writing. Also, one can only observe a very low concentration of DNA. That's why it is required to have an effective protocol to conduct studies in this type of matrix. This protocol includes steps of cell lysis by saline buffer with ionic/non-ionic detergents, and enzymatic digestion with lysozyme and proteases, complemented with organic extraction and alcohol precipitation. Additionally, it requires purification to eliminate the inhibitory substances of the extract that cause PCR inhibition. The method of DNA extraction proposed in this study is easy to handle and low cost. It allows the extraction of DNA from different bacteria and fungi, associated with soil contaminated with extra heavy crude.

RevDate: 2021-03-03

Aouizerat T, Maeir AM, Paz Y, et al (2020)

Isolation and Characterization of Live Yeast Cells from Ancient Clay Vessels.

Bio-protocol, 10(1):e3473 pii:3473.

Ancient fermented food has been studied mainly based on residue analysis and recipes and reconstruction attempts were performed using modern domesticated yeast. Furthermore, microorganisms which participated in fermentation were studied using ancient-DNA techniques. In a recent paper, we presented a novel approach based on the hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. Here we present a pipeline for isolation of yeast from clay vessels uncovered in archeological sites and transferred to the microbiology lab where they can be isolated and characterized. This method opens new avenues for experimental archeology and enables attempts to recreate ancient food and beverages using the original microorganisms.

RevDate: 2021-03-03

Dubinsky V, Reshef L, Rabinowitz K, et al (2021)

Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease.

mSystems, 6(2):.

Crohn's disease (CD), ulcerative colitis (UC), and pouchitis are multifactorial and chronic inflammatory bowel diseases (IBD). Pouchitis develops in former UC patients after proctocolectomy and ileal-pouch-anal anastomosis and is characterized by inflammation of the previously normal small intestine comprising the pouch. The extent to which microbial functional alteration (dysbiosis) in pouchitis resembles that of CD or UC has not been investigated, and the pathogenesis of pouchitis remains unknown. We collected 208 fecal metagenomes from 69 patients with a pouch (normal pouch and pouchitis) and compared them to publicly available metagenomes of patients with CD (n = 88), patients with UC (n = 76), and healthy controls (n = 56). Patients with pouchitis presented the highest alterations in species, metabolic pathways, and enzymes, which was correlated with intestinal inflammation. Ruminococcus gnavus strains encoding mucin-degrading glycoside hydrolases were highly enriched in pouchitis. Butyrate and secondary bile acid biosynthesis pathways were decreased in IBD phenotypes and were especially low in pouchitis. Pathways such as amino acid biosynthesis and degradation of aromatic compounds and sugars, encoded by members of the Enterobacteriaceae, were enriched in pouch and CD but not in UC. We developed microbial feature-based classifiers that can distinguish between patients with a normal pouch and pouchitis and identified species and genes that were predictive of pouchitis. We propose that the noninflamed pouch is already dysbiotic and microbially is similar to CD. Our study reveals microbial functions that outline the pathogenesis of pouchitis and suggests bacterial groups and functions that could be targeted for intervention to attenuate small intestinal inflammation present in pouchitis and CD.IMPORTANCE Crohn's disease (CD), ulcerative colitis (UC), and pouchitis are chronic inflammatory conditions of the bowel. Pouchitis develops in former UC patients after proctocolectomy and ileal-pouch-anal anastomosis and is characterized by inflammation of the previously normal small intestine comprising the pouch. The extent to which microbial dysbiosis in patients with pouchitis resembles that of CD or UC and the pathogenesis of pouchitis remains unclear. We investigated the functions in the gut microbiomes of these patients using metagenomics. We found that the noninflamed pouch is already dysbiotic and microbially is similar to CD. Our study reveals microbial functions with a potential role in pouchitis pathogenesis such as depletion in butyrate and secondary bile acid synthesis and enrichment of amino acid synthesis and degradation of aromatic compounds, encoded by members of the Enterobacteriaceae We developed microbial feature-based classifiers that can distinguish between patients with a normal pouch and pouchitis and identified species and genes that were predictive of pouchitis. We suggest species and functions that could be targeted for intervention to attenuate small intestinal inflammation present in pouchitis and CD.

RevDate: 2021-03-03

Yanuka-Golub K, Dubinsky V, Korenblum E, et al (2021)

Anode Surface Bioaugmentation Enhances Deterministic Biofilm Assembly in Microbial Fuel Cells.

mBio, 12(2):.

Microbial fuel cells (MFCs) generate energy while aiding the biodegradation of waste through the activity of an electroactive mixed biofilm. Metabolic cooperation is essential for MFCs' efficiency, especially during early colonization. Thus, examining specific ecological processes that drive the assembly of anode biofilms is highly important for shortening startup times and improving MFC performance, making this technology cost-effective and sustainable. Here, we use metagenomics to show that bioaugmentation of the anode surface with a taxonomically defined electroactive consortium, dominated by Desulfuromonas, resulted in an extremely rapid current density generation. Conversely, the untreated anode surface resulted in a highly stochastic and slower biofilm assembly. Remarkably, an efficient anode colonization process was obtained only if wastewater was added, leading to a nearly complete replacement of the bioaugmented community by Geobacter lovleyi Although different approaches to improve MFC startup have been investigated, we propose that only the combination of anode bioaugmentation with wastewater inoculation can reduce stochasticity. Such an approach provides the conditions that support the growth of specific newly arriving species that positively support the fast establishment of a highly functional anode biofilm.IMPORTANCE Mixed microbial communities play important roles in treating wastewater, in producing renewable energy, and in the bioremediation of pollutants in contaminated environments. While these processes are well known, especially the community structure and biodiversity, how to efficiently and robustly manage microbial community assembly remains unknown. Moreover, it has been shown that a high degree of temporal variation in microbial community composition and structure often occurs even under identical environmental conditions. This heterogeneity is directly related to stochastic processes involved in microbial community organization, similarly during the initial stages of biofilm formation on surfaces. In this study, we show that anode surface pretreatment alone is not sufficient for a substantial improvement in startup times in microbial fuel cells (MFCs), as previously thought. Rather, we have discovered that the combination of applying a well-known consortium directly on the anode surface together with wastewater (including the bacteria that they contain) is the optimized management scheme. This allowed a selected colonization process by the wastewater species, which improved the functionality relative to that of untreated systems.

RevDate: 2021-03-03

Choo KSO, Bollen M, Ravensdale JT, et al (2021)

Effect of chitosan and gum Arabic with natamycin on the aroma profile and bacterial community of Australian grown black Périgord truffles (Tuber melansoporum) during storage.

Food microbiology, 97:103743.

