Microbial Community Profiles Research Articles

Deterministic effect of oxygen level variation on shaping antibiotic resistome

An increase in acquisition of antibiotic resistance genes (ARGs) by pathogens under antibiotic selective pressure poses public health threats. Sub-inhibitory antibiotics induce bacteria to generate reactive oxygen species (ROS) dependent on dissolved oxygen (DO) levels, while molecular connection between ROS-mediated ARG emergence through DNA damage and metabolic changes remains elusive. Thus, the study investigates antibiotic resistome dynamics, microbiome shift, and pathogen distribution in hyperoxic (5–7 mg L−1), normoxic (2–4 mg L−1), and hypoxic (0.5–1 mg L−1) conditions using lab-scale bioreactor. Composite inoculums in the reactor were designed to represent comprehensive microbial community and AR profile from selected activated sludge. RT-qPCR and metagenomic analysis showed an increase in ARG count (100.98 ppm) with enrichment of multidrug efflux pumps (acrAB, mexAB) in hyperoxic condition. Conversely, total ARGs decreased (0.11 ppm) under hypoxic condition marked by a major decline in int1 abundance. Prevalence of global priority pathogens increased in hyperoxic (22.5%), compared to hypoxic (0.9%) wherein major decrease were observed in Pseudomonas, Shigella, and Borrelia. The study observed an increase in superoxide dismutase (sodA, sodB), DNA repair genes (nfo, polA, recA, recB), and ROS (10.4 µmol L−1) in adapted biomass with spiked antibiotics. This suggests oxidative damage that facilitates stress-induced mutagenesis providing evidence for observed hyperoxic enrichment of ARGs. Moreover, predominance of catalase (katE, katG) likely limit oxidative damage that deplete ARG breeding in hypoxic condition. The study proposes a link between oxygen levels and AR development that offers insights into mitigation and intervention of AR by controlling oxygen-related stress and strategic selection of bacterial communities.

The Microbial Communities of Anaerobic Respiration and Fermentation Degrading Chitin Exist in the Anaerobic Sludge of Microbial Fuel Cell Anodes

Chitin is one of the most abundant polymers in nature, with chitinous biomass often discarded as food waste and marine debris. To explore an effective way to degrade chitin, in this work, anaerobic sludge was inoculated at the anode of a two-chamber microbial fuel cell (MFC), and chitin was degraded via anaerobic respiration and fermentation. The results showed that the anaerobic sludge could degrade chitin under both the anaerobic respiration and fermentation modes, with similar degradation rates (7.10 ± 0.96 and 6.96 ± 0.23 C-mg/L·d−1). The open-circuit voltage and output current density could roughly reflect the degradation of chitin in the MFC. The maximum current density generated through the anaerobic sludge degradation of chitin via anaerobic respiration was 160 mA/m2, and the maximum power density was 26.29 mW/m2. The microbial sequencing results revealed substantially different microbial community profiles, with electroactive bacteria (EAB) flora and fermentative bacteria (Longilinea) as the main microbial groups that degraded chitin via anaerobic respiration and fermentation, respectively. Therefore, anaerobic sludge may be a good choice for the treatment of refractory biomass due to its abundant electroactive and fermentative flora.

Combined contribution of biochar and introduced AM fungi on lead stability and microbial community in polluted agricultural soil.

Lead (Pb) pollution in agricultural soil has been accelerated by industrial development and human activities, and poses a major threat to agricultural ecosystems. Both biochar and arbuscular mycorrhiza (AM) fungi are considered to play an important role in remediation of Pb contaminated soil. The combined remediation effects of introduced AM fungi and biochar on soil properties, Pb availability, microbial community and functional profiles were systematically investigated in unsterilized Pb-polluted agricultural soil. Results indicated that soil nutrients were significantly improved through the combined application of biochar and introduced AM fungi. The introduced AM fungi combined with biochar prepared at 400°C and 500°C promoted the transformation of Pb to a more stable state with low bioavailability. Moreover, the addition of AM fungi and biochar affected the relative abundances of dominant bacteria and fungi at the phylum and genus levels. Biochar mainly affected soil bacterial community and obviously increased the relative abundance of Actinobacteria and Blastococcus. The interactions between biochar and introduced AM fungi mainly affected fungal community, and increased the abundance of Ascomycota and Botryotrichum. Further, PICRUSt analysis indicated biochar amendment supported stronger bacterial metabolic functional potentials. Therefore, the combined application of biochar and Therefore, the combined application of biochar and introduced AM fungi could improve soil nutrients, reduce Pb introduced AM fungi could improve soil nutrients, reduce Pb availability, availability, and show and show a positive effect on a positive effect on indigenous microbial communities and indigenous microbial communities and metabolic functions in metabolic functions in farmland soil.

