Role Of Microbes Research Articles

Fractions of traditionally brewed rice beverage relieve anxiety and improve spatial memory in mice

Rice beverages are traditionally prepared and consumed popularly by the different ethnic groups of North East India and claimed to have several health benefits. In an attempt to validate the traditional claims, effects of different fractions of the beverage were studied using mouse model. To investigate its effects on behavior, mice were treated with different fractions of rice beverage that included the beverage as a whole, insoluble and soluble fractions. Intragastric treatments of these fractions were given to the mice (n = 6 per group) for 30 days, and behavioral studies were performed on elevated plus and Y maze to evaluate anxiety and spatial memory, respectively. Next-generation sequencing of metagenomic DNA of the beverage indicated the presence of 157 OTUs, and 26 bacterial genera were dominant with an abundance of 0.1%. The insoluble fraction and the whole beverage treatments reduced the anxiety-like symptoms in animals indicating the probable role of microbes. Spatial memory improved in all the treatments compared to the control, of which the rice beverage treatment showed the highest levels (p < 0.05). Gas chromatography and mass spectroscopy-based metabolite profiling of the beverage revealed 10 alcohols, 29 sachharides, 43 acids, and 13 amino acids. Findings of this study suggest a positive effect of rice beverage on anxiety and spatial memory of mice, justifying the claims by ethnic communities on its role on mood regulation.

Microbiome pattern of Lucilia sericata (Meigen) (Diptera: Calliphoridae) and feeding substrate in the presence of the foodborne pathogen Salmonella enterica

The microbial diversity and quantitative dynamics during the insect’s development stages constitute recently developed putative tools in forensic and medical studies. Meanwhile, little is known on the role of insects in spreading foodborne pathogenic bacteria and on the impact of these pathogens on the overall insects and feeding substrate microbiome composition. Here, we provide the first characterization of the bacterial communities harbored in adult and immature stages of Lucilia sericata, one of the first colonizers of decomposed human remains, in the presence of the foodborne pathogen Salmonella enterica using 16S rRNA Illumina sequencing and qPCR. The pathogen transmission from the wild adults to the second generation was observed, with a 101.25× quantitative increase. The microbial patterns from both insect and liver samples were not influenced by the artificial introduction of this pathogenic foodborne bacteria, being dominated by Firmicutes and Proteobacteria. Overall, our results provided a first detailed overview of the insect and decomposed substrate microbiome in the presence of a human pathogen, advancing the knowledge on the role of microbes as postmortem interval estimators and the transmission of pathogenic bacteria.

Microbial Identification, High-Resolution Microscopy and Spectrometry of the Rhizosphere in Its Native Spatial Context.

During the past decades, several stand-alone and combinatorial methods have been developed to investigate the chemistry (i.e., mapping of elemental, isotopic, and molecular composition) and the role of microbes in soil and rhizosphere. However, none of these approaches are currently applicable to characterize soil-root-microbe interactions simultaneously in their spatial arrangement. Here we present a novel approach that allows for simultaneous microbial identification and chemical analysis of the rhizosphere at micro− to nano-meter spatial resolution. Our approach includes (i) a resin embedding and sectioning method suitable for simultaneous correlative characterization of Zea mays rhizosphere, (ii) an analytical work flow that allows up to six instruments/techniques to be used correlatively, and (iii) data and image correlation. Hydrophilic, immunohistochemistry compatible, low viscosity LR white resin was used to embed the rhizosphere sample. We employed waterjet cutting and avoided polishing the surface to prevent smearing of the sample surface at nanoscale. The quality of embedding was analyzed by Helium Ion Microscopy (HIM). Bacteria in the embedded soil were identified by Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) to avoid interferences from high levels of autofluorescence emitted by soil particles and organic matter. Chemical mapping of the rhizosphere was done by Scanning Electron Microscopy (SEM) with Energy-dispersive X-ray analysis (SEM-EDX), Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), nano-focused Secondary Ion mass Spectrometry (nanoSIMS), and confocal Raman spectroscopy (μ-Raman). High-resolution correlative characterization by six different techniques followed by image registration shows that this method can meet the demanding requirements of multiple characterization techniques to identify spatial organization of bacteria and chemically map the rhizosphere. Finally, we presented individual and correlative workflows for imaging and image registration to analyze data. We hope this method will be a platform to combine various 2D analytics for an improved understanding of the rhizosphere processes and their ecological significance.