This study aimed to assess the effect of chitosan or gum Arabic edible coatings, with natamycin (200, 300, 400 mg/L) on the aroma profiles of Western Australian grown truffles at five storage intervals: 0, 7, 14, 21, and 28 days using solid-phase microextraction (SPME)-followed by gas chromatography-mass spectrometry (GC-MS). The population structure of the bacterial community of both untreated and chitosan-natamycin (400 mg/L) coated truffles were assessed using metagenomic sequencing analysis alongside GC-MS. The results demonstrated that all the coating treatments were able to have a positive impact in halting or delaying the changes of truffle aroma throughout the storage period, with chitosan-natamycin (400 mg/L) coating having the best preservation results compared to the other coatings. Only 9 volatile organic compounds (VOCs) were found to have significant changes in chitosan-natamycin (400 mg/L) coated truffles throughout the storage period compared to 11 VOCs in untreated controls. The result also demonstrated the gradual change of fresh truffle's bacteria communities over the storage period. Over 4 weeks of storage, the dominant bacterial classes of the truffles (α-Proteobacteria, Bacteroidia or Actinobacteria classes) were replaced by Bacteroidia, Actinobacteria, Deltaprotobacteria and γ-Proteobacteria classes. The preliminary results from this study show that edible coatings can affect the VOC and bacterial communities of the truffles which may have implications for future research into truffle preservation techniques.

RevDate: 2021-03-03

Constantinou A, Kanti V, Polak-Witka K, et al (2021)

The Potential Relevance of the Microbiome to Hair Physiology and Regeneration: The Emerging Role of Metagenomics.

Biomedicines, 9(3): pii:biomedicines9030236.

Human skin and hair follicles are recognized sites of microbial colonization. These microbiota help regulate host immune mechanisms via an interplay between microbes and immune cells, influencing homeostasis and inflammation. Bacteria affect immune responses by controlling the local inflammatory milieu, the breakdown of which can result in chronic inflammatory disorders. Follicular microbiome shifts described in some inflammatory cutaneous diseases suggest a link between their development or perpetuation and dysbiosis. Though the hair follicle infundibulum is an area of intense immunological interactions, bulb and bulge regions represent immune-privileged niches. Immune privilege maintenance seems essential for hair growth and regeneration, as collapse and inflammation characterize inflammatory hair disorders like alopecia areata and primary cicatricial alopecia. Current research largely focuses on immunological aberrations. However, studies suggest that external stimuli and interactions across the follicular epithelium can have profound effects on the local immune system, homeostasis, and cycling. Herein, we review hair follicle bacterial colonization, its possible effects on the underlying tissue, and links to the pathogenesis of alopecia, beyond the pure investigation of specific species abundance. As skin microbiology enters the metagenomics era, multi-dimensional approaches will enable a new level of investigations on the effects of microorganisms and metabolism on host tissue.

RevDate: 2021-03-03
CmpDate: 2021-03-03

Morgan-Lang C, McLaughlin R, Armstrong Z, et al (2020)

TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler.

Bioinformatics (Oxford, England), 36(18):4706-4713.

MOTIVATION: Microbial communities drive matter and energy transformations integral to global biogeochemical cycles, yet many taxonomic groups facilitating these processes remain poorly represented in biological sequence databases. Due to this missing information, taxonomic assignment of sequences from environmental genomes remains inaccurate.

RESULTS: We present the Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software for functionally and taxonomically classifying genes, reactions and pathways from genomes of cultivated and uncultivated microorganisms using reference packages representing coding sequences mediating multiple globally relevant biogeochemical cycles. TreeSAPP uses linear regression of evolutionary distance on taxonomic rank to improve classifications, assigning both closely related and divergent query sequences at the appropriate taxonomic rank. TreeSAPP is able to provide quantitative functional and taxonomic classifications for both assembled and unassembled sequences and files supporting interactive tree of life visualizations.

TreeSAPP was developed in Python 3 as an open-source Python package and is available on GitHub at

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2021-03-02
CmpDate: 2021-03-02

Klimina KM, Voroshilova VN, Poluektova EU, et al (2020)

Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota.

Toxins, 12(6):.

The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species and strains. Yet many studies stop at characterizing the HGM at the family level. This is mainly due to lack of adequate methods for a high-resolution profiling of the HGM. One way to characterize the strain diversity of the HGM is to look for strain-specific functional markers. Here, we propose using type II toxin-antitoxin systems (TAS). To identify TAS systems in the HGM, we previously developed the software TAGMA. This software was designed to detect the TAS systems, MazEF and RelBE, in lactobacilli and bifidobacteria. In this study, we updated the gene catalog created previously and used it to test our software anew on 1346 strains of bacteria, which belonged to 489 species and 49 genera. We also sequenced the genomes of 20 fecal samples and analyzed the results with TAGMA. Although some differences were detected at the strain level, the results showed no particular difference in the bacterial species between our method and other classic analysis software. These results support the use of the updated catalog of genes encoding type II TAS as a useful tool for computer-assisted species and strain characterization of the HGM.

RevDate: 2021-03-02

Park SY, Lee ES, Lee SR, et al (2021)

Vaginal Microbiome Is Associated With Vulvodynia, Vulvar Pain Syndrome: A Case-Control Study.

Sexual medicine, 9(2):100314 pii:S2050-1161(20)30202-6 [Epub ahead of print].

INTRODUCTION: Vulvodynia, vulvar pain syndrome, is defined as vulvar pain of at least a 3-month duration without a clear identifiable cause, which may have associated factor and the etiology and treatment of this challenging disease is still unclear. Dyspareunia is a relevant symptom of patients with vulvodynia. Vaginal microbiome has known an important role in local immune-inflammatory responses and it may be important pathogenic mechanism in vulvodynia.

AIM: The objective of this study was to investigate the association of vaginal microbiome and vulvodynia.

METHODS: We analyzed the microbial compositions of the vestibule and vagina among women with clinically diagnosed vulvodynia (n = 22) and age-matched healthy controls (n = 22) without vulvodynia. The compositions of bacterial microbiomes were compared by pyrosequencing of the 16S rRNA.

MAIN OUTCOME MEASURE: Vaginal microbiome alpha and beta diversity were assessed using the Shannon diversity index and Heat map. Linear discriminant analysis effect size was used to find out marker for vulvodynia.

RESULTS: There were no significant differences in the age, duration of marriage, history of gynecologic surgery, parity, and menopause status between cases and controls. A total of 1,661,934 high-quality pyrosequencing reads was obtained to evaluate bacterial diversity, and 50,246 unique sequences represented all phylotypes. The type and mean number of the genera were not different between cases and controls. However, the most predominant phyla of bacteria were significantly different between cases and controls. 3 phyla (Firmicutes, Actinobacteria, and Tenericutes) and 11 genera including Gardnerella, Ureaplasma, Achromobacter, Mycoplasma, and Bifidobacteria were significantly more prevalent in cases than in controls (P < .05). Linear discriminant analysis effect size analysis suggest the Bifidobacterium, Mycoplasma, and Fenollaria species can be potential markers for vulvodynia.

CONCLUSION: Our results suggest the differences in vaginal microbiome can be associated with the vulvodynia. Park SY, Lee ES, Lee SR, et al. Vaginal Microbiome Is Associated With Vulvodynia, Vulvar Pain Syndrome: A Case-Control Study. Sex Med 2021;XX:XXX-XXX.