Metagenomic 16S rDNA reads of in situ preserved samples revealed microbial communities in the Yongle blue hole.

Our knowledge on biogeochemistry and microbial ecology of marine blue holes is limited due to challenges in collecting multilayered water column and oxycline zones. In this study, we collected samples from 16 water layers in Yongle blue hole (YBH) located in the South China Sea using the in situ microbial filtration and fixation (ISMIFF) apparatus. The microbial communities based on 16S rRNA metagenomic reads for the ISMIFF samples showed high microbial diversity and consistency among samples with similar dissolved oxygen levels. At the same depth of the anoxic layer, the ISMIFF samples were dominated by sulfate-reducing bacteria from Desulfatiglandales (17.96%). The sulfide concentration is the most significant factor that drives the division of microbial communities in YBH, which might support the prevalence of sulfate-reducing microorganisms in the anoxic layers. Our results are different from the microbial community structures of a Niskin sample of this study and the reported samples collected in 2017, in which a high relative abundance of Alteromonadales (26.59%) and Thiomicrospirales (38.13%), and Arcobacteraceae (11.74%) was identified. We therefore demonstrate a new profile of microbial communities in YBH probably due to the effect of sampling and molecular biological methods, which provides new possibilities for further understanding of the material circulation mechanism of blue holes and expanding anoxic marine water zones under global warming.

Soil microbiome analysis reveals effects of periodic waterlogging stress on sugarcane growth.

Sugarcane is one of the major agricultural crops with high economic importance in Thailand. Periodic waterlogging has a long-term negative effect on sugarcane development, soil properties, and microbial diversity, impacting overall sugarcane production. Yet, the microbial structure in periodically waterlogged sugarcane fields across soil compartments and growth stages in Thailand has not been documented. This study investigated soil and rhizosphere microbial communities in a periodic waterlogged field in comparison with a normal field in a sugarcane plantation in Ratchaburi, Thailand, using 16S rRNA and ITS amplicon sequencing. Alpha diversity analysis revealed comparable values in periodic waterlogged and normal fields across all growth stages, while beta diversity analysis highlighted distinct microbial community profiles in both fields throughout the growth stages. In the periodic waterlogged field, the relative abundance of Chloroflexi, Actinobacteria, and Basidiomycota increased, while Acidobacteria and Ascomycota decreased. Beneficial microbes such as Arthrobacter, Azoarcus, Bacillus, Paenibacillus, Pseudomonas, and Streptomyces thrived in the normal field, potentially serving as biomarkers for favorable soil conditions. Conversely, phytopathogens and growth-inhibiting bacteria were prevalent in the periodic waterlogged field, indicating unfavorable conditions. The co-occurrence network in rhizosphere of the normal field had the highest complexity, implying increased sharing of resources among microorganisms and enhanced soil biological fertility. Altogether, this study demonstrated that the periodic waterlogged field had a long-term negative effect on the soil microbial community which is a key determining factor of sugarcane growth.