FUNCTIONAL APPRAISAL OF ORAL MICROBES IN OSCC PROGRESSION: A SYSTEMATIC REVIEW AND META-ANALYSIS

<h3>Background</h3> Oral squamous cell carcinoma (OSCC) is the most common malignancy, representing up to 80% to 90% of all malignant neoplasms of the oral cavity. The role of microbes in association with the host is known to promote cancer progression, which is considered a prominent risk factor for oral OSCC. In view of a recent systematic review on microbial involvement, a proficient conclusion was derived associating microbes in OSCC progression. <h3>Objective</h3> Identification of most relevant microbial species associated in OSCC progression using statistical meta-analysis. <h3>Methods</h3> A preliminary search was primed through different literature databases including PubMed, Embase, and Cochrane for a systematic review by using different MeSH terminologies for microbial association with OSCC progression. A meta-analysis was done to identify statistically significant bacterial species. <h3>Results</h3> Results of this analysis presented the forest plots with statistically evaluated odds ratios and confidence intervals for each considered bacterial concentration. According to the results, no single or clustered microbial entity evaluated could confirm its significant association with OSCC progression. This could be because of a lack of qualitative and quantitative data and needs extensive evaluation using throughput research techniques. <h3>Conclusions</h3> The observations of the bacterial risk factors of OSCC through meta-analysis have been concluded with the identification of statistically insignificant association of microbes with OSCC progression. But, among those possibly consistent species, <i>Prevotella melaninogenica</i> might play a sensitive role in propagating OSCC progression.

Role of Microbes in Plant Growth and Food Preservation

&#x0D; Introduction: Microbes perform better functions for agricultural production by promoting various direct and indirect mechanisms in soil and plants. If agricultural development is to satisfy the needs of an increasing global population, a deeper understanding of soil microbiology is needed. Furthermore, microbial biota such as yeast, bacteria etc., plays a significant role in food preservation by various mechanisms.&#x0D; Review results: Despite their pathogenicity, microbes play a substantial role in dispensing an assortment of fermented drinks and foods in the food industry and home. Probiotics, fermented foods and alcoholic beverages are flattering extra popular due to their health benefits and flavour. Furthermore, they increase the yield and growth of plants by improving mineral availability to the plants and by another mechanism.&#x0D; Review implementation: This present review also discusses the various organisms used in the agricultural processing of beverages and food and the benefits of using the following microbes in the beverage and food industry.&#x0D;

The Landscape of Microbial Composition and Associated Factors in Pancreatic Ductal Adenocarcinoma Using RNA-Seq Data.

Recent research studies on interrogation of the tumor microbiome (including bacteria, viruses, and fungi) have yielded important insights into the role of microbes in carcinogenesis, therapeutic responses, and resistance. Once thought to be a sterile organ, a number of studies have showed the presence of microbes within this organ in PDAC status. A microbiome–pancreas axis for PDAC (pancreatic ductal adenocarcinoma) carcinogenesis is proposed. However, the microbial composition of localized PDAC tissue is still unclear. The associations between microbiome and PDAC reported in previous studies were detected in an indirect way, which mostly used samples from stool, oral saliva, and intestinal samples. This study integrated 582 samples derived from PDAC tissues across four datasets and presented a landscape of tumor microbiome at the genus level in PDAC based on remining of RNA-Seq data. On average, there are hundreds of genera distributed in the PDAC tissue, and dozens of core microbiota were identified by PDAC tissue. The pan-microbiome of PDAC tissue was also estimated, which might surpass 2,500 genera. In addition, sampling sites (stroma vs. epithelium) and tissue source (human tissue vs. PDX) were found to have great effects on the microbial composition of PDAC tissue, but not the traditional risk factors (sex and age). It is the first study to systematically focus on exploring the microbial composition of PDAC tissue and is helpful to have a deep understanding of tumor microbiome. The identified specific taxa might be potential biomarkers for follow-up research studies.