RevDate: 2021-03-02

Ruuskanen MO, Åberg F, Männistö V, et al (2021)

Links between gut microbiome composition and fatty liver disease in a large population sample.

Gut microbes, 13(1):1-22.

Fatty liver disease is the most common liver disease in the world. Its connection with the gut microbiome has been known for at least 80 y, but this association remains mostly unstudied in the general population because of underdiagnosis and small sample sizes. To address this knowledge gap, we studied the link between the Fatty Liver Index (FLI), a well-established proxy for fatty liver disease, and gut microbiome composition in a representative, ethnically homogeneous population sample of 6,269 Finnish participants. We based our models on biometric covariates and gut microbiome compositions from shallow metagenome sequencing. Our classification models could discriminate between individuals with a high FLI (≥60, indicates likely liver steatosis) and low FLI (<60) in internal cross-region validation, consisting of 30% of the data not used in model training, with an average AUC of 0.75 and AUPRC of 0.56 (baseline at 0.30). In addition to age and sex, our models included differences in 11 microbial groups from class Clostridia, mostly belonging to orders Lachnospirales and Oscillospirales. Our models were also predictive of the high FLI group in a different Finnish cohort, consisting of 258 participants, with an average AUC of 0.77 and AUPRC of 0.51 (baseline at 0.21). Pathway analysis of representative genomes of the positively FLI-associated taxa in (NCBI) Clostridium subclusters IV and XIVa indicated the presence of, e.g., ethanol fermentation pathways. These results support several findings from smaller case-control studies, such as the role of endogenous ethanol producers in the development of the fatty liver.

RevDate: 2021-03-02

Brubaker L, Putonti C, Dong Q, et al (2021)

The human urobiome.

Mammalian genome : official journal of the International Mammalian Genome Society [Epub ahead of print].

Traditionally, the healthy urinary bladder has been considered to be sterile. Several teams have used metagenomic (DNA-dependent) and metaculturomic (culture-dependent) methods to debunk this longstanding dogma. In fact, resident microbial communities (urobiome) have been detected in both adult females and males. Although the field is young, several observations have been made. For example, the urobiome differs between men and women, likely due to anatomical and hormonal differences. Importantly, the urobiome has been associated with a variety of lower urinary tract disorders, including overactive bladder and post-operative urinary tract infection, raising the possibility that clinicians might one day treat symptoms by modifying the urobiome instead of killing the suspected uropathogen. Little is known concerning the relationship between the urobiome and host genetics; so far, only a single paper has reported such a study. However, major efforts have gone into understanding the genomics of the urobiome itself, a process facilitated by the fact that many urobiome studies have used metaculturomic methods to detect and identify microbes. In this narrative review, we will introduce the urobiome with separate sections on the female and male urobiomes, discuss challenges specific to the urobiome, describe newly discovered associations between the urobiome and lower urinary tract symptoms, and highlight the one study that has attempted to relate host genetics and the urobiome. We will finish with a section on how metagenomic surveys and whole genome sequencing of bacterial isolates are improving our understanding of the urobiome and its relationship to lower urinary tract health and disorders.

RevDate: 2021-03-02

Dalcin Martins P, de Jong A, Lenstra WK, et al (2021)

Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen-limited methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments.

MicrobiologyOpen, 10(1):e1175.

Microbial methane oxidation is a major biofilter preventing larger emissions of this powerful greenhouse gas from marine coastal areas into the atmosphere. In these zones, various electron acceptors such as sulfate, metal oxides, nitrate, or oxygen can be used. However, the key microbial players and mechanisms of methane oxidation are poorly understood. In this study, we inoculated a bioreactor with methane- and iron-rich sediments from the Bothnian Sea to investigate microbial methane and iron cycling under low oxygen concentrations. Using metagenomics, we investigated shifts in microbial community composition after approximately 2.5 years of bioreactor operation. Marker genes for methane and iron cycling, as well as respiratory and fermentative metabolism, were identified and used to infer putative microbial metabolism. Metagenome-assembled genomes representing novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria were recovered and revealed a potential for methane oxidation, organic matter degradation, and iron cycling, respectively. This work brings new hypotheses on the identity and metabolic versatility of microorganisms that may be members of such functional guilds in coastal marine sediments and highlights that microorganisms potentially composing the methane biofilter in these sediments may be more diverse than previously appreciated.

RevDate: 2021-03-02

Maclot F, Candresse T, Filloux D, et al (2021)

[From boots on the ground to nucleotides in the sequencer: a century of advances in the study of the plant virus ecology].

Virologie (Montrouge, France), 25(1):29-42.

Plant virus ecology began to be explored at the end of the 19th century. Since then, major advances have revealed complex virus-host-vector interactions in a variety of environments. These advances have been accelerated by development of new technologies for virus detection and characterization, the latest of which being high-throughput sequencing (HTS). HTS technologies have proved to be effective for non-targeted characterization of all or nearly all viruses present in a sample without requiring prior information about virus identity, as would be needed for virus-targeted tests. Phytoviromic studies have thus made important advances, including characterization of the complex interactions between phytovirus dynamics and the structure of multi-species host communities, and documentation of the effects of anthropogenic ecosystem simplification on plant virus emergence and diversity. However, such studies must overcome challenges at every stage, from plant sampling to bioinformatics analysis. This review summarizes major advances in plant virus ecology, in association with technological developments, and presents key considerations for use of HTS in the study of the ecology of phytovirus communities.

RevDate: 2021-03-02

Oyewusi HA, Wahab RA, F Huyop (2021)

Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria.

Molecular biology reports [Epub ahead of print].

An integral approach to decoding both culturable and uncultured microorganisms' metabolic activity involves the whole genome sequencing (WGS) of individual/complex microbial communities. WGS of culturable microbes, amplicon sequencing, metagenomics, and single-cell genome analysis are selective techniques integrating genetic information and biochemical mechanisms. These approaches transform microbial biotechnology into a quick and high-throughput culture-independent evaluation and exploit pollutant-degrading microbes. They are windows into enzyme regulatory bioremediation pathways (i.e., dehalogenase) and the complete bioremediation process of organohalide pollutants. While the genome sequencing technique is gaining the scientific community's interest, it is still in its infancy in the field of pollutant bioremediation. The techniques are becoming increasingly helpful in unraveling and predicting the enzyme structure and explore metabolic and biodegradation capabilities.

RevDate: 2021-03-02

Milani C (2021)

Metagenomic Analyses of Bifidobacterial Communities.

Methods in molecular biology (Clifton, N.J.), 2278:183-193.

Bifidobacteria represent highly prevalent and abundant members of the gut microbiota during mammalian infancy. In this context, bifidobacterial species have been shown to be correlated with many aspects of host health by means of direct interactions with the host and cohabiting microbes. Metagenomic sequencing of fecal DNA represents a valuable approach for taxonomic and functional profiling of bacterial populations, and has allowed us to appreciate the relevance of bifidobacterial taxa in such complex bacterial communities, especially during the first stages of life.