Biofilm formation on microplastics in wastewater: insights into factors, diversity and inactivation strategies

Microplastic (MP) occurrence in wastewater poses serious threats to aquatic organisms due to their ecological impact. Additionally, these microplastics may provide a unique habitat for microbial biofilms. This study explored the possible factors that facilitate biofilm formation on different MPs in a wastewater environment. Biofilm formation was determined via measurement of optical density (OD) and confirmed using scanning electron microscopy. Furthermore, microbial community profiling was performed via 16S rRNA amplicon sequencing. The highest biofilm formation occurred after 3 weeks of exposure, followed by a decline to its lowest after 5 weeks. Biofilms were predominant on MPs that were exposed to dark conditions, mesophilic temperature (25 °C) and aerobic conditions. Under these conditions, a positive correlation was observed between the OD value and ammonia (NH3) (r = 0.824) and nitrite (NO2) concentrations (r = 0.1). However, a negative correlation (r = −0.673) was found between the OD value and nitrate (NO3) levels in the medium. Furthermore, the highest biofilm formation was observed on polyethylene particles. The most dominant phyla in both the biofilms and wastewater medium were Proteobacteria, Bacteroidetes and Planctomycetes, with Methylotenera being the most abundant genera in the biofilms. In general, the polypropylene particles supported the most diverse bacterial community (H' = 2.51138 and Simpson index = 11.096), while high-density polyethylene supported the least diverse bacterial community (H' = 0.88779 and Simpson index = 1.5324). The study also demonstrated that both UV and chlorine treatments were effective in inactivating these biofilms, within 30 and 10 min, respectively.

Effects of Enterotoxigenic Escherichia coli Challenge on Jejunal Morphology and Microbial Community Profiles in Weaned Crossbred Piglets.

Pathogenic enterotoxigenic Escherichia coli (ETEC) is a major cause of bacterial diarrhea in weaning piglets, which are vulnerable to changes in environment and feed. This study aimed to determine the effects of the ETEC challenge on piglet growth performance, diarrhea rate, jejunal microbial profile, jejunal morphology and goblet cell distribution. A total of 13 piglets from one litter were selected on postnatal day 21 and assigned to treatments with or without ETEC challenge at 1 × 108 CFUs, as ETEC group or control group, respectively. On postnatal day 28, samples were collected, followed by the detection of serum biochemical indexes and inflammatory indicators, HE staining, PAS staining and 16S rDNA gene amplicon sequencing. Results showed that the growth performance decreased, while the diarrhea rate increased for the ETEC group. The jejunum is the main segment of the injured intestine during the ETEC challenge. Compared with the control, the ETEC group displayed fewer goblet cells in the jejunum, where goblet cells are more distributed at the crypt and less distributed at the villus. In addition, ETEC piglets possessed higher abundances of the genus Desulfovibrio, genus Oxalobacter and genus Peptococus and lower abundances of the genus Prevotella 2, genus Flavonifractor and genus Blautra. In terms of alpha diversity, Chao 1 and observed features indexes were both increased for the ETEC group. Our study provides insights into jejunal histopathological impairment and microbial variation in response to ETEC infection for weaned piglets and is a valuable reference for researchers engaged in animal health research to select stress models.

Dynamic Changes in the Microbial Community and Metabolite Profile during the Pile Fermentation Process of Fuzhuan Brick Tea.

The pile fermentation process of Fuzhuan brick tea is unique in that it involves preheating without the use of starter cultures. The detailed metabolite changes and their drivers during this procedure are not known. Characterizing these unknown changes that occur in the metabolites and microbes during pile fermentation of Fuzhuan brick tea is important for industrial modernization of this traditional fermented food. Using microbial DNA amplicon sequencing, mass spectrometry-based untargeted metabolomics, and feature-based molecular networking, we herein reveal that significant changes in the microbial community occur before changes in the metabolite profile. These changes were characterized by a decrease in Klebsiella and Aspergillus, alongside an increase in Bacillus and Eurotium. The decrease in lysophosphatidylcholines, unsaturated fatty acids, and some astringent flavan-3-ols and bitter amino acids, as well as the increase in some less astringent flavan-3-ols and sweet or umami amino acids, contributed importantly to the overall changes observed in the metabolite profile. The majority of these changes was caused by bacterial metabolism and the corresponding heat generated by it.

Livestock grazing is associated with the gut microbiota and antibiotic resistance genes in sympatric plateau pika (Ochotona curzoniae).