DOM degradation by light and microbes along the Yukon River-coastal ocean continuum

The Arctic is experiencing rapid warming, resulting in fundamental shifts in hydrologic connectivity and carbon cycling. Dissolved organic matter (DOM) is a significant component of the Arctic and global carbon cycle, and significant perturbations to DOM cycling are expected with Arctic warming. The impact of photochemical and microbial degradation, and their interactive effects, on DOM composition and remineralization have been documented in Arctic soils and rivers. However, the role of microbes, sunlight and their interactions on Arctic DOM alteration and remineralization in the coastal ocean has not been considered, particularly during the spring freshet when DOM loads are high, photoexposure can be quite limited and residence time within river networks is low. Here, we collected DOM samples along a salinity gradient in the Yukon River delta, plume and coastal ocean during peak river discharge immediately after spring freshet and explored the role of UV exposure, microbial transformations and interactive effects on DOM quantity and composition. Our results show: (1) photochemical alteration of DOM significantly shifts processing pathways of terrestrial DOM, including increasing relative humification of DOM by microbes by > 10%; (2) microbes produce humic-like material that is not optically distinguishable from terrestrial humics; and (3) size-fractionation of the microbial community indicates a size-dependent role for DOM remineralization and humification of DOM observed through modeled PARAFAC components of fluorescent DOM, either through direct or community effects. Field observations indicate apparent conservative mixing along the salinity gradient; however, changing photochemical and microbial alteration of DOM with increasing salinity indicate changing DOM composition likely due to microbial activity. Finally, our findings show potential for rapid transformation of DOM in the coastal ocean from photochemical and microbial alteration, with microbes responsible for the majority of dissolved organic matter remineralization.

The role of microbes in organic material decomposition and formation of compost bacterial communities

The application of microbial decomposers and bio-stimulant into agriculture wastes influence the abundance of microorganisms and their biological diversity of the compost. The study was conducted to determine the role of microbial in the decomposition of agricultural wastes that produces compost and its effect on the diversity and function of microbes that inhabited the compost product. Agricultural wastes used straw, leaves and grass from the Cibinong Science Center-Botanical Garden. Decomposer microbes used fungi (Trichoderma), and bacteria (Azospirillum brasilense and Agrobacterium sp.). The composting process was conducted anaerobically and the compost beds were reversed every 7 days. The diversity and function of inhabiting microbes resulted from the composting process was determined and identified by conducting microbial isolation and 16S rRNA genes identification. The ability of the microbes as decomposers was also analyzed. The results showed that the genus Bacillus tended to dominate. The microbial consortia have a high enzyme activity to degrade material waste agriculture. Of the three sources of compost used, the grass produced a better compost, forming a diverse and beneficial bacterial community. Therefore, it can be stated that the use of microbial decomposers for composting the agriculture wastes is an appropriate method for forming the beneficial microbial ecosystems.

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease.

Inflammatory bowel disease (IBD) is a chronic relapsing–remitting systemic disease of the gastrointestinal tract. It is well established that the gut microbiome has a profound impact on IBD pathogenesis. Our aim was to systematically review the literature on the IBD gut microbiome and its usefulness to provide microbiome-based biomarkers. A systematic search of the online bibliographic database PubMed from inception to August 2020 with screening in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was conducted. One-hundred and forty-four papers were eligible for inclusion. There was a wide heterogeneity in microbiome analysis methods or experimental design. The IBD intestinal microbiome was generally characterized by reduced species richness and diversity, and lower temporal stability, while changes in the gut microbiome seemed to play a pivotal role in determining the onset of IBD. Multiple studies have identified certain microbial taxa that are enriched or depleted in IBD, including bacteria, fungi, viruses, and archaea. The two main features in this sense are the decrease in beneficial bacteria and the increase in pathogenic bacteria. Significant differences were also present between remission and relapse IBD status. Shifts in gut microbial community composition and abundance have proven to be valuable as diagnostic biomarkers. The gut microbiome plays a major role in IBD, yet studies need to go from casualty to causality. Longitudinal designs including newly diagnosed treatment-naïve patients are needed to provide insights into the role of microbes in the onset of intestinal inflammation. A better understanding of the human gut microbiome could provide innovative targets for diagnosis, prognosis, treatment and even cure of this relevant disease.

