Metagenomic Analysis Research Articles

Circular Utilization of Coffee Grounds as a Bio-Nutrient through Microbial Transformation for Leafy Vegetables

This study explores the production of bio-nutrients from bioactive compound-rich spent coffee grounds (SCG) and biochar (BC) through composting after inoculation with a biological agent and its impact on the growth performance of garden cress and spinach. The SCG was composted with six doses of BC (0, 5, 10, 15, 20, and 25%). The compost with 10% BC exhibited the best maturity, humification, and phytotoxicity index values of dissolved organic carbon (DOC), humification index (E4/E6), and germination index (GI). A metagenome analysis showed that compost starter enhanced the bacterial community’s relative abundance, richness, and diversity in SCG and BC treatments. This improvement included increased Patescibacteria, which can break down noxious phenolic compounds found in SCG and BC. The BC enriched the compost with phosphorus and potassium while preserving the nitrogen. In plant growth experiments, the total chlorophyll content in compost-treated garden cress and spinach was 2.47 and 4.88 mg g−1, respectively, which was significantly greater (p ≤ 0.05) than in unfertilized plants and similar to the plants treated with traditional fertilizer. Overall, the results show that the compost of SCG + BC was well-suited for promoting the growth of garden cress and spinach, providing adequate nutrients as a fertilizer for these leafy vegetables.

A Multi-Strain Oral Probiotic Improves the Balance of the Vaginal Microbiota in Women with Asymptomatic Bacterial Vaginosis: Preliminary Evidence

Background/Objectives: the vaginal microbiota is known to confer protection in the genital ecosystem, due to the predominance of different Lactobacillus species, playing a crucial role in women’s health; alterations in the composition of the microbial communities in the vagina can be associated with the development of bacterial vaginosis (BV). Current therapy for BV involves oral or intravaginal administration of metronidazole or clindamycin, albeit the high recurrence rates suggest a need for alternative therapeutic tools, such as probiotics. Herein, the diversity and composition of vaginal microbiota in women with asymptomatic BV was investigated before and after the oral administration of a multi-strain probiotic formulation. Methods: a prospective observational pilot study with pre–post design was carried out from 1 June 2022, to 31 December 2022, on reproductive-age women with asymptomatic BV, as diagnosed via Nugent score, and matched healthy controls. The probiotic was administered to all study participants as acid-resistant oral capsules (twice daily), and a vaginal swab was collected at baseline and after 2 months of treatment, for the metagenomic analysis of 16s rDNA. Results: the diversity and richness of the vaginal microbiota in women with BV were significantly reduced after 2 months of supplementation with the oral probiotic, as evidenced by measures of α-diversity. Interestingly, some bacterial genera typically associated with dysbiosis, such as Megasphaera spp., were significantly decreased; whereas, at the same time, Lactobacillus spp. Doubled. Conclusions: our preliminary results suggest that the multi-strain oral probiotic is a beneficial treatment specifically targeting the dysbiotic vaginal microenvironment.

Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.

Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which in turn are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the Lachnospiraceae , then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as Veillonella and Haemophilus , unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the Lachnospira eligens pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses.

Uncovering the toxic effects and adaptive mechanisms of aminated polystyrene nanoplastics on microbes in sludge anaerobic digestion system: Insight from extracellular to intracellular