RevDate: 2021-03-02

McDonnell B, Casey E, Milani C, et al (2021)

Phageome Analysis of Bifidobacteria-Rich Samples.

Methods in molecular biology (Clifton, N.J.), 2278:71-85.

Bifidobacteria are important early colonizers of the human intestinal tract. The relative abundance of bifidobacterial species may be modulated, in part, by bacteriophage activity. Metagenomic studies of these populations is a crucial step in understanding this important interaction. This chapter outlines the technical instructions required to analyze the virome of a bifidobacteria-rich sample, for example, an infant fecal sample.

RevDate: 2021-03-02

Meyer F, Lesker TR, Koslicki D, et al (2021)

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit.

Nature protocols [Epub ahead of print].

Computational methods are key in microbiome research, and obtaining a quantitative and unbiased performance estimate is important for method developers and applied researchers. For meaningful comparisons between methods, to identify best practices and common use cases, and to reduce overhead in benchmarking, it is necessary to have standardized datasets, procedures and metrics for evaluation. In this tutorial, we describe emerging standards in computational meta-omics benchmarking derived and agreed upon by a larger community of researchers. Specifically, we outline recent efforts by the Critical Assessment of Metagenome Interpretation (CAMI) initiative, which supplies method developers and applied researchers with exhaustive quantitative data about software performance in realistic scenarios and organizes community-driven benchmarking challenges. We explain the most relevant evaluation metrics for assessing metagenome assembly, binning and profiling results, and provide step-by-step instructions on how to generate them. The instructions use simulated mouse gut metagenome data released in preparation for the second round of CAMI challenges and showcase the use of a repository of tool results for CAMI datasets. This tutorial will serve as a reference for the community and facilitate informative and reproducible benchmarking in microbiome research.

RevDate: 2021-03-02

Michoud G, Ngugi DK, Barozzi A, et al (2021)

Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline.

The ISME journal [Epub ahead of print].

Deep-sea hypersaline anoxic basins are polyextreme environments in the ocean's interior characterized by the high density of brines that prevents mixing with the overlaying seawater, generating sharp chemoclines and redoxclines up to tens of meters thick that host a high concentration of microbial communities. Yet, a fundamental understanding of how such pycnoclines shape microbial life and the associated biogeochemical processes at a fine scale, remains elusive. Here, we applied high-precision sampling of the brine-seawater transition interface in the Suakin Deep, located at 2770 m in the central Red Sea, to reveal previously undocumented fine-scale community structuring and succession of metabolic groups along a salinity gradient only 1 m thick. Metagenomic profiling at a 10-cm-scale resolution highlighted spatial organization of key metabolic pathways and corresponding microbial functional units, emphasizing the prominent role and significance of salinity and oxygen in shaping their ecology. Nitrogen cycling processes are especially affected by the redoxcline with ammonia oxidation processes being taxa and layers specific, highlighting also the presence of novel microorganisms, such as novel Thaumarchaeota and anammox, adapted to the changing conditions of the chemocline. The findings render the transition zone as a critical niche for nitrogen cycling, with complementary metabolic networks, in turn underscoring the biogeochemical complexity of deep-sea brines.

RevDate: 2021-03-02

Francis TB, Bartosik D, Sura T, et al (2021)

Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom.

The ISME journal [Epub ahead of print].

Algal blooms produce large quantities of organic matter that is subsequently remineralised by bacterial heterotrophs. Polysaccharide is a primary component of algal biomass. It has been hypothesised that individual bacterial heterotrophic niches during algal blooms are in part determined by the available polysaccharide substrates present. Measurement of the expression of TonB-dependent transporters, often specific for polysaccharide uptake, might serve as a proxy for assessing bacterial polysaccharide consumption over time. To investigate this, we present here high-resolution metaproteomic and metagenomic datasets from bacterioplankton of the 2016 spring phytoplankton bloom at Helgoland island in the southern North Sea, and expression profiles of TonB-dependent transporters during the bloom, which demonstrate the importance of both the Gammaproteobacteria and the Bacteroidetes as degraders of algal polysaccharide. TonB-dependent transporters were the most highly expressed protein class, split approximately evenly between the Gammaproteobacteria and Bacteroidetes, and totalling on average 16.7% of all detected proteins during the bloom. About 93% of these were predicted to take up organic matter, and for about 12% of the TonB-dependent transporters, we predicted a specific target polysaccharide class. Most significantly, we observed a change in substrate specificities of the expressed transporters over time, which was not reflected in the corresponding metagenomic data. From this, we conclude that algal cell wall-related compounds containing fucose, mannose, and xylose were mostly utilised in later bloom stages, whereas glucose-based algal and bacterial storage molecules including laminarin, glycogen, and starch were used throughout. Quantification of transporters could therefore be key for understanding marine carbon cycling.

RevDate: 2021-03-02

Sonbol S, R Siam (2021)

The association of group IIB intron with integrons in hypersaline environments.

Mobile DNA, 12(1):8.

BACKGROUND: Group II introns are mobile genetic elements used as efficient gene targeting tools. They function as both ribozymes and retroelements. Group IIC introns are the only class reported so far to be associated with integrons. In order to identify group II introns linked with integrons and CALINS (cluster of attC sites lacking a neighboring integron integrase) within halophiles, we mined for integrons in 28 assembled metagenomes from hypersaline environments and publically available 104 halophilic genomes using Integron Finder followed by blast search for group II intron reverse transcriptases (RT)s.

RESULTS: We report the presence of different group II introns associated with integrons and integron-related sequences denoted by UHB.F1, UHB.I2, H.ha.F1 and H.ha.F2. The first two were identified within putative integrons in the metagenome of Tanatar-5 hypersaline soda lake, belonging to IIC and IIB intron classes, respectively at which the first was a truncated intron. Other truncated introns H.ha.F1 and H.ha.F2 were also detected in a CALIN within the extreme halophile Halorhodospira halochloris, both belonging to group IIB introns. The intron-encoded proteins (IEP) s identified within group IIB introns belonged to different classes: CL1 class in UHB.I2 and bacterial class E in H.ha.Fa1 and H.ha.F2. A newly identified insertion sequence (ISHahl1) of IS200/605 superfamily was also identified adjacent to H. halochloris CALIN. Finally, an abundance of toxin-antitoxin (TA) systems was observed within the identified integrons.

CONCLUSION: So far, this is the first investigation of group II introns within integrons in halophilic genomes and metagenomes from hypersaline environments. We report the presence of group IIB introns associated with integrons or CALINs. This study provides the basis for understanding the role of group IIB introns in the evolution of halophiles and their potential biotechnological role.

RevDate: 2021-03-02

Plichta DR, Somani J, Pichaud M, et al (2021)

Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis.

Genome medicine, 13(1):35.