Prenatal Stress Leads to Intrauterine Dysfunction: The Role of Microbes and Microglia

Prenatal stress is deleterious to both mother and fetus and is associated with offspring neurodevelopmental deficits. There is emerging evidence that disruption of the maternal gut microbiome and subsequent immunomodulation is a potential mechanism by which prenatal stress affects neurodevelopment. Previously, we demonstrated that prenatal stress induced fetal neuroinflammation and adult offspring social behavioral deficits, but not in the absence of the chemokine CCL2. However, the specific role of CCL2 in the intrauterine environment and its interplay with maternal microbes remains to be elucidated.

Lignin-Degrading Microorganisms from Organic Soils

The most prevalent aromatic polymer in nature is lignin, produced by higher plants and thought to make up 30-35 percent of the non-fossil organic carbon on the planet. Lignin hydrolyzing enzymes such as lignin peroxidase, laccase, manganese peroxidase, and others produce a variety of aromatic monomers, including ferulic and vanillic acids. However, very little research has been done on the role of microbes in lignin degradation. In the present work, we have isolated 25 ligninolytic bacteria and 25 ligninolytic fungi from organic soils of Koppal, Raichur districts of Karnataka. The bacterial isolates were identified as Pseudomonas putida, Bacillus subtilis, based on biochemical tests, and fungi were identified as Aspergillus niger, Trichoderma viridae, Phanerochaete chrysosporium and Pleurotus ostreatus based on morphological characters. The ligninolytic activity of bacterial isolates was high when compared to fungal isolates. All the isolates produced detectable amounts of lignin peroxidase, manganese peroxidase, and laccase under in vitro conditions. In dye decolorization test, fungal isolates KGST-1, KGST-2, and KKSP could decolorize Ramazol Brilliant Blue R and Congo red.

The change of water content and role of microbe in the sludge drying process

In this study, the pure terephthalic acid sludge was treated by a drying process which was an economical and environmentally method. The water change and metabolic pathways for bacterial community function prediction were analyzed. The microbial community changes were studied by high-throughput sequencing to draw the dynamic succession model. Then multiple statistics was used to determine the key factors of the reduction. The results showed that the main stage of water loss in the PTA sludge drying process was the high temperature period where the water lost by evaporation accounted for more than 90% of the total removal. The main metabolic pathways for bacterial community function were amino acid (7.72%–8.71% of Kyoto encyclopedia of genes and genomes relative abundance and 8.26%–9.51% of Cluster of orthologous groups of proteins relative abundance) and carbohydrate metabolism. The model describing the dynamic succession of microbial communities showed that the dominant bacteria changed from Nitrospira, Novosphingobium and Azohydromonas to Pseudomonas, Paeniglutamicibac and Pelotomaculum. The key factors for water loss were Gemmatimonas, Novosphingobium and Azohydromonas with the correlation coefficients of 0.887, 0.772, 0.783, respectively; the key factors for dry matter loss were Pelotomaculum, total organic matter, dissovlved organic carbon and carbon/nitrogen ratio; the key factors for toxic substance loss were Brevundimonas, Novosphingobium and Gemmatimonas. These results provided theoretical support for the application and demonstration for hazardous waste sludge reduction.

Fe and S-isotope compositions of hydrothermal deposits from Kings Triple Junction, Lau Basin, southwest Pacific Ocean

We analyzed iron and sulfur isotopic compositions of polymetallic sulfides from an extinct hydrothermal mound near the Kings Triple Junction of the northern Lau basin belonging to a back-arc basin for understanding the origin and mineral zoning processes in this study. Sulfides from the hydrothermal mound's pedestal slab consisting of chalcopyrite and pyrite show enrichment of heavy S-isotope (δ34SV-CDT = +8.3 to +9.6‰). Sphalerite-dominated chimney on the mound's slope also has variable δ34S values between +5.5 and + 8.3‰ from central orifice to outer wall. These isotopic ratios indicate the substantial contribution of heavy isotope rich sulfate-S in seawater circulating within the mound. Low Δ33S values in these sulfides also indicate that the sulfate reduction is of thermal origin, with minimal or no role for microbes. Circulating seawater induced changes in fluid composition and post-depositional zone refinement of certain minerals can explain the variation in δ34S in different layers within the chimney and pedestal slab. The Fe-isotopic compositions (δ56FeIRMM-014) show a range from −1.1 to −0.3‰ in the pedestal slab while they vary between −1.7 and − 0.6‰ at different parts of the peripheral chimney section. We explain such changes are mostly due to redox processes and mineral zoning development during these sulfide deposit formation. The tree-like FeMn oxide growth structures in the vicinity of the hydrothermal mound having a thin birnessite top layer and amorphous iron oxide bottom part show distinct δ56Fe values of −3.0 and − 0.8‰, respectively.

A review of clothing microbiology: the history of clothing and the role of microbes in textiles.

Humans have worn clothing for thousands of years, and since its invention, clothing has evolved from its simple utilitarian function for survival to become an integral part of society. While much consideration has been given to the broad environmental impacts of the textile and laundering industries, little is known about the impact wearing clothing has had on the human microbiome, particularly that of the skin, despite our long history with clothing. This review discusses the history of clothing and the evolution of textiles, what is and is not known about microbial persistence on and degradation of various fibres, and what opportunities for the industrial and environmental application of clothing microbiology exist for the future.

Microbiome and acne vulgaris

Acne vulgaris is a highly prevalent inflammatory skin disease involving sebaceous follicle. Although the pathogensis of acne remains uncertain, skin microbes are considered to plays an essential role in acne vulgaris. Cutibacterium acnes is the most important microbe in acne pathogenesis and its several processes: colonization, over-proliferation and inflammation have long been thought to contribute to the disease. Moreover, Staphylococcus epidermidis and Malassezia also synergistically collaborate with Cutibacterium acnes. Besides, given the growing number of patients who are treatment resistant, assessments are needed on phenotypic changes in the skin microbiome with retinoids and antibacterial therapy. Further research on the role of microbes in the pathogenesis of acne and the relationship between pathogenic microbes is expected to provide a new theoretical basis for clinical treatment of acne.

Species identity, rather than species mixtures, drives cover crop effects on nutrient partitioning in unfertilized agricultural soil

AimsPrevious cover crop studies mainly focused on the links between plant uptake and soil fertility, and there is a clear knowledge gap regarding the role of microbes in these processes. Our aim was then to better understand the effects of plant mixtures (versus monoculture) and the specific effects of each plant species on nitrogen (N) and phosphorus (P) partitioning between plant, soil, and more particularly microbial pools.MethodsMonocultures and mixtures composed of black oat, field pea and Indian mustard were grown during two months in a greenhouse. The concentrations of carbon (C), N and P were measured in both plant and microbial biomass at final harvest, together with soil available N and P.ResultsOverall, our findings highlight stronger selection effect (i.e., presence of key species) rather than complementarity effects (i.e., species mixture) to affect the measured parameters. The presence of pea increased the biomass production of oat and mustard, as well as the nutrient concentration of oat, whereas pea P concentration decreased in presence of oat and mustard N and P concentrations were negatively impacted respectively by the presence of oat and pea. We also observed a strong competition between plants and microbes for both soil N and P.ConclusionsThe oat-pea and the oat-pea-mustard mixtures represented the best compromise between biomass production, nutrient storage and biomass C:N ratio, thus insuring a good organic matter decomposition and nutrient provision for the following main crop.

Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes

Small open reading frames (smORFs) and their encoded microproteins play central roles in microbes. However, there is a vast unexplored space of smORFs within human-associated microbes. A recent bioinformatic analysis used evolutionary conservation signals to enhance prediction of small protein families. To facilitate the annotation of specific smORFs, we introduce SmORFinder. This tool combines profile hidden Markov models of each smORF family and deep learning models that better generalize to smORF families not seen in the training set, resulting in predictions enriched for Ribo-seq translation signals. Feature importance analysis reveals that the deep learning models learn to identify Shine-Dalgarno sequences, deprioritize the wobble position in each codon, and group codon synonyms found in the codon table. A core-genome analysis of 26 bacterial species identifies several core smORFs of unknown function. We pre-compute smORF annotations for thousands of RefSeq isolate genomes and Human Microbiome Project metagenomes and provide these data through a public web portal.

Biodiversity of pesticides degrading microbial communities and their environmental impact

A number of hazardous pesticides (pure substances or mixtures of chemicals) are being used by the farmers in agricultural fields to control undesired microbes during production, harvesting and storage of food stuff. These potent chemicals are jeopardizing not only the crop fertility and productivity but affecting human health, directly or indirectly. As far as in the interest of people, such hazardous chemicals are gaining access to get inside the food chain indirectly leading to adversely affecting individual's health with passage of time. The microbial resources in consortia or alone are able to degrade them upto considerable extent and converting them less hazardous. The field workers especially the farmers, whose health status is most compromised due chronic exposure of such hazardous chemicals leading to various chronic diseases like diabetes, hypertension etc. which farmers may not aware of until they have been tested for it. There are different groups of microbes including the members of phylum Actinobacteria, Ascomycota, Bacteroidetes, Basidiomycota, Chlorophyta, Cyanobacteria, Firmicutes and Proteobacteria were found to be best sources for degradation of diverse groups of pesticide (Carbamate, Organochlorine, Organophosphate and Pyrethroids). Among different groups of microbes, Arthrobacter, Aspergillus, Bacillus, Burkholderia, Chlamydomonas, Methylobacterium, Nocardioides, Nostoc, Phanerochaete, Pseudomonas, Sphingobacterium, Sphingomonas and Trichoderma were isolated and characterised for the degradation of different pesticides. The role of microbes, in the remediation and degradation of chemical pesticides are elaborated into this compilation with the recent insights.

The evolution of biogeochemistry: revisited

The evolution of biogeochemistry, retraces the important historical steps in part, covered by Gorham (Biogeochemistry 13:199–239, 1991) in the 18–19th centuries—with new emergent linkages and trends in 20–21st centuries. In the post-phlogiston period, key synthetic connections are made between weathering, atmospheric chemistry, carbon cycling, and climate change. Early work in the 19th century, focused on weathering and the importance of organisms in the exchange of carbon dioxide between the rocks and the atmosphere, provided foundations for new analytical approaches. The role microbes in connecting abiotic and biotic processes begins to emerge, based largely on the existing knowledge of stoichiometry in agricultural soils and plants. This in part, leads to the founding of ecology and its linkages with evolution and biogeography. Verandsky boldly emerges in the 20th century, with his concepts of a biosphere and a noosphere, as concerns begin to arise about human impacts on nature. The development of organic geochemistry as a discipline, allowed for new roots to develop in the evolution of biogeochemistry through linkages between short and long-term carbon cycles. In the 20th century, a new interesting stoichiometry emerges in biogeochemistry—as related to the Green Revolution, human population growth, and eutrophication problems. The advent of long-term and large-scale experiments help to constrain the complexity of non-linearity and regional differences in fluxes and rates in biogeochemical work. A new age begins in the 21st century whereby molecular approaches (e.g. omics) combined with large-scale satellite, monitoring, survey, observatory approaches are combined in the development of Earth System models. These new connections with ecological/evolutionary genetics are one of the more dramatic and important aspects of biogeochemistry in modern times.

Identification and Characterization of the Intra-Articular Microbiome in the Osteoarthritic Knee.

Osteoarthritis (OA) is the most common joint disorder in the United States, and the gut microbiome has recently emerged as a potential etiologic factor in OA development. Recent studies have shown that a microbiome is present at joint synovia. Therefore, we aimed to characterize the intra-articular microbiome within osteoarthritic synovia and to illustrate its role in OA disease progression. RNA-sequencing data from OA patient synovial tissue was aligned to a library of microbial reference genomes to identify microbial reads indicative of microbial abundance. Microbial abundance data of OA and normal samples was compared to identify differentially abundant microbes. We computationally explored the correlation of differentially abundant microbes to immunological gene signatures, immune signaling pathways, and immune cell infiltration. We found that microbes correlated to OA are related to dysregulation of two main functional pathways: increased inflammation-induced extracellular matrix remodeling and decreased cell signaling pathways crucial for joint and immune function. We also confirmed that the differentially abundant and biologically relevant microbes we had identified were not contaminants. Collectively, our findings contribute to the understanding of the human microbiome, well-known OA risk factors, and the role microbes play in OA pathogenesis. In conclusion, we present previously undiscovered microbes implicated in the OA disease progression that may be useful for future treatment purposes.