The impacts of polystyrene nanoplastics (PS NPs) with amino functional groups on sludge anaerobic digestion process and the underlying microbial feedbacks remains unclear. Herein, PS NPs coated with and without amino functional groups were employed to explore their impacts on the sludge digestion performance. Experimental results showed that aminated PS NPs (PS-NH2) deteriorated the methane yield and hydrolysis rate. The Derjaguin-Landau-Verwey-Overbeek theory analysis suggested that the PS-NH2 decreased the interaction energy barrier, making it easier to contact with sludge and disrupting the structure of extracellular polymeric substances. Metagenomic analysis showed that the abundance of functional microbes (e.g., Longilinea, Leptolinea, and Methanosarcina) decreased, accompanied with lower network complexity and fewer keystone taxa. Molecular docking revealed that PS-NH2 occupy the antioxidant enzyme active binding sites through hydrogen bonding and hydrophobic interactions, impairing degradation of reactive oxygen species. The severe intracellular oxidative stress up-regulated genes associated with quorum sensing (e.g., luxI and luxR) and protein biosynthesis (e.g., algA, trpG and trpE), and further inducing compact tryptophan-like proteins as a defense against NPs. These findings provide new understanding of the toxic effects from PS-NH2 in biological systems and offer valuable insights into the regulation strategies aimed at alleviating NPs inhibition.

Metagenomic Analysis of Bacterial Communities in Bee Bread in Türkiye

This study aims to investigate the bacterial community structure in bee bread samples collected from 10 provinces of Türkiye using next-generation sequencing (NGS) and metagenomic analysis. Bacterial genomic DNA was extracted and sequenced using Illumina MiSeq. Bioinformatic analysis involved quality assessment, OTU classification, principal coordinate analysis (PCoA), and diversity index calculations. Heatmap and PCoA were utilized to explore the impact of locality and ecological zones on microbial diversity. Metagenomic analysis of 12 bee bread samples revealed 276,583 high-quality sequencing reads. The dominant bacterial phyla identified were Proteobacteria, Actinobacteria, Cyanobacteria, and Firmicutes. At the genus level, Streptomyces, Streptococcus, Bacillus, and Synechococcus were the most abundant, with Streptomyces and Bacillus playing key roles in the fermentation process of bee bread. The Shannon diversity index (ranging from 2.92 to 4.26) and Simpson's index (0.83 to 0.95) indicated high species diversity and relative abundance in bee bread. The study underscores the need for locality-specific approaches in beekeeping management and highlights the potential significance of beneficial bacterial taxa, particularly those involved in fermentation, in contributing to the nutritional and health properties of bee bread. These findings provide a foundation for further research on the microbial dynamics that support bee colony health.

Metagenomic Analysis: Alterations of Soil Microbial Community and Function due to the Disturbance of Collecting Cordyceps sinensis

Soil microorganisms are critical to the occurrence of Cordyceps sinensis (Chinese Cordyceps), a medicinal fungi used in Traditional Chinese Medicine. The over-collection of Chinese Cordyceps has caused vegetation degradation and impacted the sustainable occurrence of Cordyceps. The effects of Chinese Cordyceps collection on soil microorganisms have not been reported. Metagenomic analysis was performed on the soil of collecting and non-collecting areas of production and non-production areas, respectively. C. sinensis collection showed no alteration in alpha-diversity but significantly affected beta-diversity and the community composition of soil microorganisms. In Cordyceps production, Thaumarchaeota and Crenarchaeota were identified as the dominant archaeal phyla. DNA repair, flagellar assembly, propionate metabolism, and sulfur metabolism were affected in archaea, reducing the tolerance of archaea in extreme habitats. Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Nitrospirae were identified as the dominant bacterial phyla. The collection of Chinese Cordyceps enhanced the bacterial biosynthesis of secondary metabolites and suppressed ribosome and carbon metabolism pathways in bacteria. A more complex microbial community relationship network in the Chinese Cordyceps production area was found. The changes in the microbial community structure were closely related to C, N, P and enzyme activities. This study clarified soil microbial community composition and function in the Cordyceps production area and established that collection clearly affects the microbial community function by altering microbial community structure. Therefore, it would be important to balance the relationship between cordyceps production and microbiology.

Metagenomic analysis reveals metabolic mechanism of enhancing lignocellulosic anaerobic digestion mediated by CO2/O2-nanobubble water

Nanobubble water (NW) has been reported to enhance anaerobic digestion (AD), but its influence on the metabolic pathways of microorganisms remains unclear. In this study, the specific methane yields of rice straw in the CO2NW and O2NW treatments increased by 6.9% and 18.3%, respectively. The electron transport system (ETS) and coenzyme F420 activities were enhanced by the addition of NW. Metagenomic analysis showed that the abundances of most enzymes in the acidification were significantly increased by both CO2NW and O2NW. Regarding methanogenesis, CO2NW promoted the expression of genes encoding enzymes of hydrogenotrophic methanogenesis, while O2NW stimulated both the acetoclastic and hydrogenotrophic methanogenesis. With the addition of O2NW, the expressions of modules related to the tricarboxylic acid (TCA) cycle and oxidative phosphorylation were enhanced, resulting in increased ATP production. This study provided fundamental evidence of the metabolic pathways of microorganisms mediated by NW at each stage of AD.

Environmental Driving of Adaptation Mechanism on Rumen Microorganisms of Sheep Based on Metagenomics and Metabolomics Data Analysis.

Natural or artificial selection causes animals to adapt to their environment. The adaptive changes generated by the rumen population and metabolism form the basis of ruminant evolution. In particular, the adaptive drive for environmental adaptation reflects the high-quality traits of sheep that have migrated from other places or have been distant from their origins for a long time. The Hu sheep is the most representative sheep breed in the humid and low-altitude environments (Tai Lake region) in East Asia and has been widely introduced into the arid and high-altitude environments (Tibetan Plateau and Hotan region), resulting in environmental adaptive changes in the Hu sheep. In this study, a joint analysis of the rumen microbial metagenome and metabolome was conducted on Hu sheep from different regions (area of origin and area of introduction) with the objective of investigating the quality traits of Hu sheep and identifying microorganisms that influence the adaptive drive of ruminants. The results demonstrated that the growth performance of Hu sheep was altered due to changes in rumen tissue and metabolism following their introduction to the arid area at relatively high altitude. Metagenomic and metabolomic analyses (five ramsper area) revealed that 3580 different microorganisms and 732 different metabolites were identified in the rumen fluid of arid sheep. Among these, the representative upregulated metabolites were 4,6-isocanedione, methanesulfonic acid and N2-succinyl-L-arginine, while the dominant microorganism was Prevotella ruminicola. The downregulated metabolites were identified as campesterol, teprenone and dihydroclavaminic acid, while the disadvantaged microorganisms were Dialister_succinatiphilus, Prevotella_sp._AGR2160, Prevotella_multisaccharivorax and Selenomonas_bovis. The results of the Pearson analysis indicated that the rumen microbiota and metabolite content of sheep were significantly altered and highly correlated following their relocation from a humid lowland to an arid upland. In particular, the observed changes in rumen microorganisms led to an acceleration of body metabolism, rendering sheep highly adaptable to environmental stress. Prevotella_ruminicola was identified as playing an important role in this process. These findings provide insights into the environmental adaptation mechanisms of sheep.

Dysbiotic signatures and diagnostic potential of gut microbial markers for inflammatory bowel disease in Korean population

Fecal samples were collected from 640 individuals in Korea, including 523 patients with IBD (223 with Crohn’s disease [CD] and 300 with ulcerative colitis [UC]) and 117 healthy controls. The samples were subjected to cross-sectional gut metagenomic analysis using 16 S rRNA sequencing and bioinformatics analysis. Patients with IBD, particularly those with CD, exhibited significantly lower alpha diversities than the healthy subjects. Differential abundance analysis revealed dysbiotic signatures, characterized by an expansion of the genus Escherichia-Shigella in patients with CD. Functional annotations showed that functional pathways related to bacterial pathogenesis and production of hydrogen sulfide (H2S) were strongly upregulated in patients with CD. A dysbiosis score, calculated based on functional characteristics, highly correlated with disease severity. Markers distinguishing between healthy subjects and patients with IBD showed accurate classification based on a small number of microbial taxa, which may be used to diagnose ambiguous cases. These findings confirm the taxonomic and functional dysbiosis of the gut microbiota in patients with IBD, especially those with CD. Taxa indicative of dysbiosis may have significant implications for future clinical research on the management and diagnosis of IBD.

Groundwater resistant gene accumulation in mining-agriculture complex zones: Insights from metagenomic analysis of subterranean mineral and terrestrial agricultural interactions

During the Mining-Agriculture Complex Areas, the mining and agriculture activities could lead to an excessive presence of sulfate content in the regional groundwater. Sulfate exhibits the potential to influence the positive accumulation of RGs, although its mechanisms remain inadequately explored. To address this gap, this study analyzed the RGs buildup mechanisms in the groundwater of the mining-agriculture complex area. Results showed a widespread presence of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs), especially in coal-seams crevice groundwater. And iron and sulfur are primary environmental factors conducive to RGs accumulation through a synergistic interaction. Microbial annotation of gene sets sourced from coal-seams crevice groundwater samples unveiled part of sulfur-metabolizing microorganisms that were hosts of both ARGs and MRGs. Mechanistic insights revealed that iron may stimulates reactive oxygen species (ROS) generation, facilitating RGs accumulation, while adjusting sulfur metabolism and the synthesis of iron-sulfur clusters, thereby augmenting microbial growth which as predominant hosts of RGs, thereby intensifying the buildup of RGs.

Removal of sulfamethoxazole in an algal-bacterial membrane aerated biofilm reactor: Microbial responses and antibiotic resistance genes

Antibiotics are frequently detected in wastewater, but often are poorly removed in conventional wastewater treatment processes. Combining microalgal and nitrifying bacterial processes may provide synergistic removal of antibiotics and ammonium. In this research, we studied the removal of the antibiotic sulfamethoxazole (SMX) in two different reactors: a conventional nitrifying bacterial membrane aerated biofilm reactor (bMABR) and algal-bacterial membrane aerated biofilm reactor (abMABR) systems. We investigated the synergistic removal of antibiotics and ammonium, antioxidant activity, microbial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and their potential hosts. Our findings show that the abMABR maintained a high sulfamethoxazole (SMX) removal efficiency, with a minimum of 44.6 % and a maximum of 75.8 %, despite SMX inhibition, it maintained a consistent 25.0 % ammonium removal efficiency compared to the bMABR. Through a production of extracellular polymeric substances (EPS) with increased proteins/polysaccharides (PN/PS), the abMABR possibly allowed the microalgae-bacteria consortium to protect the bacteria from SMX inactivation. The activity of antioxidant enzymes caused by SMX was reduced by 62.1–98.5 % in the abMABR compared to the bMABR. Metagenomic analysis revealed that the relative abundance of Methylophilus, Pseudoxanthomonas, and Acidovorax in the abMABR exhibited a significant positive correlation with SMX exposure and reduced nitrate concentrations and SMX removal. Sulfonamide ARGs (sul1 and sul2) appeared to be primarily responsible for defense against SMX stress, and Hyphomicrobium and Nitrosomonas were the key carriers of ARGs. This study demonstrated that the abMABR system has great potential for removing SMX and reducing the environmental risks of ARGs.

Metagenomics Analysis of the Gut Microbiome Structure and Function in Black Soldier Fly (Hermetia illucens) Larvae Reared With Different Types of Diet1

Metagenomics Analysis of the Gut Microbiome Structure and Function in Black Soldier Fly (Hermetia illucens) Larvae Reared With Different Types of Diet1

Fulvic Acid Enhances Nitrogen Fixation and Retention in Paddy Soils through Microbial-Coupled Carbon and Nitrogen Cycling.

Fulvic acid, the most soluble and active humic substance, is widely used as an agent to remediate contaminated soils and improve soil fertility. However, the influence of fulvic acid (FA), as a microbial carbon source, on carbon and nitrogen cycles in paddy soils remains elusive. Therefore, to investigate it, an incubation experiment was conducted. Gas analyses indicated that the carbon dioxide and methane emissions were enhanced in FA treatment, which increased up to 94.08-fold and 5.06-fold, respectively. 15N-labeling experiments revealed that nitrogen fixation capability was promoted (1.2-fold) to reduce the carbon and nitrogen imbalance due to fulvic acid amendment. Metagenomic analysis further revealed that gene abundances of degradation of lignin-like compounds, gallate degradation, methanogenesis, nitrogen fixation, and urea hydrolysis increased, while the bacterial ammonia oxidation and anaerobic ammonium oxidation decreased, caused by FA application. Metabolic reconstruction of metagenome-assembled genomes revealed that Azospirillaceae, Methanosarcinaceae, and Bathyarchaeota, with higher abundance in FA treatment, were the key microorganisms to maintain the carbon and nitrogen balance. The metabolic pathways of fulvic acid degradation and coupled nitrogen fixation and retention were constructed. Collectively, our results provided novel insights into the theoretical basis of the use of humic substances for reducing nitrogen fertilization and climate change.

Genome-Centric Metagenomics Insights into the Plastisphere-Driven Natural Degradation Characteristics and Mechanism of Biodegradable Plastics in Aquatic Environments.

Biodegradable plastics (BPs) are pervasively available as alternatives to traditional plastics, but their natural degradation characteristics and microbial-driven degradation mechanisms are poorly understood, especially in aquatic environments, the primary sink of plastic debris. Herein, the three-month dynamic degradation process of BPs (the copolymer of poly(butylene adipate-co-terephthalate) and polylactic acid (PLA) (PBAT/PLA) and single PLA) in a natural aquatic environment was investigated, with nonbiodegradable plastics polyvinyl chloride, polypropylene, and polystyrene as controls. PBAT/PLA showed the weight loss of 47.4% at 50 days and severe fragmentation within two months, but no significant decay for other plastics. The significant increase in the specific surface area and roughness and the weakening of hydrophobicity within the first month promoted microbial attachment to the PBAT/PLA surface. Then, a complete microbial succession occurred, including biofilm formation, maturation, and dispersion. Metagenomic analysis indicated that plastispheres selectively enriched degraders. Based on the functional genes involved in BPs degradation, a total of 16 high-quality metagenome-assembled genomes of degraders (mainly Burkholderiaceae) were recovered from the PBAT/PLA plastisphere. These microbes showed the greatest degrading potential at the biofilm maturation stage and executed the functions by PLA_depolymerase, polyesterase, hydrolase, and esterase. These findings will enhance understanding of BPs' environmental behavior and microbial roles on plastic degradation.

Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change

The gut microbiome is implicated in the pathogenesis of colorectal cancer (CRC), but the full scope of this dialogue is unknown. Here we aimed to define the scale and membership of the body of CRC- and health-associated gut bacteria in global populations. We performed a microbiome-CRC correlation analysis of published ultra-deep shotgun metagenomic sequencing data from global microbiome surveys, utilizing a de novo (reference-agnostic) gene-level clustering approach to identify protein-coding co-abundant gene (CAGs) clusters. We link an unprecedented ~ 23–40% of gut bacteria to CRC or health, split nearly evenly as CRC- or health-associated. These microbes encode 2319 CAGs encompassing 427,261 bacterial genes significantly enriched or depleted in CRC. We identified many microbes that had not previously been linked to CRC, thus expanding the scope of “known unknowns” of CRC-associated microbes. We performed an agnostic CAG-based screen of bacterial isolates and validated predicted effects of previously unimplicated bacteria in preclinical models, in which we observed differential induction of precancerous adenomas and field effects. Single-cell RNA sequencing disclosed microbiome-induced senescence-associated gene expression signatures in discrete colonic populations including fibroblasts. In organoid co-cultures, primary colon fibroblasts from mice with microbiomes promoted significantly greater growth than fibroblasts from microbiome-depleted mice. These results offer proof-of-principle for gene-level metagenomic analysis enabling discovery of microbiome links to health and demonstrate that the microbiome can drive precancer states, thereby potentially revealing novel cancer prevention opportunities.

Evidence for high-risk pollutants and emerging microbial contaminants at two major bathing ghats of the river Ganga using high-resolution mass spectrometry and metagenomics

An efficient wastewater treatment plant is imperative to limit the entry of emerging pollutants (EPs) and emerging microbial contaminants (EMCs) in the river ecosystem. The detection of emerging EPs in aquatic environments is challenging due to complex sample preparation methods, and the need for sophisticated accurate analytical tools. In Varanasi (India), the river Ganga holds immense significance as a holy river but is consistently polluted with municipal (MWW) and hospital wastewater (HWW). We developed an efficient method for untargeted detection of EPs in the water samples using High-resolution mass spectrometry (HRMS), and identified 577 and 670 chemicals (or chemical components) in the water samples from two major bathing ghats, Assi Ghat (AG) and Dashashwamedh Ghat (DG), respectively. The presence of EPs of different categories viz chemicals from research labs, diagnostic labs, lifestyle and industrial chemicals, toxins, flavor and food additives indicated the unsafe disposal of MWW and HWW or inefficient wastewater treatment plants (WWTPs). Besides, shotgun metagenomic analysis depicted the presence of bacteria associated with MWW viz Cloacibacterium normanse, Sphaerotilus natans (sewage fungi), E. coli, and Prevotella. Also, the presence of human pathogens Arcobacter, Polynucleobacter, Pseudomonas, Klebsiella, Aeromonas, Acinetobacter, Vibrio, and Campylobacter suggests the discharge of HWW. EPs are linked to the development, and transmission of antimicrobial resistance (AMR). Occurrence of antibiotic resistance genes (ARGs), plasmid-borne β-lactamases, aminoglycoside transferases, and ARGs associated with integrons, transposons and plasmids viz mcr-3 gene that confer resistance to colistin, the last resort of antibiotics confirmed the presence of emerging microbial contaminants. Subsequent genome reconstruction studies showed the presence of uncultivable ARB and transmission of ARGs through horizontal gene transfer. This study can be used to monitor the health of aquatic bodies as well as the efficiency of WWTPs and raise an urgent need for efficient WWTPs to safeguard the river, Ganga.

Effects of Prebiotic Dietary Fibers on the Stimulation of the Mucin Secretion in Host Cells by In Vitro Gut Microbiome Consortia.

The gastrointestinal microbiota are important for human health. Dietary intake may modulate the composition and metabolic function of the gut microbiome. We examined how the breakdown of prebiotic dietary fibers by the gut microbiome affects mucin secretion by intestinal epithelial cells. Metagenomic analyses of in vitro gut microbiome consortia revealed taxonomic profiles and genetic diversity of carbohydrate-active enzymes that digest polysaccharides. Two independent consortia exhibited different abilities to produce acetic acid, propionic acid, and butyric acid via the fermentation of polysaccharides derived from dietary fibers of grains and mushrooms. Although acetic acid generally had the highest concentration, the ratios of butyric acid and propionic acid to acetic acid varied depending on the polysaccharide source. These short-chain fatty acids affected morphological differentiation and mucin secretion in HT-29 human intestinal epithelial cells. These results suggest that prebiotic dietary fibers can be digested and metabolized by the gut microbiome to short-chain fatty acids, which can affect gut epithelial cells both directly and indirectly via the modulation of the gut microbiota and their enzymes.

Sustainable farming practices enhance bacterial diversity and nutrient levels in sorghum rhizosphere soil

This research employs metagenomic analysis to explore bacterial diversity in sorghum rhizosphere soil in response to various sustainable farming practices and their impact on soil fertility. The field experiment with cotton-sorghum cropping system was conducted since 2020 and from 3rd cycle sorghum experiment, the soils were collected and subjected to metagenomics and nutrients availability analysis. We evaluated the impact of different farming approaches: Natural Farming (NF), Organic Farming (OF), integrated crop management (ICM), along with a control (No input farming). The results underscores the prevalence of Proteobacteria phylum across all farming practices, while Actinobacteria, Bacteroidetes and Firmicutes showed increased presence due to altered soil management and nutrient availability changes. Genus-level analysis revealed shifts in dominant genera, including Acinetobacter, Sphingomonas, Bacillus, and Candidatus nitrososphaera, across different farming practices. Post-harvest soil analysis indicated varied nutrient levels, with ICM showing enhanced nitrogen, phosphorus, and potassium availability. ICM, utilizing a balanced mix of organic and inorganic fertilizers, promoted sorghum growth, yielding higher plant height and total dry matter compared to OF and NF, which performed similarly. The study emphasizes the efficacy of a balanced approach like ICM for improving crop production and soil nutrient availability. However, all diversified farming practices exhibited high soil biological diversity compared to the control, highlighting the necessity for continuous long-term soil monitoring across different farming practices to stabilize soil microbiomes, ensure nutrient availability, and support sustainable crop production.

Comparative analysis of the duodenojejunal microbiome with the oral and fecal microbiomes reveals its stronger association with obesity and nutrition

ABSTRACT The intestinal microbiota is increasingly recognized as a crucial player in the development and maintenance of various chronic conditions, including obesity and associated metabolic diseases. While most research focuses on the fecal microbiota due to its easier accessibility, the small intestine, as a major site for nutrient sensing and absorption, warrants further investigation to determine its microbiota composition and functions. Here, we conducted a clinical research project in 30 age- and sex-matched participants with (n = 15) and without (n = 15) obesity. Duodenojejunal fluid was obtained by aspiration during endoscopy. Phenotyping included clinical variables related to metabolic status, lifestyle, and psychosocial factors using validated questionnaires. We performed metagenomic analyses of the oral, duodenojejunal, and fecal microbiome, alongside metabolomic data from duodenojejunal fluid and feces, integrating these data with clinical and lifestyle information. Our results highlight significant associations between duodenojejunal microbiota composition and usual dietary intake, as well as clinical phenotypes, with larger effect sizes than the associations between these variables and fecal microbiota. Notably, we found that the duodenojejunal microbiota of patients with obesity exhibited higher diversity and showed distinct differences in the abundance of several duodenojejunal microbiota species compared with individuals without obesity. Our findings support the relevance of studying the role of the small intestinal microbiota in the pathogenesis of nutrition-related diseases.

The variation of resistome, mobilome and pathogen in domestic and industrial wastewater treatment systems

Wastewater treatment plants (WWTPs), including both domestic and industrial facilities, are key contributors to antibiotic resistance genes (ARGs) and human pathogens in the environment. However, the characteristics and dissemination mechanisms of ARGs in domestic (SD) and industrial (SI) wastewater treatment systems remain unclear, leading to uncertainties in risk assessment. Based on metagenomic analysis, we observed significant differences in the compositions of resistome (ARGs and metal resistance genes, MRGs), mobilome (mobile genetic elements, MGEs), and bacterial community between SD and SI. SI exhibited lower diversity of ARGs but higher abundance of MRGs compared to SD. The removal efficiency of resistome was lower in the SI than that in the SD. MGEs emerged as the primary driver of ARG dissemination in the WWTPs, followed by the bacterial community. Environmental conditions (physicochemical parameters, heavy metals, and antibiotics) indirectly influenced the variation of resistome. Significantly, environmental conditions and MGEs highly influenced the composition of resistome in the SI, while bacterial community more associated with resistome in the SD. Additionally, we identified 36 human bacterial pathogens as potential hosts of ARGs, MRGs, and MGEs in wastewater samples. This study provides new insights on the dissemination mechanisms and risk assessment of antimicrobial resistance in the different types of WWTPs.