BACKGROUND: Immunoglobulin G4-related disease (IgG4-RD) and systemic sclerosis (SSc) are rare autoimmune diseases characterized by the presence of CD4+ cytotoxic T cells in the blood as well as inflammation and fibrosis in various organs, but they have no established etiologies. Similar to other autoimmune diseases, the gut microbiome might encode disease-triggering or disease-sustaining factors.

METHODS: The gut microbiomes from IgG4-RD and SSc patients as well as healthy individuals with no recent antibiotic treatment were studied by metagenomic sequencing of stool DNA. De novo assembly-based taxonomic and functional characterization, followed by association and accessory gene set enrichment analysis, were applied to describe microbiome changes associated with both diseases.

RESULTS: Microbiomes of IgG4-RD and SSc patients distinctly separated from those of healthy controls: numerous opportunistic pathogenic Clostridium and typically oral Streptococcus species were significantly overabundant, while Alistipes, Bacteroides, and butyrate-producing species were depleted in the two diseases compared to healthy controls. Accessory gene content analysis in these species revealed an enrichment of Th17-activating Eggerthella lenta strains in IgG4-RD and SSc and a preferential colonization of a homocysteine-producing strain of Clostridium bolteae in SSc. Overabundance of the classical mevalonate pathway, hydroxyproline dehydratase, and fibronectin-binding protein in disease microbiomes reflects potential functional differences in host immune recognition and extracellular matrix utilization associated with fibrosis. Strikingly, the majority of species that were differentially abundant in IgG4-RD and SSc compared to controls showed the same directionality in both diseases. Compared with multiple sclerosis and rheumatoid arthritis, the gut microbiomes of IgG4-RD and SSc showed similar signatures; in contrast, the most differentially abundant taxa were not the facultative anaerobes consistently identified in inflammatory bowel diseases, suggesting the microbial signatures of IgG4-RD and SSc do not result from mucosal inflammation and decreased anaerobism.

CONCLUSIONS: These results provide an initial characterization of gut microbiome ecology in fibrosis-prone IgG4-RD and SSc and reveal microbial functions that offer insights into the pathophysiology of these rare diseases.

RevDate: 2021-03-02

Baburam C, NA Feto (2021)

Mining of two novel aldehyde dehydrogenases (DHY-SC-VUT5 and DHY-G-VUT7) from metagenome of hydrocarbon contaminated soils.

BMC biotechnology, 21(1):18.

BACKGROUND: Aldehyde dehydrogenases are vital for aerobic hydrocarbon degradation and is involved in the last step of catalysing the oxidation of aldehydes to carboxylic acids. With the global increase in hydrocarbon pollution of different environments, these enzymes have the potential to be used in enzymatic bioremediation applications.

RESULTS: Fifteen fosmid clones with hydrocarbon degrading potential were functionally screened to identify dehydrogenase enzymes. Accordingly, the fosmid insert of the positive clones were sequenced using PacBio next generation sequencing platform and de novo assembled using CLC Genomic Work Bench. The 1233 bp long open reading frame (ORF) for DHY-SC-VUT5 was found to share a protein sequence similarity of 97.7% to short-chain dehydrogenase from E. coli. The 1470 bp long ORF for DHY-G-VUT7 was found to share a protein sequence similarity of 23.9% to glycine dehydrogenase (decarboxylating) (EC from Caulobacter vibrioides (strain NA1000 / CB15N) (Caulobacter crescentus). The in silico analyses and blast against UNIPROT protein database with the stated similarity show that the two dehydrogenases are novel. Biochemical characterization revealed, that the highest relative activity was observed at substrate concentrations of 150 mM and 50 mM for DHY-SC-VUT5 and DHY-G-VUT7, respectively. The Km values were found to be 13.77 mM with a Vmax of 0.009135 μmol.min- 1 and 2.832 mM with a Vmax of 0.005886 μmol.min- 1 for DHY-SC-VUT5 and DHY-G-VUT7, respectively. Thus, a potent and efficient enzyme for alkyl aldehyde conversion to carboxylic acid.

CONCLUSION: The microorganisms overexpressing the novel aldehyde dehydrogenases could be used to make up microbial cocktails for biodegradation of alkanes. Moreover, since the discovered enzymes are novel it would be interesting to solve their structures by crystallography and explore the downstream applications.

RevDate: 2021-03-02

Yang Y, Wang ST, Lu ZM, et al (2021)

Metagenomics unveils microbial roles involved in metabolic network of flavor development in medium-temperature daqu starter.

Food research international (Ottawa, Ont.), 140:110037.

As a widely used Asian starter culture, the quality of daqu can significantly affect the organoleptic characteristics of the final products, yet the microbial metabolic network involved in flavor development remains unclear. This study aims to investigate that network based on the dynamics of physicochemical properties, microbial community, and volatile compounds in medium-temperature daqu (MT-daqu) during spontaneous fermentation. Analyses using the metagenomic data set facilitated the gene repertoire overview of this ecosystem, indicating that Lactobacillales (mainly Weissella, Lactobacillus, and Pediococcus), Mucorales (mainly Lichtheimia), and Eurotiales (mainly Aspergillus, Rasamsonia and Byssochlamys) were the potential predominant populations successively responsible for the production of lytic enzymes and flavor precursors/compounds in MT-daqu. Flavor-relevant pathways were found to exist in multiple species, but only bacteria showed the potential to participate in butane-2,3-diol (e.g. Weissella, Lactobacillus, and Staphylococcus) and butanoate (Thermoactinomyces) metabolism, and only fungi were potentially involved in biosynthesis of guaiacol (Byssochlamys) and 4-vinylguaiacol (Aspergillus). Furthermore, a combined analysis revealed that the acidic thermal environment present in early phases was mainly due to the catabolic activities of Lactobacillales and Lichtheimia, which could contribute to the effective self-domestication of microbiota. The study helps elucidate the different metabolic roles of microorganisms and disclose the formation mechanism of daqu's partial functions, namely providing various aromatic substances/precursors and enzymes.

RevDate: 2021-03-02

Ongmu Bhutia M, Thapa N, Nakibapher Jones Shangpliang H, et al (2021)

Metataxonomic profiling of bacterial communities and their predictive functional profiles in traditionally preserved meat products of Sikkim state in India.

Food research international (Ottawa, Ont.), 140:110002.

