Related Microbes Research Articles

Responses of N2O production pathways and related functional microbes to temperature across greenhouse vegetable field soils

Greenhouse vegetable field is one of the main sources of agricultural nitrous oxide (N2O) emissions via multiple pathways regulated by different microbes. However, the relative contributions of nitrifier nitrification, nitrifier denitrification, nitrification-coupled denitrification and heterotrophic denitrification to N2O production with temperature change in different greenhouse vegetable soils are poorly understood. In this study, combined approaches of the 15N–18O labeling technique and transcriptome analyses were applied to investigate the pathways of N2O production (nitrifier nitrification, nitrifier denitrification, nitrification-coupled denitrification and heterotrophic denitrification) under 15, 25 and 35 °C in six greenhouse vegetable field soils in mainland China. The results show that heterotrophic denitrification was an important source of N2O in acidic greenhouse vegetable soils, whereas nitrifier nitrification was the dominant source of N2O in alkaline greenhouse vegetable soils. In addition, the contribution of nitrifier denitrification and nitrification-coupled denitrification to N2O production in alkaline greenhouse vegetable soils were higher than in acidic greenhouse vegetable soils. The contribution of nitrification-coupled denitrification increased with temperature at 15–35 °C, whereas nitrifier denitrification increased with temperature at 15–25 °C. Overall, high temperature decreased the contribution of nitrifier nitrification to N2O production. These results have important implications for understanding the temperature-dependent N2O production pathways and for mitigating agricultural N2O emissions under different soil and temperature conditions.

Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae

The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters (“Ca. Methylopumilus”) and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteria), from sediment microbes with medium-sized genomes (2–3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or is encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome streamlining as such a collection of evolutionarily related microbes from different habitats is rare in the microbial world.

“Breathing” Hemagglutinin Reveals Cryptic Epitopes for Universal Influenza Vaccine Design

A universal vaccine against influenza remains a critical target, and efforts have recently focused on the stem of the hemagglutinin glycoprotein. In this issue of Cell and a related Cell Host & Microbe article, three studies identify broad protective epitopes in the hemagglutinin head domain that are exposed by trimer “breathing.”

Biostimulation of in situ microbial degradation processes in organically-enriched sediments mitigates the impact of aquaculture

Fish farm deposition, resulting in organic matter accumulation on bottom sediments, has been identified as among the main phenomena causing negative environmental impacts in aquaculture. An in situ bioremediation treatment was carried out in order to reduce the organic matter accumulation in the fish farm sediments by promoting the natural microbial biodegradation processes. To assess the effect of the treatment, the concentration of organic matter in the sediment and its microbial degradation, as well as the response of the benthic prokaryotic community, were investigated. The results showed a significant effect of the treatment in stimulating microbial degradation rates, and the consequent decrease in the concentration of biochemical components beneath the cages during the treatment. During the bioremediation process, the prokaryotic community in the fish farm sediment responded to the overall improvement of the sediment conditions by showing the decrease of certain anaerobic taxa (e.g. Clostridiales, Acidaminobacteraceae and Caldilinaceae). This suggested that the bioactivator was effective in promoting a shift from an anaerobic to an aerobic metabolism in the prokaryotic community. However, the larger importance of Lachnospiraceae (members of the gut and faecal microbiota of the farmed fishes) in treated compared to non-treated sediments suggested that the bioactivator was not efficient in reducing the accumulation of faecal bacteria from the farmed fishes. Our results indicate that bioremediation is a promising tool to mitigate the aquaculture impact in fish farm sediments, and that further research needs to be oriented to identifying more successful interventions able to specifically target also fish-faeces related microbes.

Fermenting Sculptures: Edges and Encounters of the Vessel and the Body

The significance of microbes in relation to a queer perspective on being is central to my thought process around this work. They/Them/Their was titled in reference to my gender pronouns and also to the multitude of microbes we coexist with. When framing the human in relation to prokaryotes (bacteria), we learn that they outnumber us in our own bodies as well as in the population on Earth, not just in numbers of individuals, but in total biomass as well. Microbes reproduce in myriad ways and cannot be defined by gender. If microbes are without gender and they make up at least half of our human selves, then are we are all pluralities? Are we are all they, them, and their?