With the overuse of antibiotics in health care and animal husbandry, antibiotic resistance becomes a serious threat to public health. Antibiotic residues from veterinary medicine have increased the dissemination of antibiotic resistance genes (ARGs) by horizontal gene transfer globally, leading to the enrichment of ARGs in wildlife. Plateau pika (Ochotona curzoniae) is a small herbivore endemic to the Qinghai-Tibetan Plateau. Previous studies reveal that pika evolves a coprophagy behavior toward cohabitated yak, which makes the pika population a potential reservoir of ARGs. Yet, little is known about the resistome of pika under different grazing intensities. Here, we sampled the cecum content of pika from three different grazing intensity areas in the Qinghai-Tibetan Plateau to evaluate the effect of grazing on its gut microbiota and resistome. By using the 16S full-length amplicon and metagenomic sequencing, our study revealed that livestock grazing significantly altered the gut microbial community of plateau pika as compared to prohibited grazing areas. We found bacterial lineage Prevotellaceae, Lachnospirales, and RF39 increased in grazing areas. Analysis of the resistome revealed that pika from continuous grazing areas enriched a higher abundance of colistin (MCR) and streptogramin (vat) resistance genes. Moreover, we observed significant correlations between the gut microbial community, ARGs, and mobile genetic element profiles, hinting that pika gut microbiota was an important shaping force of the resistome. In future studies, the continuous monitoring of wildlife gut resistome and environmental antibiotic residues is imperative for a better understanding and for tackling the horizontal gene transfer of ARGs across the wildlife-livestock interface.

Intra-tumoral microbial community profiling and associated metabolites alterations of TNBC.

Triple-negative breast cancer (TNBC) presents significant challenges to female health owing to the lack of therapeutic targets and its poor prognosis. In recent years, in the field of molecular pathology, there has been a growing focus on the role of intra-tumoral microbial communities and metabolic alterations in tumor cells. However, the precise mechanism through which microbiota and their metabolites influence TNBC remains unclear and warrants further investigation. In this study, we analyzed the microbial community composition in various subtypes of breast cancer through 16S rRNA MiSeq sequencing of formalin-fixed, paraffin-embedded (FFPE) tissue samples. Notably, Turicibacter, a microbe associated with cancer response, exhibited a significantly higher abundance in TNBC. Similarly, mass spectrometry-based metabolomic analysis revealed substantial differences in specific metabolites, such as nutriacholic, pregnanetriol, and cortol. Furthermore, we observed significant correlations between the intra-tumoral microbiome, clinicopathological characteristics, and human epidermal growth factor receptor-2 expression(HER2). Three microbial taxa (Cytophagaceae, Conexibacteraceae, and Flavobacteriaceae) were associated with tumor-infiltrating lymphocytes(TILs), which are indicative of antitumor immunity. This study creatively utilized FFPE tissue samples to assess intra-tumoral microbial communities and their related metabolic correlations, presenting avenues for the identification of novel diagnostic biomarkers, the development of therapeutic strategies, and the early clinical diagnosis of TNBC.

Microbiome depiction through user-adapted bioinformatic pipelines and parameters.

Introduction. The role of the microbiome in health and disease continues to be increasingly recognized. However, there is significant variability in the bioinformatic protocols for analysing genomic data. This, in part, has impeded the potential incorporation of microbiomics into the clinical setting and has challenged interstudy reproducibility. In microbial compositional analysis, there is a growing recognition for the need to move away from a one-size-fits-all approach to data processing.Gap Statement. Few evidence-based recommendations exist for setting parameters of programs that infer microbiota community profiles despite these parameters significantly impacting the accuracy of taxonomic inference.Aim. To compare three commonly used programs (DADA2, QIIME2, and mothur) and optimize them into four user-adapted pipelines for processing paired-end amplicon reads. We aim to increase the accuracy of compositional inference and help standardize microbiomic protocol.Methods. Two key parameters were isolated across four pipelines: filtering sequence reads based on a whole-number error threshold (maxEE) and truncating read ends based on a quality score threshold (QTrim). Closeness of sample inference was then evaluated using a mock community of known composition.Results. We observed that raw genomic data lost were proportionate to how stringently parameters were set. Exactly how much data were lost varied by pipeline. Accuracy of sample inference correlated with increased sequence read retention. Falsely detected taxa and unaccounted for microbial constituents were unique to pipeline and parameter. Implementation of optimized parameter values led to better approximation of the known mock community.Conclusions. Microbial compositions generated based on the 16S rRNA marker gene should be interpreted with caution. To improve microbial community profiling, bioinformatic protocols must be user-adapted. Analysis should be performed with consideration for the select target amplicon, pipelines and parameters used, and taxa of interest.

Characterization of the bacterial microbiota of cattle ticks in northeastern Thailand through 16S rRNA amplicon sequencing

Ticks are vectors of a variety of pathogens that can infect humans and animals. Ticks also harbor non-pathogenic microbiota. This study characterized the microbiota of the ticks infesting beef cattle in Thailand. Two species of ticks; Rhipicephalus microplus (n = 15) and Haemaphysalis bispinosa (n = 5), were collected in seven provinces in northeastern Thailand. Microbial community profile of ticks was examined based on sequences of the V3-V4 region of 16S rRNA gene. Proteobacteria (Pseudomonadota) was the most abundant phylum, followed by Firmicutes (Bacillota), and Actinobacteriota. Coxiella-like endosymbiont was the most abundant bacterial taxon overall (49% of sequence reads), followed by Anaplasma (8.5%), Corynebacterium (5.5%), Ehrlichia (3.9%), and Castellaniella (3.4%). Co-infections of the pathogenic bacteria Ehrlichia and Anaplasma were detected in 19/20 (95%) female ticks. The tick with the lowest number of bacteria had the lowest abundance of the Coxiella-like endosymbiont, and the pathogenic bacteria Anaplasma and Ehrlichia were absent. This study provides baseline information of the microbiota of cattle ticks in northeastern Thailand, suggesting that ticks carry a few dominant bacterial taxa that are primarily non-pathogenic but can co-occur with pathogenic microorganisms. The information obtained is useful for monitoring disease outbreaks in the future and informing prevention and control strategies against cattle tick-borne diseases.

The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling.

The long-read amplicon provides a species-level solution for the community. With the improvement of nanopore flowcells, the accuracy of Oxford Nanopore Technologies (ONT) R10.4.1 has been substantially enhanced, with an average of approximately 99%. To evaluate its effectiveness on amplicons, three types of microbiomes were analyzed by 16S ribosomal RNA (hereinafter referred to as "16S") amplicon sequencing using Novaseq, Pacbio sequel II, and Nanopore PromethION platforms (R9.4.1 and R10.4.1) in the current study. We showed the error rate, recall, precision, and bias index in the mock sample. The error rate of ONT R10.4.1 was greatly reduced, with a better recall in the case of the synthetic community. Meanwhile, in different types of environmental samples, ONT R10.4.1 analysis resulted in a composition similar to Pacbio data. We found that classification tools and databases influence ONT data. Based on these results, we conclude that the ONT R10.4.1 16S amplicon can also be used for application in environmental samples. IMPORTANCE The long-read amplicon supplies the community with a species-level solution. Due to the high error rate of nanopore sequencing early on, it has not been frequently used in 16S studies. Oxford Nanopore Technologies (ONT) introduced the R10.4.1 flowcell with Q20+ reagent to achieve more than 99% accuracy as sequencing technology advanced. However, there has been no published study on the performance of commercial PromethION sequencers with R10.4.1 flowcells on 16S sequencing or on the impact of accuracy improvement on taxonomy (R9.4.1 to R10.4.1) using 16S ONT data. In this study, three types of microbiomes were investigated by 16S ribosomal RNA (rRNA) amplicon sequencing using Novaseq, Pacbio sequel II, and Nanopore PromethION platforms (R9.4.1 and R10.4.1). In the mock sample, we displayed the error rate, recall, precision, and bias index. We observed that the error rate in ONT R10.4.1 is significantly lower, especially when deletions are involved. First and foremost, R10.4.1 and Pacific Bioscience platforms reveal a similar microbiome in environmental samples. This study shows that the R10.4.1 full-length 16S rRNA sequences allow for species identification of environmental microbiota.

The Protective Effect of Roseburia faecis Against Repeated Water Avoidance Stress-induced Irritable Bowel Syndrome in a Wister Rat Model.

Roseburia faecis, a butyrate-producing, gram-positive anaerobic bacterium, was evaluated for its usefulness against repeated water avoidance stress (WAS)-induced irritable bowel syndrome (IBS) in a rat model, and the underlying mechanism was explored. We divided the subjects into three groups: one without stress exposure, another subjected to daily 1-hour WAS for 10 days, and a third exposed to the same WAS regimen while also receiving two different R. faecis strains (BBH024 or R22-12-24) via oral gavage for the same 10-day duration. Fecal pellet output (FPO), a toluidine blue assay for mast cell infiltration, and fecal microbiota analyses were conducted using 16S rRNA metagenomic sequencing. Predictive functional profiling of microbial communities in metabolism was also conducted. FPO and colonic mucosal mast cell counts were significantly higher in the WAS group than in the control group (male, P = 0.004; female, P = 0.027). The administration of both BBH024 (male, P = 0.015; female, P = 0.022) and R22-12-24 (male, P = 0.003; female, P = 0.040) significantly reduced FPO. Submucosal mast cell infiltration in the colon showed a similar pattern in males. In case of fecal microbiota, the WAS with R. faecis group showed increased abundance of the Roseburia genus compared to WAS alone. Moreover, the expression of a gene encoding a D-methionine transport system substrate-binding protein was significantly elevated in the WAS with R. faecis group compared to that in the WAS (male, P = 0.028; female, P = 0.025) group. These results indicate that R. faecis is a useful probiotic for treating IBS and colonic microinflammation.

Stable microbial community in compacted bentonite after 5 years of exposure to natural granitic groundwater.

The Materials Corrosion Test (MaCoTe) at the Underground Research Laboratory in Grimsel, Switzerland, assesses the microbiology and corrosion behavior of engineered barrier components of a deep geological repository (DGR) for long-term disposal of high-level nuclear waste. Diversity and temporal changes of bentonite-associated microbial community profiles were assessed under DGR-like conditions for compacted Wyoming MX-80 bentonite (1.25 g/cm3 and 1.50 g/cm3 targeted dry densities) exposed to natural groundwater. Using culture-dependent and molecular techniques, samples taken from the outside layer of 5-year borehole modules revealed up to 66% and 23% of 16S rRNA gene sequences affiliated with Desulfosporosinus and Desulfovibrio, respectively. Putatively involved in sulfate reduction, these taxa were almost undetectable within the bentonite core. Instead, microbial profiles of the inner bentonite core were similar to uncompacted bentonite used to pack modules years earlier, and were consistent with a previously published 1-year time point, revealing no detectable microbial growth. Abundances of culturable aerobic and anaerobic heterotrophic bacteria in the uncompacted bentonite were relatively low, with less than 1,000 and 100 colony-forming units (CFUs) per gram dry weight, respectively. Nearly 5 years after emplacement, culturable heterotrophic bacterial CFUs and sulfate-reducing bacteria did not change significantly inside the bentonite core. Phospholipid fatty acid data indicated similar lipid abundance, and corresponding cell abundance estimates, for inner 5-year MaCoTe bentonite samples compared to those previously obtained for 1-year incubations. Collectively, our results provide complementary evidence for microbial stability inside highly compacted bentonite exposed to conditions that mimic engineered barrier components of a deep geological repository. IMPORTANCE The long-term safety of a deep geological repository for used nuclear fuel is dependent on the performance of the engineered and natural barriers. Microbial activity can produce chemical species that can influence the corrosion of the disposal containers for used nuclear fuel. Although previous studies have evaluated the microbiology of compacted bentonite clay within subsurface environments, these have been limited to relatively short incubations (i.e., 1 year). The current study provides a unique 5-year perspective that reinforces previous findings of growth inhibition for bentonite clay exposed to in situ subsurface conditions.

Modeling host–microbiome interactions to improve mechanistic understanding of aphid vectored plant pathogens

Insect transmission of plant pathogens involves multi-layered interactions between vectors, viruses, host plants and environmental factors. Adding to the complexity of vector–virus relationships are diverse microbial communities, which are hypothesized to influence pathogen transmission. Although vector–virus interaction research has flourished, the role played by microbes in vector competence and disease epidemiology remains unclear in many pathosystems. We therefore aimed to develop a novel ecological modeling approach to identify environmental drivers of complex vector–virus–microbiome interactions, particularly differences in the abundance of microbial symbionts within vector microbiomes and relationships between symbionts and the probability of virus acquisition. Our approach combines established molecular tools for profiling microbial communities with underutilized Bayesian hierarchical modeling and data integration techniques. We used a globally relevant aphid–virus pathosystem to develop custom vector–microbiome models that incorporate environmental covariates (e.g., temperature, landcover) and applied them to individual vector symbionts to identify the extent to which environmental factors drive changes in microbial communities that then influence virus acquisition by the host aphid. Specifically, we focus on the aphid obligate symbiont (Buchnera) and a wide-spread facultative symbiont (Serratia) as proof of concept to develop models for two major vector species that include a single environmental covariate (i.e., temperature). Overall, we demonstrate how community-level modeling and microbiome profiling can identify candidate microbes and environmental variables associated with vector competence. Our modeling framework can accommodate a range of microbial symbionts with different abundances, overcome spatial misalignment of data streams, and is robust to varying levels of disease incidence. Results show Buchnera relative abundance is strongly negatively associated with virus acquisition by the vector S.avenae, but not R. padi. Although Serratia was not associated with R. padi vector competence, relative abundance was influenced by differences in spring temperatures. This work lays the foundation for developing a broader modeling framework for predicting disease dynamics in agroecosystems and deploying microbiome-targeted pest management tactics.

Morel (Morchella spp.) intake alters gut microbial community and short-chain fatty acid profiles in mice.

Morels (Morchella spp.) are highly nutritious and consumed as both edible mushrooms and traditional Chinese medicine. This study aimed to investigate the effects of dietary supplementation with morel mushrooms on the gut bacterial microbiota and short-chain fatty acids (SCFAs) profiles in healthy mice. Healthy mice were randomly assigned to five groups: a control group (0% morel) and four intervention groups supplemented with different levels of morel mushrooms (5% for M5, 10% for M10, 15% for M15, and 20% for M20) over a period of 4 weeks. Fecal samples were collected at the end of the experiment to characterize the microbiota and assess the SCFAs levels. The morel intervention significantly altered the bacterial community composition, increasing Bacteroides, Lachnospiraceae NK4A136 group and Parabacteroides, while decreasing Staphylococcus and the Firmicutes to Bacteroidetes ratio (F/B ratio). Moreover, increased morel intake was associated with weight loss. All SCFAs content was upregulated in the morel-intervention groups. Potential SCFAs-producing taxa identified by regression analysis were distributed in the families Muribaculaceae, Lachnospiraceae, and in the genera Jeotgalicoccus, Gemella, Odoribacter, Tyzzerella 3 and Ruminococcaceae UCG-014. The functional categories involved with SCFAs-production or weight loss may contain enzymes such as beta-glucosidase (K05349), beta-galactosidase (K01190), and hexosaminidase (K12373) after morel intervention. The exploration of the impact of morel mushrooms on gut microbiota and metabolites contributes to the development of prebiotics for improving health and reducing obesity.

Metagenomics reveals the effects of glyphosate on soil microbial communities and functional profiles of C and P cycling in the competitive vegetation control process of Chinese fir plantation

Although considerable efforts have been devoted to investigate the behavior of glyphosate on microbiome in various environment, knowledge about the soil microbial community and functional profile in weeds control process of the Chinese fir plantation are limited. In this study, shotgun metagenomic sequencing was used to determine the abundance and diversity of microbial communities and functional genes after foliar application of glyphosate for 1, 2, 3 and 4 months in a Chinese fir plantation. The results showed that glyphosate increased the copy numbers (qPCR) of 16S rRNA gene for 16.9%, improved the bacterial diversity (Shannon index) and complexity of bacterial co-occurrence network, and changed the abundances of some bacterial and fungal taxa, but had no effects on ITS gene copy numbers, fungal Shannon index, and bacterial and fungal communities (PCoA). Glyphosate application significantly decreased the amount of microbial function potentials involved in organic P mineralization for 10.7%, chitin degradation for 13.1%, and CAZy gene families with an exception of PL for 11.5% at the first month, while did not affect the profile of microbial genes response to P and C cycling in longer term. In addition, glyphosate reduced the contents of soil TOC, DOC and NH4+-H for 17.6%, 52.3% and 44.6% respectively, and decreased the starch, soluble sugar, Zn and Fe of Chinese fir leaves for 20.6%, 19.8%, 32.8% and 48.4% respectively. Mantle test, Spearman's correlation, and PLS-PM model revealed the connections among soil properties, tree nutrients, bacterial and fungal communities, and microbial function potentials were influenced by glyphosate. While our findings need to be validated in other filed and mechanistic studies, they may indicate that the foliar application of glyphosate has a potential effect on Chinese fir seedlings, and this effect may contribute to the changes of the bacterial community and soil properties including AN, DON and NH4+-H.

Integrating the Soil Microbiota and Metabolome Reveals the Mechanism through Which Controlled Release Fertilizer Affects Sugarcane Growth.

Root-soil underground interactions mediated by soil microorganisms and metabolites are crucial for fertilizer utilization efficiency and crop growth regulation. This study employed a combined approach of soil microbial community profiling and non-targeted metabolomics to investigate the patterns of root-associated microbial aggregation and the mechanisms associated with metabolites under varying controlled-release fertilizer (CRF) application rates. The experimental treatments included five field application rates of CRF (D1: 675 kg/ha; D15: 1012.5 kg/ha; D2: 1350 kg/ha; D25: 1687.5 kg/ha; and D3: 2025 kg/ha) along with traditional fertilizer as a control (CK: 1687.5 kg/ha). The results indicated that the growth of sugarcane in the field was significantly influenced by the CRF application rate (p < 0.05). Compared with CK, the optimal field application of CRF was observed at D25, resulting in a 16.3% to 53.6% increase in sugarcane yield. Under the condition of reducing fertilizer application by 20%, D2 showed a 13.3% increase in stem yield and a 6.7% increase in sugar production. The bacterial ACE index exhibited significant differences between D25 and D1, while the Chao1 index showed significance among the D25, D1, and CK treatments. The dominant bacterial phyla in sugarcane rhizosphere aggregation included Proteobacteria, Actinobacteriota, and Acidobacteriota. Fungal phyla comprised Rozellomycota, Basidiomycota, and Ascomycota. The annotated metabolic pathways encompassed biosynthesis of secondary metabolites, carbohydrate metabolism, and lipid metabolism. Differential analysis and random forest selection identified distinctive biomarkers including Leotiomycetes, Cercospora, Anaeromyxobacter, isoleucyl-proline, and methylmalonic acid. Redundancy analysis unveiled soil pH, soil organic carbon, and available nitrogen as the primary drivers of microbial communities, while the metabolic profiles were notably influenced by the available potassium and phosphorus. The correlation heatmaps illustrated potential microbial-metabolite regulatory mechanisms under CRF application conditions. These findings underscore the significant potential of CRF in sugarcane field production, laying a theoretical foundation for sustainable development in the sugarcane industry.

Metaproteomics revealing microbial diversity and activity in the spontaneous fermentation of maize dough

Maize was spontaneously fermented and metaproteomic analysis was performed on the maize dough to investigate the profile of microbial communities. pH decreased (5.36, 4.44, and 4.42 after 24, 72, and 12 h), while lactic acid increased (0.03, 0.2, and 0.31 after 24, 72, and 120 h).The number of lactic acid bacteria (179 × 106 CFU/g) and mesophilic bacteria (213 × 106 CFU/g) was high. Based on metaproteomic analysis, Actinobacteria, Proteobacteria, and Firmicutes phyla dominated the fermentation medium, and the Actinobacteria was associated with the matrix of maize during starch degradation. Fermentation parameters (pH, lactic acid and titratable sugar) were considered to be regulated during the first 24 h of the fermentation process for ensure the microbiological safety of maize dough. Assuming that metaproteomics as culture-free methods can be an excellent tool for find mechanisms for faster optimization of a new product, is indeed a good tool for investigating fermentative microbiota.