Traditionally preserved meat products are common food items in Sikkim state of India. We studied the high-throughput sequencing of four traditionally preserved meat products viz. beef kargyong, pork kargyong, yak satchu and khyopeh to profile the bacterial communities and also inferred their predictive functional profiles. Overall abundant OTUs in samples showed that Firmicutes was the abundant phylum followed by Proteobacteria and Bacteroidetes. Abundant species detected in each product were Psychrobacter pulmonis in beef kargyong, Lactobacillus sakei in pork kargyong, Bdellovibrio bacteriovorus and Ignatzschinera sp. in yak satchu and Lactobacillus sakei and Enterococcus sp. in khyopeh. Several genera unique to each product, based on analysis of shared OTUs contents, were observed among the samples except in khyopeh. Goods coverage recorded to 1.0 was observed, which reflected the maximum bacterial diversity in the samples. Alpha diversity metrics showed a maximum bacterial diversity in khyopeh and lowest in pork kargyong Community dissimilarities in the products were observed by PCoA plot. A total of 133 KEGG predictive functional pathways was observed in beef kargyong, 131 in pork kargyong, 125 in yak satchu and 101 in khyopeh. Metagenome contribution of the OTUs was computed using PICTRUSt2 and visualized by BURRITO software to predict the metabolic pathways. Several predictive functional profiles were contributed by abundant OTUs represented by Enterococcus, Acinetobacter, Agrobacterium, Bdellovibrio, Chryseobacterium, Lactococcus, Leuconostoc, Psychrobacter, and Staphylococcus.

RevDate: 2021-03-02

Hu Y, Yang Q, Chen D, et al (2021)

Study on microbial communities and higher alcohol formations in the fermentation of Chinese Xiaoqu Baijiu produced by traditional and new mechanical technologies.

Food research international (Ottawa, Ont.), 140:109876.

Microorganisms play an important role in the flavor formation of Chinese Baijiu. Mechanization is the way to develop Baijiu. Therefore, it is necessary to study the effects of mechanization on microbial community and flavor in Baijiu production. The microbial communities exhibited differences between two technologies with the fermentation, and the numbers of yeasts and bacteria in new mechanical technology were significantly higher than those in traditional technology at the peak of fermentation. Both metagenomic and metatranscriptomic analyses showed 5 core microorganisms in the fermentation, namely Saccharomyces cerevisiae, Rhizopus delemar, Pichia kudriavzevii, Lactobacillus helveticus, and Rhizopus oryzae. S. cerevisiae was generally regarded to be the most dominant yeast in Baijiu fermentation, but our metatranscriptomic data showed that P. kudriavzevii was more active than S. cerevisiae. These two analyses indicated that higher initiation abundance of S. cerevisiae and P. kudriavzevii and lower initiation abundance of R. delemar and R. oryzae were observed in traditional technology than in new technology, and that Lactobacillus displayed apparent advantages in traditional technology, whereas Lactobacillus and yeast exhibited obvious advantages in new technology at the end of fermentation. In addition to S. cerevisiae, other microorganisms including non-saccharomyces yeasts, molds, and bacteria were involved in higher alcohol formation. This work provides insight into the microbial dynamics and higher alcohol formation, as well as an efficient strategy for process improvement in Baijiu fermentation.

RevDate: 2021-03-02

Bai X, Shen L, Gao X, et al (2021)

Differential structures and enterotype-like clusters of Bifidobacterium responses to probiotic fermented milk consumption across subjects using a Bifidobacterium-target procedure.

Food research international (Ottawa, Ont.), 140:109839.

The health-promoting attributes of bifidobacteria have piqued interest of researchers worldwide. However, scant published studies are available pertinent to bifidobacteria in microbiota/metagenomics datasets due to its intrinsic low abundance and limitations of detection methods. In this work, we designed a procedure to optimize the detection of the bifidobacterial population in complex biological samples with single-molecule real-time sequencing (SMRT) technology, including one primer pair designated as Bif-6 and a Bifidobacterium-specific database. The optimized procedure detected 14 bifidobacterial species/subspecies in ten human stool samples (2024 sequences per sample) and eight breast milk samples (3473 sequences per sample), respectively. Furthermore, by using the optimized procedure of SMRT, we investigated the effect of a 4-week-intervention of probiotic fermented milk (PFM; 200 g/day) on the gut bifidobacteria population of adults. The results showed that consuming PFM changed the structure and enterotype-like clusters of Bifidobacterium. After the consumption of PFM, the level of gut Bifidobacterium animalis increased significantly, replacing several originally dominating taxa in some subjects, including B. catenulatum, B. breve, and B. bifidum. On the other hand, B. adolescentis was, unaffectedly, the representative species in subjects having an original enterotype-like cluster of B. adolescentis. In conclusion, our work designed a procedure for detecting the bifidobacterial population in complex samples. By applying the currently designed procedure, we found that the PFM intervention changed the bifidobacterial enterotype-like cluster of some subjects, and such change was dependent on the basal bifidobacterial population.

RevDate: 2021-03-01

Tsamis KI, Sakkas H, Giannakis A, et al (2021)

Evaluating Infectious, Neoplastic, Immunological, and Degenerative Diseases of the Central Nervous System with Cerebrospinal Fluid-Based Next-Generation Sequencing.

Molecular diagnosis & therapy [Epub ahead of print].

Cerebrospinal fluid (CSF) is a clear and paucicellular fluid that circulates within the ventricular system and the subarachnoid space of the central nervous system (CNS), and diverse CNS disorders can impact its composition, volume, and flow. As conventional CSF testing suffers from suboptimal sensitivity, this review aimed to evaluate the role of next-generation sequencing (NGS) in the work-up of infectious, neoplastic, neuroimmunological, and neurodegenerative CNS diseases. Metagenomic NGS showed improved sensitivity-compared to traditional methods-to detect bacterial, viral, parasitic, and fungal infections, while the overall performance was maximized in some studies when all diagnostic modalities were used. In patients with primary CNS cancer, NGS findings in the CSF were largely concordant with the molecular signatures derived from tissue-based molecular analysis; of interest, additional mutations were identified in the CSF in some glioma studies, reflecting intratumoral heterogeneity. In patients with metastasis to the CNS, NGS facilitated diagnosis, prognosis, therapeutic management, and monitoring, exhibiting higher sensitivity than neuroimaging, cytology, and plasma-based molecular analysis. Although evidence is still rudimentary, NGS could enhance the diagnosis and pathogenetic understanding of multiple sclerosis in addition to Alzheimer and Parkinson disease. To conclude, NGS has shown potential to aid the research, facilitate the diagnostic approach, and improve the management outcomes of all the aforementioned CNS diseases. However, to establish its role in clinical practice, the clinical validity and utility of each NGS protocol should be determined. Lastly, as most evidence has been derived from small and retrospective studies, results from randomized control trials could be of significant value.

RevDate: 2021-03-01

Shi T, Wu L, Cai J, et al (2021)

An Iris Tumor Secondary to Talaromyces Marneffei Infection in a Patient with AIDS and Syphilis.

Ocular immunology and inflammation [Epub ahead of print].

Purpose: To report a case of iris tumor secondary to Talaromyces marneffei infection in a patient with AIDS and syphilis.Case report: A 25-year-old man presented with gradual vision decrease in the right eye for 2 months. Ocular examination revealed best-corrected visual acuity (BCVA) of 0.12 and a vascularized and solid tumor at inferotemporal iris base in the right eye. There were some papulonecrotic skin lesions. Both serum treponema pallidum particle agglutination and human immunodeficiency virus antibody were positive. Non-target metagenome next-generation sequencing detected Talaromyces marneffei in the skin lesion and aqueous humor. After 8 weeks of oral voriconazole and fluconazole eyedrop treatment, the iris tumor completely subsided, and the BCVA improved to 1.0.Conclusion: Talaromyces marneffei infection may present as an iris tumor. Metagenome next-generation sequencing is helpful in diagnosis. Oral and topical anti-fungus therapy was sufficient to regress the disease without intraocular injection.