Characterizing the microbial diversity and major metabolites of Sichuan bran vinegar augmented by Monascus purpureus

This research aimed to evaluate the impacts of Monascus purpureus on the microbial community and major metabolites of Cupei and vinegar of Sichuan bran vinegar (SBV). Cupei is the mixture of fermented materials and vinegar is the liquid leached from Cupei. The characteristics of microbial community were revealed by Illumina-MiSeq. The result suggested that inoculation of M. purpureus decreased the microbial diversities and inhibited several pathogens related microbes including Erwinia, Proteus and Ignatzschineria of Cupei. The dominant genera of SBV were Lactobacillus, Acetobacter, Trichoderma and Candida. With addition of M. purpureus, the total relative abundance of Lactobacillus and Acetobacter was increased from 75.14% to 99.79%. Furthermore, the major metabolites in corresponding vinegar were investigated by HPLC and HS-SPME-GC–MS. The result indicated that the addition of M. purpureus significantly promoted the accumulation of organic acids, aromatic esters and alcohols, whose contents were increased by 1.95, 2.30 and 3.55 times, respectively. Meanwhile acetic acid, lactic acid, phenethyl acetate and β-phenethyl alcohol were the dominant components in organic acids, esters and alcohols, respectively. In addition, the relationship between dominant microbes and major metabolites explored by redundancy analysis displayed that Lactobacillus, Acetobacter, Candida and Monascus were closely related with seven volatiles and five organic acids. This study provided an insight on regulation of microbial community and metabolic function of traditional fermented foods by bioaugmentation.

NTSHMDA: Prediction of Human Microbe-Disease Association Based on Random Walk by Integrating Network Topological Similarity.

Accumulating clinic evidences have demonstrated that the microbes residing in human bodies play a significantly important role in the formation, development, and progression of various complex human diseases. Identifying latent related microbes for disease could provide insight into human disease mechanisms and promote disease prevention, diagnosis, and treatment. In this paper, we first construct a heterogeneous network by connecting the disease similarity network and the microbe similarity network through known microbe-disease association network, and then develop a novel computational model to predict human microbe-disease associations based on random walk by integrating network topological similarity (NTSHMDA). Specifically, each microbe-disease association pair is regarded as a distinct relationship level and, thus, assigned different weights based on network topological similarity. The experimental results show that NTSHMDA outperforms some state-of-the-art methods with average AUCs of 0.9070, 0.8896 ± 0.0038 in the frameworks of Leave-one-out cross validation and 5-fold cross validation, respectively. In case studies, 9, 18, 38 and 9, 18, 45 out of top-10, 20, 50 candidate microbes are verified by recently published literatures for asthma and inflammatory bowel disease, respectively. In conclusion, NTSHMDA has potential ability to identify novel disease-microbe associations and can also provide valuable information for drug discovery and biological researches.

Predominance of methanogens over methanotrophs in rewetted fens characterized by high methane emissions

Abstract. The rewetting of drained peatlands alters peat geochemistry and often leads to sustained elevated methane emission. Although this methane is produced entirely by microbial activity, the distribution and abundance of methane-cycling microbes in rewetted peatlands, especially in fens, is rarely described. In this study, we compare the community composition and abundance of methane-cycling microbes in relation to peat porewater geochemistry in two rewetted fens in northeastern Germany, a coastal brackish fen and a freshwater riparian fen, with known high methane fluxes. We utilized 16S rRNA high-throughput sequencing and quantitative polymerase chain reaction (qPCR) on 16S rRNA, mcrA, and pmoA genes to determine microbial community composition and the abundance of total bacteria, methanogens, and methanotrophs. Electrical conductivity (EC) was more than 3 times higher in the coastal fen than in the riparian fen, averaging 5.3 and 1.5 mS cm−1, respectively. Porewater concentrations of terminal electron acceptors (TEAs) varied within and among the fens. This was also reflected in similarly high intra- and inter-site variations of microbial community composition. Despite these differences in environmental conditions and electron acceptor availability, we found a low abundance of methanotrophs and a high abundance of methanogens, represented in particular by Methanosaetaceae, in both fens. This suggests that rapid (re)establishment of methanogens and slow (re)establishment of methanotrophs contributes to prolonged increased methane emissions following rewetting.

RETRACTED ARTICLE: Evaluating polymicrobial immune responses in patients suffering from tick-borne diseases

There is insufficient evidence to support screening of various tick-borne diseases (TBD) related microbes alongside Borrelia in patients suffering from TBD. To evaluate the involvement of multiple microbial immune responses in patients experiencing TBD we utilized enzyme-linked immunosorbent assay. Four hundred and thirty-two human serum samples organized into seven categories followed Centers for Disease Control and Prevention two-tier Lyme disease (LD) diagnosis guidelines and Infectious Disease Society of America guidelines for post-treatment Lyme disease syndrome. All patient categories were tested for their immunoglobulin M (IgM) and G (IgG) responses against 20 microbes associated with TBD. Our findings recognize that microbial infections in patients suffering from TBDs do not follow the one microbe, one disease Germ Theory as 65% of the TBD patients produce immune responses to various microbes. We have established a causal association between TBD patients and TBD associated co-infections and essential opportunistic microbes following Bradford Hill’s criteria. This study indicated an 85% probability that a randomly selected TBD patient will respond to Borrelia and other related TBD microbes rather than to Borrelia alone. A paradigm shift is required in current healthcare policies to diagnose TBD so that patients can get tested and treated even for opportunistic infections.

Metagenomic characterisation of ruminal bacterial diversity in buffaloes from birth to adulthood using 16S rRNA gene amplicon sequencing

Microbial colonisation in the forestomach of a ruminant is one of the most crucial factors in determining many of its physiological developments and digestive capabilities. The present study attempts to identify establishment pattern of microbes in relation to food, age and rumen development in the buffalo calves at every fortnight interval from birth to 6months of age, followed by every month till animals became 1year of age. Diversity study based on 16S rRNA gene sequencing identified rapidly changing bacterial population during initial 60days of life, which got assemblage as rumen became physiologically mature with increasing age of animals. A lactate fermenting aerobic to facultative anaerobic genera found during initial 30days of life were expeditiously replaced by strict anaerobic cellulolytic bacterial population with increasing age. The study confirms that initial colonisation mainly depends on the oral cavity and skin of the mother, followed by the surrounding environment and feed offered, which is reversed in order once animal gets older. Some of the well-described genera based on culture-dependent studies like Ruminococcus spp. were found to be in lesser proportion suggesting an additional role of other microbes or niche in cellulose degradation. We report the presence of Porphyromonas spp. and Mannheimia glucosidal for the first time in bovine infants.

State feedback impulsive therapy to SIS model of animal infectious diseases

Controlling animal infectious diseases and its related infra microbes is of great significance to public health, since a lot of infectious diseases originate from animal epidemics and they often threaten human health. A state feedback impulsive model is constructed to depict the transmission and treatment of animal epidemics. Basing on the impulsive model, the existence of order-1 periodic solution and its stability are proved with a novel method. The theoretical results indicate that the impulsive treatment triggered by the number of infectious is an efficient approach to control animal infectious disease from breakout. Numerical simulation is presented to support the theoretical conclusion in the end.

Human Microbe-Disease Association Prediction Based on Adaptive Boosting.

There are countless microbes in the human body, and they play various roles in the physiological process. There is growing evidence that microbes are closely associated with human diseases. Researching disease-related microbes helps us understand the mechanisms of diseases and provides new strategies for diseases diagnosis and treatment. Many computational models have been proposed to predict disease-related microbes, in this paper, we developed a model of Adaptive Boosting for Human Microbe-Disease Association prediction (ABHMDA) to reveal the associations between diseases and microbes by calculating the relation probability of disease-microbe pair using a strong classifier. Our model could be applied to new diseases without any known related microbes. In order to assess the prediction power of the model, global and local leave-one-out cross validation (LOOCV) were implemented. As shown in the results, the global and local LOOCV values reached 0.8869 and 0.7910, respectively. What’s more, 10, 10, and 8 out of the top 10 microbes predicted to be most likely to be associated with Asthma, Colorectal carcinoma and Type 1 diabetes were all verified by relevant literatures or database HMDAD, respectively. The above results verify the superior predictive performance of ABHMDA.

A systematic literature review of the effect of anthocyanins on gut microbiota populations.

Evidence has shown that anthocyanins, a subclass of polyphenol, are metabolised in the gut, modulate bacterial species and exert bioactive effects through this interaction. A systematic literature review was undertaken to determine the level of current evidence for the association between anthocyanin intake and changes in gut microbiota populations. The studies included were also assessed for the different techniques used in microbiota determination. Following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, scientific databases, including Scopus, PubMed, ScienceDirect, Web of Science and MEDLINE, were searched up to June 2017. Details on population/sample, study design, intervention/control, dosage and method of microbiota determination were extracted. Six studies (three in vitro, two animal and one human trials) were included in the review, which showed that anthocyanins induced a significant proliferative effect on Bifidobacterium spp., known for their wide use in probiotics and for the treatment of irritable bowel syndrome. There was also an observed inhibition of Clostridium histolyticum, which was shown to be pathogenic in humans. The depth of analysis is an important consideration for the choice of microbiota determination technique with respect to a comprehensive, high-resolution microbiota analysis or analysis of the main microbiota taxa. Very limited research has been carried out in the area of anthocyanins and gut microbiota; beneficial effects have generally been observed, and further clinical trials in humans are needed to confirm changes to gut microbes in relation to dietary anthocyanin intake and potential health benefits.

Research progress on the relationship between oral microbes and digestive system diseases

The human microbiome project promoted further understanding on human oral microbes. Besides oral diseases such as dental caries, periodontal disease, and oral cancer, oral microbes are closely associated with systematic diseases. They have a close connection with digestive system diseases and even contribute to the origination and progression of colorectal cancer. By reviewing recent studies involving oral microbe-related digestive systemic diseases, we aim to propose the considerable role of oral microbes in relation to digestive systemic diseases and the way of oral microbes to multiple organs of digestive system.

Two-year microbial adaptation during hydrogen-mediated biogas upgrading process in a serial reactor configuration

Microbial dynamics in an upgrading biogas reactor system undergoing a more than two years-period at stable operating conditions were explored. The carbon dioxide generated during biomass degradation in the first reactor of the system was converted to methane into the secondary reactor by addition of external hydrogen. Considering the overall efficiency, the long-term operation period resulted in an improved biogas upgrading performance (99% methane content). However, a remarkable accumulation of acetate was revealed, indicating the enhancement of homoacetogenic activity. For this reason, a shift in the anaerobic digestion microbiome was expected and evaluated by 16S rRNA amplicon analysis. Results demonstrated that the most abundant archaeal species identified in the first time point, Candidatus Methanoculleus thermohydrogenotrophicum, was replaced by Methanothermobacter thermautotrophicus, becoming dominant after the community adaptation. The most interesting taxonomic units were clustered by relative abundance and six main long-term adaptation trends were found, characterizing functionally related microbes (e.g. homoacetogens).

Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles.

ABSTRACTDuring the first weeks of life, microbial colonization of the gut impacts human immune system maturation and other developmental processes. In premature infants, aberrant colonization has been implicated in the onset of necrotizing enterocolitis (NEC), a life-threatening intestinal disease. To study the premature infant gut colonization process, genome-resolved metagenomics was conducted on 343 fecal samples collected during the first 3 months of life from 35 premature infants housed in a neonatal intensive care unit, 14 of whom developed NEC, and metaproteomic measurements were made on 87 samples. Microbial community composition and proteomic profiles remained relatively stable on the time scale of a week, but the proteome was more variable. Although genetically similar organisms colonized many infants, most infants were colonized by distinct strains with metabolic profiles that could be distinguished using metaproteomics. Microbiome composition correlated with infant, antibiotics administration, and NEC diagnosis. Communities were found to cluster into seven primary types, and community type switched within infants, sometimes multiple times. Interestingly, some communities sampled from the same infant at subsequent time points clustered with those of other infants. In some cases, switches preceded onset of NEC; however, no species or community type could account for NEC across the majority of infants. In addition to a correlation of protein abundances with organism replication rates, we found that organism proteomes correlated with overall community composition. Thus, this genome-resolved proteomics study demonstrated that the contributions of individual organisms to microbiome development depend on microbial community context.

Cathodic microbial community adaptation to the removal of chlorinated herbicide in soil microbial fuel cells

The microbial fuel cell (MFC) that uses a solid electrode as the inexhaustible electron acceptor is an innovative remediation technology that simultaneously generates bioelectricity. Chlorinated pollutants are better metabolized by reductive dechlorination in proximity to the cathode. Here, the removal efficiency of the herbicide metolachlor (ML) increased by 262 and 176% in soil MFCs that were spiked with 10 (C10) and 20mg/kg (C20) of ML, respectively, relative to the non-electrode controls. The bioelectricity output of the C10 and C20 increased by over two- and eightfold, respectively, compared to that of the non-ML control, with maximum current densities of 49.6 ± 2.5 (C10) and 78.9 ± 0.6mA/m2 (C20). Based on correlations between ML concentrations and species abundances in the MFCs, it was inferred that Azohydromonas sp., Sphingomonas sp., and Pontibacter sp. play a major role in ML removal around the cathode, with peak removal efficiencies of 56±1% (C10) and 58±1% (C20). Moreover, Clostridium sp., Geobacter sp., Bacillus sp., Romboutsia sp., and Terrisporobacter sp. may be electricigens or closely related microbes due to the significant positive correlation between the bioelectricity generation levels and their abundances around the anode. This study suggests that a directional adaptation of the microbial community has taken place to increase both the removal of chlorinated herbicides around the cathode and the generation of bioelectricity around the anode in bioelectrochemical remediation systems.

Prolonged Saturation Exposure Alters Human Gut Microbiota: A Case Report

PURPOSEProlonged saturation exposure induces digestive disorders, affecting health related life quality of divers. The diversity of the gut microbiota has been associated with various health parameters. Therefore, we hypothesized that prolonged saturation diving would result intestinal microbiota dysbiosis in human. In this case report, the feces of elite divers were collected after a saturation diving mission to examine the gut microbiome.METHODTwo elite male divers were recruited for this study. This study was approved by the Research Ethics Committee of Naval Medical Research Institute. Exclusion criteria included having antibiotic treatment within previous month, drinking alcoholic within one week, or suffering from any gastrointestinal or immunological disease. During the entire experiment, divers were provided the same diet and living condition. Divers were compressed to depth of 300 m with helium‐oxygen, and held for 24 hours to saturation. During the saturation stay, they made an excursion diving to 330 m undersea, then surfaced after a 15‐day decompression. Their feces were collected within 24 hours before compression (0–1, 0–2), immediately (1–1, 1–2) and a one‐month recovery after decompression (2–1, 2–2). The fecal microbial DNA was extracted and sequenced on an Illumina MiSeq platform. Principal coordinates analysis was applied to detect the differences of gut microbiota compositions of all samples. The similarity of all gut microbiota compositions were analyzed, and presented in the Heatmap.RESULTSPre‐mission (one week before mission) physical examination was applied. Diver 1: age 26, 56 kg, BMI 20.5; Diver 2: age 30, 74 kg, BMI 23.9. The gut microbiota composition and diversity baseline of two divers were no different. Shown in Venn diagram of diver 1, 49 genera were shared by samples of all three periods, while 6 in 0‐1, 13 in 1‐1 and 18 in 2‐1 were unique. And in diver 2, 49 genera were found in samples of all periods, while 7 in 0‐2, 9 in 1‐2 and 12 in 2‐2 were not overlapped. The relative abundances of gut flora in each sample were presented in phylum and genus levels. The major alteration of gut microbiota occurred in phylum of Firmicutes. The relative abundances of Terrisporobacter genus, in which some species were related to infections, turned from 0.047±0.032% before compression, to 4.293±3.381% after decompression, then drop to 0.077±0.052. On the contrary, the genus of Ruminococcaceae, which have several beneficial bacteria, took 0.496±0.087% of microflora before compression, decreased to 0.015±0.009%, and increased to 0.747±0.005% after recovery. Significant changes of some nutrients and energy metabolism related microbes were found in both saturation exposure and recovery. Despite the variation of the microbiota relative abundances, 0‐2 and 1‐2, as well as 2‐1 and 2‐2, showed notable similarity. Meanwhile, after living together for nearly two months, the mircrobiota compositions tended to be similar.CONCLUSIONIn our study, saturation exposure or recovery remarkably influenced divers' gut flora. As the change pattern of some pathogens, divers may be vulnerable to infectious diseases or digestive disorders during saturation exposure. Compositions of nutrients and energy metabolism related microbes were changed notably, but presented large interpersonal variations. Analysis of related physiological indices and further studies are needed in order to illustrate the effects of saturation exposure on divers' microbiota and health.Support or Funding InformationFound: PLA Youth Training Project for Medical Science (16QNP022), Major Logistics Projects of PLA ( AHJ11J004, AWS16J033), National Natural Science Foundation of China (31471135, 31701040), Shanghai Sailing Program (17YF1418000) and Chenguang Program (16CG57).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

FusionDB: assessing microbial diversity and environmental preferences via functional similarity networks.

Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across taxa. While microbial similarities are often reported in terms of taxonomic relationships, no existing databases directly link microbial functions to the environment. We previously developed a method for comparing microbial functional similarities on the basis of proteins translated from their sequenced genomes. Here, we describe fusionDB, a novel database that uses our functional data to represent 1374 taxonomically distinct bacteria annotated with available metadata: habitat/niche, preferred temperature, and oxygen use. Each microbe is encoded as a set of functions represented by its proteome and individual microbes are connected via common functions. Users can search fusionDB via combinations of organism names and metadata. Moreover, the web interface allows mapping new microbial genomes to the functional spectrum of reference bacteria, rendering interactive similarity networks that highlight shared functionality. fusionDB provides a fast means of comparing microbes, identifying potential horizontal gene transfer events, and highlighting key environment-specific functionality.

FusionDB: assessing microbial diversity and environmental preferences via functional similarity networks.

Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across taxa. While microbial similarities are often reported in terms of taxonomic relationships, no existing databases directly link microbial functions to the environment. We previously developed a method for comparing microbial functional similarities on the basis of proteins translated from their sequenced genomes. Here, we describe fusionDB, a novel database that uses our functional data to represent 1374 taxonomically distinct bacteria annotated with available metadata: habitat/niche, preferred temperature, and oxygen use. Each microbe is encoded as a set of functions represented by its proteome and individual microbes are connected via common functions. Users can search fusionDB via combinations of organism names and metadata. Moreover, the web interface allows mapping new microbial genomes to the functional spectrum of reference bacteria, rendering interactive similarity networks that highlight shared functionality. fusionDB provides a fast means of comparing microbes, identifying potential horizontal gene transfer events, and highlighting key environment-specific functionality.