RevDate: 2021-03-01

Li Y, Gordon E, Idle A, et al (2021)

Astrovirus Outbreak in an Animal Shelter Associated With Feline Vomiting.

Frontiers in veterinary science, 8:628082.

An outbreak of cat vomiting was observed in an animal shelter. Testing for known enteric feline pathogens did not identify a causative agent. Viral metagenomics on four mini pools of feces from cases and controls housed in the same area revealed the presence of feline astrovirus in all pools. Also found with fewer reads in one pool each were rotavirus I, carnivore bocaparvovirus 3, norovirus (NoV) GVI, and a novel dependovirus. The genome of the highly prevalent astrovirus was sequenced and classified into mamastrovirus species two, also known as feline astrovirus. Real-time RT-PCR on longitudinally acquired fecal samples from 11 sick cases showed 10 (91%) to be shedding astrovirus for as long as 19 days. Affected cats were sick for an average of 9.8 days, with a median of 2.5 days (range = 1-31 days). Unaffected control cats housed in the same areas during the outbreak showed five out of nine (56%) to also be shedding astrovirus. Feline fecal samples collected from the same animal shelter ~1 year before (n = 8) and after (n = 10) showed none to be shedding astrovirus, indicating that this virus was temporarily associated with the vomiting outbreak and is not part of the commensal virome for cats in this shelter. Together with the absence of highly prevalent known pathogens, our results support a role for feline astrovirus infection, as well as significant asymptomatic shedding, in an outbreak of contagious feline vomiting.

RevDate: 2021-03-01

Mishra S, Lin Z, Pang S, et al (2021)

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities.

Frontiers in bioengineering and biotechnology, 9:632059.

Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.

RevDate: 2021-03-01

Sysoev M, Grötzinger SW, Renn D, et al (2021)

Bioprospecting of Novel Extremozymes From Prokaryotes-The Advent of Culture-Independent Methods.

Frontiers in microbiology, 12:630013.

Extremophiles are remarkable organisms that thrive in the harshest environments on Earth, such as hydrothermal vents, hypersaline lakes and pools, alkaline soda lakes, deserts, cold oceans, and volcanic areas. These organisms have developed several strategies to overcome environmental stress and nutrient limitations. Thus, they are among the best model organisms to study adaptive mechanisms that lead to stress tolerance. Genetic and structural information derived from extremophiles and extremozymes can be used for bioengineering other nontolerant enzymes. Furthermore, extremophiles can be a valuable resource for novel biotechnological and biomedical products due to their biosynthetic properties. However, understanding life under extreme conditions is challenging due to the difficulties of in vitro cultivation and observation since > 99% of organisms cannot be cultivated. Consequently, only a minor percentage of the potential extremophiles on Earth have been discovered and characterized. Herein, we present a review of culture-independent methods, sequence-based metagenomics (SBM), and single amplified genomes (SAGs) for studying enzymes from extremophiles, with a focus on prokaryotic (archaea and bacteria) microorganisms. Additionally, we provide a comprehensive list of extremozymes discovered via metagenomics and SAGs.

RevDate: 2021-03-01

Gonzalez E, Brereton NJB, Li C, et al (2021)

Distinct Changes Occur in the Human Breast Milk Microbiome Between Early and Established Lactation in Breastfeeding Guatemalan Mothers.

Frontiers in microbiology, 12:557180.

Human breast milk contains a diverse community of bacteria, but as breast milk microbiome studies have largely focused on mothers from high income countries where few women breastfeed to 6 months, the temporal changes in the breast milk microbiome that occur during later lactation stages have not been explored. For this cross-sectional study, microbiota from breast milk samples of Mam-Mayan mothers living in eight remote rural communities in the Western Highlands of Guatemala were analyzed. All mothers delivered vaginally and breastfed their infants for 6 months. Breast milk from 76 unrelated mothers was used to compare two lactation stages, either "early" (6-46 days post-partum, n = 33) or "late" (109-184 days post-partum, n = 43). Breast milk microbial communities were assessed using 16S ribosomal RNA gene sequencing and lactation stages were compared using DESeq2 differential abundance analysis. A total of 1,505 OTUs were identified, including 287 which could be annotated as putative species. Among several maternal factors, lactation stage explained microbiome variance and inertia in ordination with the most significance (p < 0.001). Differential abundance analysis identified 137 OTUs as significantly higher in either early or late lactation. These included a general shift from Staphylococcus and Streptococcus species in early lactation to Sphingobium and Pseudomonas species in late lactation. Species enriched in early lactation included putative commensal bacteria known to colonize the infant oral and intestinal tracts whereas species enriched in late lactation had a uniform functional trait associated with aromatic compound degradation. Differentially abundant species also included several species which have not previously been reported within breast milk, such as Janthinobacterium agaricidamnosum, Novosphingobium clariflavum, Ottowia beijingensis, and Flavobacterium cucumis. These discoveries describe temporal changes to the breast milk microbiome of healthy Guatemalan mothers from early to late lactation. Collectively, these findings illustrate how studying under-represented human populations might advance our understanding of factors that modulate the human milk microbiome in low and middle income countries (LMIC).

RevDate: 2021-03-01

Gamie Z, Karthikappallil D, Gamie E, et al (2021)

Molecular sequencing technologies in the diagnosis and management of prosthetic joint infections.

Expert review of molecular diagnostics [Epub ahead of print].

INTRODUCTION: Prosthetic Joint Infections can be challenging to eradicate and are associated with high morbidity and mortality. Current microbiology culture methods can be associated with a high false-negative rate of up to 50%. Early and accurate diagnosis is crucial for effective treatment, and negative results have been associated with a greater rate of reoperation.

AREAS COVERED: There has been increasing investigation of the use of next- generation sequencing technology such as the use of metagenomic shotgun sequencing to help identify causative organisms and decrease the uncertainty around culture-negative infections. The clinical importance of the organisms detected and their management, however, requires further study. The polymerase chain reaction has shown promise, but in recent years multiple studies have reported similar or lower sensitivity for bacteria detection in PJI when compared to traditional culture. Furthermore, issues such as high cost and complexity of sample preparation and data analysis are to be addressed before it can move further towards routine clinical practice. .

EXPERT OPINION: Metagenomic NGS has shown results that inspire cautious optimism - both in culture-positive and culture-negative cases of joint infection. Refinement of technique could revolutionize the way PJI is diagnosed, managed, and drastically improve outcomes from this currently devastating complication.

RevDate: 2021-02-28

Stevens V, Thijs S, J Vangronsveld (2021)

Diversity and plant growth-promoting potential of (un)culturable bacteria in the Hedera helix phylloplane.

BMC microbiology, 21(1):66.

BACKGROUND: A diverse community of microbes naturally exists on the phylloplane, the surface of leaves. It is one of the most prevalent microbial habitats on earth and bacteria are the most abundant members, living in communities that are highly dynamic. Today, one of the key challenges for microbiologists is to develop strategies to culture the vast diversity of microorganisms that have been detected in metagenomic surveys.

RESULTS: We isolated bacteria from the phylloplane of Hedera helix (common ivy), a widespread evergreen, using five growth media: Luria-Bertani (LB), LB01, yeast extract-mannitol (YMA), yeast extract-flour (YFlour), and YEx. We also included a comparison with the uncultured phylloplane, which we showed to be dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Inter-sample (beta) diversity shifted from LB and LB01 containing the highest amount of resources to YEx, YMA, and YFlour which are more selective. All growth media equally favoured Actinobacteria and Gammaproteobacteria, whereas Bacteroidetes could only be found on LB01, YEx, and YMA. LB and LB01 favoured Firmicutes and YFlour was most selective for Betaproteobacteria. At the genus level, LB favoured the growth of Bacillus and Stenotrophomonas, while YFlour was most selective for Burkholderia and Curtobacterium. The in vitro plant growth promotion (PGP) profile of 200 isolates obtained in this study indicates that previously uncultured bacteria from the phylloplane may have potential applications in phytoremediation and other plant-based biotechnologies.

CONCLUSIONS: This study gives first insights into the total bacterial community of the H. helix phylloplane, including an evaluation of its culturability using five different growth media. We further provide a collection of 200 bacterial isolates underrepresented in current databases, including the characterization of PGP profiles. Here we highlight the potential of simple strategies to obtain higher microbial diversity from environmental samples and the use of high-throughput sequencing to guide isolate selection from a variety of growth media.

RevDate: 2021-03-01
CmpDate: 2021-03-01

Chen YM, Holmes EC, Chen X, et al (2020)

Diverse and abundant resistome in terrestrial and aquatic vertebrates revealed by transcriptional analysis.

Scientific reports, 10(1):18870.

Despite increasing evidence that antibiotic resistant pathogens are shared among humans and animals, the diversity, abundance and patterns of spread of antibiotic resistance genes (ARGs) in wildlife remains unclear. We identified 194 ARGs associated with phenotypic resistance to 13 types of antibiotic in meta-transcriptomic data generated from a broad range of lower vertebrates residing in both terrestrial and aquatic habitats. These ARGs, confirmed by PCR, included those that shared high sequence similarity to clinical isolates of public health concern. Notably, the lower vertebrate resistome varied by ecological niche of the host sampled. The resistomes in marine fish shared high similarity and were characterized by very high abundance, distinct from that observed in other habitats. An assessment of ARG mobility found that ARGs in marine fish were frequently co-localized with mobile elements, indicating that they were likely spread by horizontal gene transfer. Together, these data reveal the remarkable diversity and transcriptional levels of ARGs in lower vertebrates, and suggest that these wildlife species might play an important role in the global spread of ARGs.

RevDate: 2021-02-02
CmpDate: 2021-02-02

Xiao D, Yang G, Wang Z, et al (2020)

Efficacy of Bacillus methylotrophicus SY200 strain as feed additive against experimental Salmonella typhimurium infection in mice.

Microbial pathogenesis, 141:103978.

To investigate the effects of Bacillus methylotrophicus SY200 on Salmonella typhimurium (STM) infection in mice, a total of 36 three-week-old male mice were selected and randomly divided into 3 equal groups (N = 12). Group A and group B were fed with basal diet while group C was fed the basal diet supplemented with 0.1% (w/w) B. methylotrophicus SY200 during the 21 days experimental period. On the 14th day of the experiment, mice of group A were intragastrically administered with 0.5 ml of normal saline, group B and C were orally administered with 0.5 ml of STM suspension. On the first day and seventh day after STM challenge, the number of total white blood cells (WBCs) and neutrophils, relative weight of visceral organs, the number of Salmonella spp., Escherichia coli, Lactobacillus spp. and Bifidobacterium spp. in ileum and cecum, and diversity of cecal microflora were measured. The results showed that: on the first day and seventh day after STM challenge, the number of WBCs and neutrophils in the blood of the mice was the highest in group B, then followed by group C, and group A. On the first day after STM challenge, the relative weight of spleen in group C was significantly higher than that in group B (p < 0.05), moreover, compared with group B, B. methylotrophicus SY200 significantly reduced the number of Salmonella spp. and E. coli (p < 0.05), and increased the number of Lactobacillus spp. and Bifidobacterium spp. (p < 0.05) in the intestines of mice, and improved the Shannon-Wiener diversity (H), Simpson (E) and richness (S) indices of cecal flora of mice (p < 0.05). The results indicated that B. methylotrophicus SY200 could alleviate the inflammatory reaction after STM infection and resist the adverse effects of STM infection on mice intestinal flora.

RevDate: 2021-02-27

Biswas T, Bhushan S, Prajapati SK, et al (2021)

An eco-friendly strategy for dairy wastewater remediation with high lipid microalgae-bacterial biomass production.

Journal of environmental management, 286:112196 pii:S0301-4797(21)00258-9 [Epub ahead of print].

The present study attempts to integrate phyco-remediation and enhanced lipid productivity using microalgae-bacterial consortium enriched from wastewater fed aquaculture pond. Metagenomic analyses and microscopic images of the consortium revealed the presence of Chlorella variabilis, Parachlorella kessleri, Thermosynechococcus elongatus, Chlamydomonas, Phaeodactylum tricornutum, Oscillatoriales, Synechocystis sp., Microcystis aeruginosa, Nostocales, Naviculales, Stramenopiles, other members of Chlorophyceae, Trebouxiophyceae, and Chroococcales along with potential bacterial bioremediants. During a 30 days trial run (15 days stabilization and 14 days remediation studies) for phyco-remediation drastic reduction in the nutrient and COD content from the tested wastewater samples was seen. There was up to 93% and 87.2% reduction in chemical oxygen demand (COD) and ammonium concentration, respectively. Further, almost 100% removal of nitrates and phosphates from the dairy wastewater upon 48 h of treatment with polyculture under ambient temperature (25 ± 2 °C) with 6309 lux illumination and mild aeration, was observed for all the seven cycles. Interestingly, the nutrient and COD concentrations in the treated water were below the discharge standards as per Central Pollution Control Board (CPCB) norms. In additions, biomass (reported as dry cell weight) was enhanced by 67% upon treatment with ammonia-rich dairy wastewater exhibiting 42% lipid, 55% carbohydrate, and 18.6% protein content enhancement. The polyculture mainly grown as attached biofilm to the surface, offered an easy harvesting and separation of grown biomass from the treated wastewater. Overall, dairy wastewater was found to be a potential nutrient source for microalgae-bacteria cultivation thereby making the treatment process sustainable and eco-friendly.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )