Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin

Early detection and population dynamics of Listeria monocytogenes in naturally contaminated drains from a meat processing plant

Listeria monocytogenes, a significant foodborne pathogen, often contaminates ready-to-eat foods through cross-contamination in food processing environments, and floor drains represent one of the most common sites of persistence. Subtyping of L. monocytogenes from food processing plants for the purpose of source tracking is usually performed on a single colony obtained after selective enrichment. This study investigates the temporal variation and population dynamics of L. monocytogenes in drains, focusing on the diversity of L. monocytogenes and the impact of the resident microbiota. Six different drains in a meat processing plant were each sampled four times over a period of 8 weeks and subjected to two-step selective enrichment in Half Fraser and Full Fraser broths. The clonal complexes (CCs) of at least 20 individual L. monocytogenes isolates from each positive sample (460 isolates in total) were determined using either the GenoListeria Multiplex qPCR assay or whole genome sequencing (WGS). The microbiota in drains and enrichment cultures was analyzed by 16S rRNA gene amplicon sequencing and metagenomic or quasimetagenomic sequencing. L. monocytogenes was detected in the majority of samples and four different CCs were identified - CC9, CC11 (ST451), CC121 and CC8 - with up to three CCs in the same sample and with different CCs dominating in different drains. The same clones of CC9, CC11, and CC121 had persisted in the facility for 3-5 years. The composition of the drain microbiota remained relatively stable over time, with Pseudomonas, Acinetobacter, Janthinobacterium, Chryseobacterium, Staphylococcus, and Sphingomonas as the most commonly identified genera. There were no apparent differences in the microbial genera present in L. monocytogenes positive and negative drains or samples. The study highlights the use of techniques such as qPCR and quasimetagenomics for monitoring and controlling the risk of L. monocytogenes contamination in processing environments.

Intestinal microbiota development in the first week of life of preterm newborns

OBJECTIVE

This study aimed to evaluate the intestinal microbiota development in the first week of life of preterm newborns (PTNB) treated at a public hospital in a municipality in the Brazilian Northeast.

METHODS

This is an observational, longitudinal, and descriptive study with 23 PTNBs. Two stool samples were collected from each neonate (fasting/meconium and seventh day of life) for stool microbiota analysis by 16S rRNA gene sequencing. The authors analyzed alpha diversity (Chao1, Shannon, and Simpson indices) and principal coordinates of beta diversity.

RESULTS

Forty-six stool samples from 23 PTNBs were analyzed at the taxonomic level. Microbiota's development was dynamic with low diversity. The authors observed a statistical association with the genera Enterobacterales, Streptococcus, Bacteroides, Clostridium_sensu_stricto_1, Enterococcus, and Bifidobacterium in the fasting samples when compared to the day-7 samples. The genus Staphylococcus also dominated at both times.

CONCLUSION

Dynamics were observed in the intestinal microbiota development, with an alpha diversity decrease in the stool samples collected at fasting/meconium and on the seventh day of life.

A microbiota pattern associated with cardiovascular events in secondary prevention: the CORDIOPREV study

BACKGROUND AND AIMS

Preventing new cardiovascular events in patients with established cardiovascular disease (CVD) is a daunting task for clinicians. Intestinal microbiota may help identify patients at risk, thus improving the strategies of secondary prevention. The aim of this study was to evaluate the baseline differences between the gut microbiota from coronary heart disease (CHD) patients suffering new major adverse cardiovascular events (MACEs) in the following 7 years, compared with CHD patients who did not undergo new MACE in this period, and to build a score associated with the risk of suffering new MACE.

METHODS

Within the framework of the CORDIOPREV study, a clinical trial that involved 1002 patients with CHD, intestinal microbiota was examined in patients with available faecal samples (n = 679, 132 MACE), through 16S metagenomics on the Illumina MiSeq and Quiime2 software. Lipopolysaccharide (LPS) was measured using limulus amoebocyte lysate test.

RESULTS

Random survival forest identified 10 bacterial taxa with a higher predictive power for MACE incidence. Receiver operating characteristic curves yielded an area under the curve of 65.2% (59.1%-71.3%) in the training set and 68.6% (59.3%-77.9%) in the validation set. The intestinal microbiota risk score was associated with a MACE incidence hazard ratio of 2.01 (95% confidence interval 1.37-3.22). Lipopolysaccharide analysis showed a greater LPS post-prandial fold change in the MACE group (P = .005).

CONCLUSIONS

These results reinforce the relationship between intestinal microbiota and CVD and suggest that a microbiota profile is associated with MACE in CHD patients, in addition to higher endotoxaemia.

Effects of pumpkin and fermented whey on fecal microbiota profile against AFB1 and OTA exposure in Wistar rats

Mycotoxins perturb the gut microbiota performance. Bioactive compounds have been recently used as a new food strategy to diminish mycotoxins bioaccessibility and prevent their toxic effects on human and animal health. Male and female Wistar rats were exposed orally to twelve different diets containing aflatoxin B1 (AFB1) and/or ochratoxin A (OTA) with or without fermented whey (FW) and pumpkin (P) for 28 days. Fecal microbiota using 16S rRNA gene sequencing and subsequent metagenomics analysis were analyzed to study the effect of 28-day exposure through diet of contaminated and enriched feed. QIIME 2 microbiome analysis package (version 2024.5) was used to analyze the demultiplexed data. Mycotoxins-functional ingredients combination contributed more to microbial phylogenetic faith α-diversity rather than the functional ingredients alone, while the same combination reported a microbial α-diversity enhancement in comparison to the mycotoxins alone. Proteobacteria phylum was reduced in rat samples fed with contaminated diets (AFB1, OTA, and AFB1+OTA), while there was an increase-although not in all groups-when adding the functional ingredients. The main difference between the sexes was found in FW+AFB1+OTA group, with males (25%) showing higher % of Proteobacteria than females (1.86%). Phylogenetic diversity faith only focuses on microbial genetic (dis)similarity, not considering the biological function. Morganella morganii, a Proteobacteria found in some groups presents anticancer activity, but it is also related to inflammatory bowel disease and colorectal cancer. To sum up, both mycotoxins and functional ingredients trigger changes in the microbiota profile of Wistar rats in a sex-specific manner.

Effects of Yeast Products on the Apparent Total Tract Macronutrient Digestibility, Oxidative Stress Markers, Skin Measures, and Fecal Characteristics and Microbiota Populations of Healthy Adult Dogs

Brewer's yeast has high nutritional value and contains bioactive compounds that may promote health. Functionalized canola meal (FCM) is a high-fiber ingredient that has been proposed as a carrier for brewer's yeast. The objective of this experiment was to determine the apparent total tract digestibility (ATTD) of diets containing yeast-enriched FCM and test their effects on the fecal characteristics and microbiota, skin measures, and serum oxidative stress markers of adult dogs. Twelve dogs were fed four extruded kibble diets (control (no FCM or yeast), FCM + low yeast dose, FCM + medium yeast dose, and FCM + high yeast dose) in a replicated 4x4 LSD. Dogs fed yeast-enriched FCM had greater wet fecal output (~15% greater than control). The ATTD of DM, OM, and fat was lower in the diets containing FCM, although the values remained >80% for all macronutrients. The yeast-enriched FCM altered the relative abundance of a few bacterial genera (Eubacterium brachy, Peptoclostridium, Ruminococcus gnavus) and fecal phenol and indole concentrations. Other fecal characteristics, metabolites, bacterial diversity indices, skin measures, or oxidative stress markers were not affected. These findings suggest that yeast-enriched FCM can be incorporated into canine diets without compromising stool quality or nutrient digestibility and may affect microbial metabolism.

Comparison of Three DNA Isolation Methods and Two Sequencing Techniques for the Study of the Human Microbiota

Breast cancer is the most commonly diagnosed cancer in women and the second leading cause of female death. Altered interactions between the host and the gut microbiota appear to play an influential role in carcinogenesis. Several studies have shown different signatures of the gut microbiota in patients with breast cancer compared to healthy women. Currently, there is disagreement regarding the different DNA isolation and sequencing methodologies for studies on the human microbiota, given that they can influence the interpretation of the results obtained. The goal of this work was to compare (1) three different DNA extraction strategies to minimize the impact of human DNA, and (2) two sequencing strategies (16S rRNA and shotgun) to identify discrepancies in microbiome results. We made use of breast tissue and fecal samples from both healthy women and breast cancer patients who participated in the MICROMA study (reference NCT03885648). DNA was isolated by means of mechanical lysis, trypsin, or saponin. The amount of eukaryotic DNA isolated using the trypsin and saponin methods was lower compared to the mechanical lysis method (mechanical lysis, 89.11 ± 2.32%; trypsin method, 82.63 ± 1.23%; saponin method, 80.53 ± 4.09%). In samples with a predominance of prokaryotic cells, such as feces, 16S rRNA sequencing was the most advantageous approach. For other tissues, which are expected to have a more complex microbial composition, the need for an in-depth evaluation of the multifactorial interaction between the various components of the microbiota makes shotgun sequencing the most appropriate method. As for the three extraction methods evaluated, when sequencing samples other than stool, the trypsin method is the most convenient. For fecal samples, where contamination by host DNA is low, no prior treatment is necessary.

The Bidirectional Effects of Periodontal Disease and Oral Dysbiosis on Gut Inflammation in Inflammatory Bowel Disease

BACKGROUND AND AIMS

Inflammatory bowel disease (IBD) flares can lead to excessive morbidity and mortality. This study aimed to determine whether oral dysbiosis/periodontal disease (PD) is common in IBD and is associated with disease activity in IBD.

METHODS

This single-center, prospective, cross-sectional, proof-of-concept, and observational study assessed the frequency of periodontal inflammatory disease and interrogated oral and stool microbiota using 16S rRNA gene amplicon sequencing of active-IBD (aIBD), inactive-IBD (iIBD), and healthy controls (HC). Questionnaires assessed diet, alcohol usage, oral hygiene behavior, and disease activity. A subset of participants underwent comprehensive dental examinations to evaluate PD.

RESULTS

Periodontal disease was severer in aIBD subjects than in HC, as aIBD had poorer quality diets (lower Mediterranean diet scores) than iIBD and HC. Significant differences in microbial community structure were observed in unstimulated saliva, stimulated saliva, gingiva, and stool samples, primarily between aIBD and HC. Saliva from aIBD had higher relative abundances of putative oral pathobionts from the genera Streptococcus, Granulicatella, Rothia, and Actinomyces relative to HC, despite similar oral hygiene behaviors between groups.

CONCLUSIONS

Our study suggests that patients with aIBD have severer periodontal disorders and higher relative abundances of putative 'pro-inflammatory' microbiota in their oral cavity, despite normal oral hygiene behaviors. Our data are consistent with the potential presence of an oral-gut inflammatory axis that could trigger IBD flare-ups in at-risk patients. Routine dental health assessments in all IBD patients should be encouraged as part of the health maintenance of IBD and as a potential strategy to decrease the risk of IBD flares.

Microbial hydrogen oxidation potential in seasonally hypoxic Baltic Sea sediments

The majority of the organic matter (OM) degradation on the seafloor occurs in coastal regions. Since oxygen (O2) becomes quickly depleted in the top sediments, most of the OM decomposition is driven by microbial sulfate reduction (SR) and fermentation, the latter generating molecular hydrogen (H2). If the H2 is not consumed by hydrogenotrophic microorganisms and accumulates in the sedimentary porewaters, OM degradation is hindered. Despite the importance of H2 scavenging microorganisms for OM mineralization, the knowledge on H2 oxidizers and their constraints in coastal marine sediments is still quite limited. Here we investigated the role of H2 oxidizers in top (2 to 5 cm, suboxic-sulfidic) and bottom (18 to 22 cm, sulfidic) coastal sediments from a location exposed to seasonal hypoxia in the SW Baltic Sea. We used sediments from April, May and August, representative of different seasons. We spiked respective sediment slurries with H2 and incubated them for up to 4 weeks under O2-free conditions. H2 consumption potential, methane production and shifts in bacterial and archaeal 16S rRNA gene amplicons (generated from RNA) were assessed over time. The seasonal variations in sedimentary community compositions and pore water geochemistry already gave distinct starting conditions for the H2 enrichments. Sediments exposed to near anoxic bottom water conditions favored a microbial starter community exhibiting the highest H2 oxidation potential. Most of the observed H2 oxidation potential appeared associated with hydrogenotrophic sulfate reducers. The putative involvement of massively enriched ANME in H2 cycling in May 18 to 22 cm sediment horizons is conspicuous. While the differences in the observed H2 oxidation potentials in the studied sediment slurries are likely related to the (season-depending) overall redox state of the sediments and interstitial waters, the influence of microbial interconnections could not be fully resolved and evaluated, demonstrating the need for further consumption- and community-based studies.

Potential of saccharomyces cerevisiae fermentation-derived postbiotic technology in mitigating multiple drug-resistant Salmonella enterica serovars in an in vitro broiler cecal model

Diamond V Original XPC® is a Saccharomyces cerevisiae fermentation-derived postbiotic technology (SCFP) designed to interact synergistically with the animal to provide health benefits by enhancing immune function, supporting digestive integrity and absorption, and maintaining gastrointestinal (GIT) microbial balance in the host. The current study investigated the effects of 1.25% SCFP on multidrug-resistant (MDR) Salmonella serovars: S. Typhimurium (ATCC 14028), S. Enteritidis, S. Infantis, S. Heidelberg, S. Typhimurium DT104, and S. Reading, and shifts in cecal microbiota populations. Using an anaerobic in vitro poultry cecal model, cecal contents were inoculated with ~ 108 colony forming units (CFU) of MDR Salmonella serovars and incubated for 24 h at 37°C anaerobically. The treatments included: control group consisting of 0.2 g of crushed poultry feed, and a treatment group 0.25 g of feed +  1.25% inclusion of Original XPC® (SCFP). The SCFP significantly reduced five of the six serovars: S. Typhimurium ATCC, S. Enteritidis, S. Infantis, S. Heidelberg, and S. Reading (P <  0.05). Time significantly impacted S. Typhimurium DT104 reduction (P <  0.001). The most significant decrease was observed for S. Enteritidis (3.9 log10 CFU/mL), followed by S. Heidelberg (3.8 log10 CFU/mL), S. Infantis (3.4 log10 CFU/mL), S. Typhimurium ATCC (3 log10 CFU/mL), and S. Reading (1.8 log10 CFU/mL) compared to controls that averaged approximately 1 log10 CFU/mL reduction. Microbiota analysis at 24 h involved genomic DNA extraction, amplification using custom dual-indexed primers, and sequencing on the Illumina MiSeq platform. Sequencing data were analyzed using QIIME2-2021.11. S. Infantis and S. Heidelberg inoculated samples were the only groups that significantly enhanced microbial richness and evenness with SCFP addition at 24 h (P <  0.05). Pairwise comparisons revealed that samples inoculated with S. Reading and S. Typhimurium DT104 exhibited a minor change in microbial composition with SCFP, compared to other serovars that demonstrated increased microbial diversity with SCFP. Additionally, S. Infantis and S. Heidelberg inoculated samples exhibited phylogenetic diversity and microbial abundance with SCFP compared to controls at 24 h (P <  0.05). Lachnospiraceae CHKCI001 was significantly more abundant in SCFP-treated samples compared to controls (ANCOM, P <  0.05), suggesting SCFP impact on cecal fermenters and production of fermentation end products that may impact the ecosystem and inhibit pathogen growth. Although various serovars may exhibit somewhat different responses, SCFP effectively mitigated multiple MDR serovars of Salmonella under in vitro incubation conditions.

Protocol of the PROMOTE study: characterization of the microbiome, the immune response, and one-carbon metabolism in preconceptional and pregnant women with and without obesity (an observational subcohort of the Rotterdam Periconception cohort)

INTRODUCTION

Preconceptional and maternal obesity are well-known risk factors for pregnancy and fetal complications including gestational diabetes, hypertensive disorders, and macrosomia. Maternal obesity is associated with offspring obesity and increased healthcare costs. To disrupt the cycle of obesity, we aim to investigate the impact of the composition of the maternal microbiota (bacteria and viruses) throughout preconception and pregnancy and the associations with the immune responses and one-carbon metabolism (1-CM) as an underlying mechanism in the pathophysiology of increased adverse pregnancy outcomes in maternal obesity.

METHODS AND ANALYSIS

The PROMOTE study is a subcohort of the Rotterdam Periconceptional Cohort, a hospital-based observational cohort study. We will include 70 women per BMI group: ≥ 30 kg/m2 or 18.5-25 kg/m2, at different time points in each group: 10 preconceptional, 50 in the first trimester (with longitudinal follow-up during pregnancy, delivery and postpartum) and 10 in the third trimester of pregnancy. Which makes a total of 140 inclusions. Vaginal and rectal bacteriome, virome, and blood samples are collected. In the third trimester inclusions, only faecal samples are collected. Microbiota samples will be analysed using 16S rRNA sequencing. Bacteriome and virome profiles are compared between the BMI subgroups, associations with general immune responses and 1-CM markers will be shown.

TRIAL REGISTRATION

ClinicalTrials.gov (NCT05754645).

Relationship Between Gut Microbiota and the Clinical Course of COVID-19 Disease

Possible early detection of people at increased risk for severe COVID-19 clinical course is extremely important so that appropriate therapy can be initiated promptly to prevent numerous deaths. Our study included 45 patients treated for COVID-19 at Dubrava University Hospital, with clinical course analysed from medical records and stool samples collected for determination of the gut microbiota diversity using 16S rRNA analysis. Sequencing was successful for 41 samples belonging to four clinical course groups (WHO guidelines): 12 samples-critical, 12-severe, 9-moderate and 8-mild group. Microbial composition was assessed between groups using two approaches-ANCOM (QIIME2) and Kruskal-Wallis (MicrobiomeAnalyst). On the genus level, two taxa were found to be differentially abundant: archaeal Halococcus and Coprococcus (for both W = 37)-the two were most abundant in the critical group (10% and 0.94% of entire abundance, respectively). Coprococcus catus was the only species identified by both methods to be differentially abundant between groups and was most abundant in the critical group. Alpha diversity indicated greater evenness of features in the critical group. Beta diversity showed clustering of samples from the critical group. A relationship between gut microbiota composition and the clinical course of COVID-19 disease was indicated, pointing towards specific distinct features of the critical group. In a broader sense, our findings might be useful in combating potential future similar pandemics and emerging virus outbreaks.

Multidimensional insights into the biodiversity of Streptomyces in soils of China: a pilot study

Streptomyces, a diverse group of filamentous bacteria found predominantly in soil, play a crucial role in nutrient cycling and produce many valuable secondary metabolites for the pharmaceutical industry. In this pilot study, we collected 19 soil samples from 14 provinces in China to preliminarily investigate the biodiversity and genetic structure of Streptomyces in soils of China from different dimensions, using recently developed cost-efficient amplicon and whole-genome library preparation methods. Amplicon analysis showed that Actinobacteria were among the most abundant bacteria, with 0.3% of amplicon sequence variants (ASVs) belonging to Streptomyces. Meanwhile, we successfully isolated 136 Streptomyces natural strains and assembled their genomes, including 26 previously unreported species, underscoring the need for further exploration of soil Streptomyces in China. Population genetics analysis revealed that homologous recombination may primarily drive the extensive genetic diversity observed in Streptomyces, as well as a complex population structure. Complementing this, pan-genome analysis shed light on gene diversity within Streptomyces and led to the discovery of rare genes, further emphasizing the vast genetic diversity of this genus. Additionally, multiple metabolic gene clusters were found in these Streptomyces strains, as well as some potentially unique or uncommon ones were found. These findings not only highlight the biological and metabolic diversity of Streptomyces but also provide a technical framework for future studies on the global biodiversity and evolution of this genus.

IMPORTANCE

Streptomyces, a prominent group of Actinobacteria, holds significant importance in ecosystems and biotechnology due to their diverse array of metabolic products. However, research on the biodiversity of soil Streptomyces across extensive geographical scales in China has been limited, and their genetic diversity has rarely been evaluated using modern population genetics principles. This pilot study successfully addresses these gaps by conducting a preliminary exploration on the biodiversity of Streptomyces in Chinese soils from multiple perspectives, providing valuable insights for a deeper understanding of their biodiversity and a novel technical framework for future large-scale explorations of its diversity.

FunVIP: Fungal Validation and Identification Pipeline based on phylogenetic analysis

The increase of sequence data in public nucleotide databases has made DNA sequence-based identification an indispensable tool for fungal identification. However, the large proportion of mislabeled sequence data in public databases leads to frequent misidentifications. Inaccurate identification is causing severe problems, especially for industrial and clinical fungi, and edible mushrooms. Existing species identification pipelines require separate validation of a dataset obtained from public databases containing mislabeled taxonomic identifications. To address this issue, we developed FunVIP, a fully automated phylogeny-based fungal validation and identification pipeline (https://github.com/Changwanseo/FunVIP). FunVIP employs phylogeny-based identification with validation, where the result is achievable only with a query, database, and a single command. FunVIP command comprises nine steps within a workflow: input management, sequence-set organization, alignment, trimming, concatenation, model selection, tree inference, tree interpretation, and report generation. Users may acquire identification results, phylogenetic tree evidence, and reports of conflicts and issues detected in multiple checkpoints during the analysis. The conflicting sample validation performance of FunVIP was demonstrated by re-iterating the manual revision of a fungal genus with a database with mislabeled sequences, Fuscoporia. We also compared the identification performance of FunVIP with BLAST and q2-feature-classifier with two mass double-revised fungal datasets, Sanghuangporus and Aspergillus section Terrei. Therefore, with its automatic validation ability and high identification performance, FunVIP proves to be a highly promising tool for achieving easy and accurate fungal identification.

Integrating temporal dynamics of both microbial taxonomic and functional characteristics as a tool for forensic time since deposition estimation

Predicting the time since deposition (TsD) of body fluid stain at a crime scene is highly valuable in forensic investigation, as it can connect a DNA-identified stain donor to a crime or estimate the post-mortem interval in forensic case involving cadaver. Previous study has demonstrated the applicability of microbial taxa for TsD prediction. In this proof-of-concept study, we explored the combined use of taxonomic and functional characteristics in human saliva microbiome for TsD prediction. We investigated the potential correlations between the temporal dynamics in microbial communities and the TsD of saliva stains, utilizing the relative abundance of microbial genera, amplicon sequence variants (AsVs), and the metabolic function pathway profiles. The results revealed that changes in the metabolic function pathway profiles of microbial communities could contribute to TsD estimation of the aged saliva stains. We developed ensemble models with multiple heterogeneous algorithms, also combined microbial species and metabolic function pathway profiles for TsD estimation. The TsD prediction model, developed using the relative abundance of the top 50 microbial genera and metabolic functional pathway profiles with the xgboost algorithm, achieved high accuracy (R2 = 0.76, mean absolute error = 6.28 days) in a 60-day deposition. Besides, we further interpreted the model and identified potential biomarkers for TsD estimation of saliva stains. The current study provided the first evidence to explore the potential of using multiple data modalities for predicting the TsD of aged saliva stains, offering valuable insight for forensic investigation.

The effects of degraded polysaccharides from Acanthopanax senticosus on growth, antioxidant and immune effects in broiler chicks based on intestinal flora

The aim of this study was to evaluate the effect of degraded polysaccharide of Acanthopanax senticosus (ASPS-1) on the immunological effects and appropriate dosage of broiler chicks with a view to developing a new feed additive. For the experimental design, 180 broiler chicks were randomly divided into six groups, ASPS-1 low, medium and high dose groups, undegraded Acanthopanax senticosus polysaccharide (ASPS) low and medium dose groups and blank control group. The drug was administered for 21 consecutive days, and the growth and data of immune organ index and immune factors were recorded on the 7th, 14th and 21st d. Finally, the effect of ASPS-1 on the intestinal flora of broiler chicks was investigated by high-throughput sequencing of the 16S rRNA gene and the correlation between the main flora and intestinal indexes was analyzed, and the function of microbial community was predicted by using PICRUSt2. The results showed that the addition of high dose of ASPS-1 could promote the body weight growth of broiler chicks, had no significant effect on immune organs, significantly promoted the increase of intestinal villi and crypt ratio, and effectively regulated the levels of serum antioxidant factors and immune indexes. Analysis of the intestinal flora showed that ASPS-1H promoted the proliferation of Lactobacillus, Faecalibacterium, Negativibacillus, and Eubacterium and inhibited the colonization of Desulfovibrio and Turicibacter, and that proliferation of Faecalibacterium, Negativibacillus and Eubacterium was associated with the development of intestinal villi. Predictive analysis of PICRUSt2 function indicates that proliferation of Lactobacillus, Faecalibacterium, Negativibacillus and Eubacterium functions through amino acid metabolism, global and overview maps, replication and repair pathways function. In summary, the addition of high doses of ASPS-1 can improve the immunity of broilers and has the potential to be used as a feed additive.

Different Land Use Systems in the Brazilian Cerrado and Their Effects on Soil Bacterial Communities

The effect of agricultural practices on soil bacterial communities is not constant and depends a lot on the climatic context, changes in the soil characteristics, land use, and agricultural strategy. Thus, knowledge about how different land use systems in the Cerrado influence the diversity and taxonomic structure of microbial communities under the same soil type remains limited. In this context, the objective of this work was to analyze and compare the bacterial communities of Cerrado soil under two different land use systems (cover crop and potato cultivation) and in a neighboring native Cerrado area. For this, we used high-throughput amplicon sequencing of 16S rRNA genes (metabarcoding) to characterize the bacterial community at different taxonomic levels in a native Cerrado area, in a potato crop area, and in an area with cover crops. Our data indicated significant impacts on soil physicochemical properties and enzymatic activity, which directly reflect the dynamics of bacterial communities. The three bacterial phyla with the highest relative abundance in the three areas were Proteobacteria, Actinobacteriota, and Acidobacteriota. At the taxonomic class level, small variations were observed among areas, while at the amplicon sequence variant (ASV) level, these variations were more pronounced. The alpha diversity indices showed that the bacterial communities among the areas are rich and diverse. Bray-Curtis and Jaccard distance-based PCoA demonstrated an overlap of bacterial communities present in the cover crop area with the native Cerrado area and separation from the potato cultivation area. The in silico prediction demonstrated that the native Cerrado area presented the highest values of functional diversity of the soil bacterial community compared to the others. Thus, our results provide a holistic view of how different land use systems in the Cerrado can influence the taxonomic and functional diversity of soil bacterial communities.

Comparative Community Ecology Reveals Conserved Ectoparasite Microbiomes Amidst Variable Host and Environment Microbiomes

The microbiome-the community of microorganisms that is associated with an individual animal-has been an important driver of insect biodiversity globally, enabling insects to specialize in narrow, nutrient-deficient diets. The importance of maternally inherited, obligate bacterial endosymbionts in provisioning nutrients missing from these narrow dietary niches has been well studied in insects. However, we know comparatively little about the processes that dictate the composition of non-maternally inherited bacteria in insect microbiomes, despite the importance of these bacteria in insect health, fitness, and vector competence. Here, we used two species of obligate insect ectoparasites of bats, the bat flies (Streblidae) Trichobius sphaeronotus and Nycterophilia coxata, to examine whether the microbiome, beyond obligate bacterial endosymbionts, is conserved or variable across geographic space, between ectoparasite species, or covaries with the external microbiome of their bat hosts or the cave environment. Our results indicate that ectoparasite microbiomes are highly conserved and specific to ectoparasite species, despite these species feeding on the blood of the same bat individuals in some cases. In contrast, we found high geographic variation in the fur microbiome of host bats and that the bat fur microbiome mimics the cave microbiomes. This research suggests that there is a constraint on blood-feeding insect ectoparasites to maintain a specific microbiome distinct from their host and the environment, potentially to meet their nutritional needs. Given that many of these bacteria are not known to be maternally inherited, this research lays the foundation for future examinations of how blood-feeding arthropods acquire and maintain bacteria in their microbiomes.

Impact of riverbed renaturalization on the attenuation of antibiotics and antimicrobial resistance in wastewater effluent-dominated streams

Mediterranean streams contain substantial proportions of wastewater treatment plant effluent, occasionally constituting the entire water flow. Here, we analysed the seasonal occurrence of 23 antibiotics (AB) and antimicrobial resistance (AMR) by tracking 3 marker genes and bacterial community dynamics in two wastewater effluent-dominated streams. One stream was renaturalized with meanders and vegetation, while the other was linear and had a low vegetation density. The concentration of ABs in the effluents ranged from 33 to 1313 ng·L-1 during summer and 4 to 2337 ng·L-1 during winter. The attenuation of ABs 3.5 km downstream varied depending on the compound, ranging from 42 to 88%. The half-lives of ABs obtained for the streams were 0.2-4.1 h in summer and 0.6-12.6 h in winter. Most ABs had a half-life of <5 h, except sulfamethoxazole, acetyl-sulfamethoxazole, and trimethoprim. The vegetated stream exhibited a higher attenuation of ABs than the unaltered stream (88% vs. 67% on average), while also showing lower half-life values (on average 1.3 vs. 3.8 h). The bacterial community profiles in both streams were typical of effluents, with greater longitudinal dynamics in the vegetated stream during summer than in the other samplings. Similarly, AMR indicator genes decreased most in the vegetated stream during summer (0.8-1.1 log units). The ecotoxicological risk and the potential microbial risk selection values downstream at 3.5 km were reduced by > 45%. Overall, the results suggest that vegetation and meanders play an important role in the in-stream attenuation of ABs and AMRs.

Evaluating the protective effects of Aurodox in a murine model of Shiga toxin-producing Escherichia coli

Shiga Toxin-Producing E. coli (STEC) are a group of acute small intestine pathogens responsible for foodborne outbreaks of bloody diarrhoea. The expression of Shiga toxins (Stx) carried by STEC can initiate Haemolytic Uremic Syndrome (HUS), a major cause of acute renal failure in children. Here, we investigate the anti-virulence potential of Aurodox - a natural product of Streptomyces goldiniensis. Previously, we have shown that Aurodox downregulates the expression of the T3SS, inhibiting epithelial cell colonisation in vitro. Here, we use the Citrobacter rodentium DBS770 (Cr Stx2dact) model of STEC infection to demonstrate that Aurodox protects mice against Citrobacter rodentium-associated colonic hyperplasia and Stx-mediated renal injury. Given antibiotic-associated dysbiosis of the gut is associated with inflammation and the emergence of opportunistic pathogens, we examined the effect of Aurodox on the faecal bacteriome. We show that although the microbial community is altered following Aurodox treatment, changes are distinct from those associated with traditional antibiotic therapies.

Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer

Diet, microbiome, inflammation and host genetics have been linked to colorectal cancer development; however, it is not clear whether and how these factors interact to promote carcinogenesis. Here we used Il10-/- mice colonized with bacteria previously associated with colorectal cancer: enterotoxigenic Bacteroides fragilis, Helicobacter hepaticus or colibactin-producing (polyketide synthase-positive (pks+)) Escherichia coli and fed either a low-carbohydrate (LC) diet deficient in soluble fibre, a high-fat and high-sugar diet, or a normal chow diet. Colonic polyposis was increased in mice colonized with pks+ E. coli and fed the LC diet. Mechanistically, mucosal inflammation was increased in the LC-diet-fed mice, leading to diminished colonic PPAR-γ signalling and increased luminal nitrate levels. This promoted both pks+ E. coli growth and colibactin-induced DNA damage. PPAR-γ agonists or supplementation with dietary soluble fibre in the form of inulin reverted inflammatory and polyposis phenotypes. The pks+ E. coli also induced more polyps in mismatch-repair-deficient mice by inducing a senescence-associated secretory phenotype. Moreover, oncogenic effects were further potentiated by inflammatory triggers in the mismatch-repair-deficient model. These data reveal that diet and host genetics influence the oncogenic potential of a common bacterium.

Combination of dietary fiber and exercise training improves fat loss in mice but does not ameliorate MASLD more than exercise alone

Lifestyle interventions, such as diet and exercise, are currently the main therapies against metabolic dysfunction-associated steatotic liver disease (MASLD). However, not much is known about the combined impact of fiber and exercise on the modulation of gut-liver axis and MASLD amelioration. Here, we studied the impact of the combination of exercise training and a fiber-rich diet on the amelioration of MASLD. Male APOE*3-Leiden.CETP mice were fed a high-fat high-cholesterol diet with or without the addition of fiber (10% inulin) and exercise trained on a treadmill, or remained sedentary. Exercise training and fiber supplementation reduced fat mass gain and lowered plasma glucose levels. Only the combination treatment, however, induced fat loss and decreased plasma triglyceride and cholesterol levels compared with sedentary control mice. Exercise training with and without the addition of fiber had a similar ameliorating effect on the MASLD score. Only exercise without fiber decreased the hepatic expression of inflammatory markers. Fiber diet was mainly responsible for remodeling the gut microbial composition, with an increase in the relative abundance of the short-chain fatty acid (SCFA)-producing genera Anaerostipes and Muribaculaceae, whereas, surprisingly, exercise training alone and with fiber resulted in the highest increase of SCFA production. Overall, the combination of exercise training and dietary fiber decreases fat mass and improves glucose and lipid homeostasis but does not have an additional synergistic positive effect on liver health compared with exercise training alone.NEW & NOTEWORTHY The combination of dietary fiber intake and exercise training has a synergetic beneficial effect on the metabolic health, resulting in fat loss, lowered blood glucose, and lowered plasma lipid levels in mice with steatotic liver disease. However, fiber supplementation, despite a positive remodulation of the gut-liver axis, does not have an additional positive effect on liver health compared with exercise training alone.

Investigation of the fingerprint-activity relationship of Tremella fuciformis polysaccharides and its mitigating effect on radiation-induced intestinal injury

The aim of this study was to conduct a comprehensive analysis of the relationship between the fingerprint of Tremella fuciformis polysaccharides (TFPs) sourced from China and their bioactivities, with an emphasis on identifying the most bioactive TFP variety that significantly mitigated radiation-induced intestinal injury (RIII). Firstly, the multi-fingerprints we developed indicated that TFPs were classified as acidic, primarily consisting of mannose, rhamnose, glucuronic acid, glucose, xylose, and fucose, with average molecular weight (Mw) ranging from 1.65 × 103 to 2.50 × 103 kDa. Subsequently, in vitro activity evaluations demonstrated variability in the antioxidant activities and the inhibitory effects on cancer cell proliferation among TFPs. Multiple linear regression analysis indicated a significant correlation between monosaccharide composition of TFPs and their bioactivity, whereas Mw did not exhibit a similar relationship. Notably, TFP sourced from Zhenjinhui (Gutian, Fujian) (i.e., TFP-2) and Shengkuo (Tongjiang, Sichuan) (i.e., TFP-23) exhibited the most significant bioactivities, both effectively mitigating RIII in mice, with TFP-23 proving to be more effective. Further investigations indicated that TFP-23 provided radioprotective benefits by rectifying RIII-induced dysbiosis of intestinal microbiota and increasing probiotic abundance. Consequently, this study not only clarifies the fingerprint-activity relationship of TFPs but also promotes the potential of TFP-23 as innovative agents for radiation protection.

Functional redundancy and niche specialization in honeybee and Varroa microbiomes

The honeybee (Apis mellifera) is a key pollinator critical to global agriculture, facing threats from various stressors, including the ectoparasitic Varroa mite (Varroa destructor). Previous studies have identified shared bacteria between Varroa mites and honeybees, yet it remains unclear if these bacteria assemble similarly in both species. This study builds on existing knowledge by investigating co-occurrence patterns in the microbiomes of both Varroa mites and honeybees, shedding light on potential interactions. Leveraging 16S rRNA datasets, we conducted co-occurrence network analyses, explored Core Association Networks (CAN) and assess network robustness. Comparative network analyses revealed structural differences between honeybee and mite microbiomes, along with shared core features and microbial motifs. The mite network exhibited lower robustness, suggesting less resistance to taxa extension compared to honeybees. Furthermore, analyses of predicted functional profiling and taxa contribution revealed that common central pathways in the metabolic networks have different taxa contributing to Varroa mites and honeybee microbiomes. The results show that while both microbial systems exhibit functional redundancy, in which different taxa contribute to the functional stability and resilience of the ecosystem, there is evidence for niche specialization resulting in unique contributions to specific pathways in each part of this host-parasite system. The specificity of taxa contribution to key pathways offers targeted approaches to Varroa microbiome management and preserving honeybee microbiome. Our findings provide valuable insights into microbial interactions, aiding farmers and beekeepers in maintaining healthy and resilient bee colonies amid increasing Varroa mite infestations.

A test for microbiome-mediated rescue via host phenotypic plasticity in Daphnia

Phenotypic plasticity is a primary mechanism by which organismal phenotypes shift in response to the environment. Host-associated microbiomes often change considerably in response to environmental variation, and these shifts could facilitate host phenotypic plasticity, adaptation, or rescue populations from extinction. However, it is unclear whether changes in microbiome composition contribute to host phenotypic plasticity, limiting our knowledge of the underlying mechanisms of plasticity and, ultimately, the fate of populations inhabiting changing environments. In this study, we examined the phenotypic responses and microbiome composition of 20 genetically distinct Daphnia magna genotypes exposed to non-toxic and toxic diets containing Microcystis, a cosmopolitan cyanobacterium and common stressor for Daphnia. Daphnia exhibited significant plasticity in survival, reproduction and population growth rates upon exposure to Microcystis. However, the effects of Microcystis exposure on the Daphnia microbiome were limited, with the primary effect being differences in abundance observed across five bacterial families. Moreover, there was no significant correlation between the magnitude of microbiome shifts and host phenotypic plasticity. Our results suggest that microbiome composition played a negligible role in driving host phenotypic plasticity or microbiome-mediated rescue.

Nutraceutical supplement slim reshaped colon histomorphology and reduces Mucispirillum schaedleri in obese mice

Introduction

Bioactive compounds and whole foods have emerged as promising interventions to address gut microbiota dysbiosis linked to obesity. Compounds such as berberine and coenzyme Q10 are well-recognized for their roles in managing metabolic syndrome and exerting antioxidant effects, while beet pulp, rich in fiber and antioxidants, enhances gut health through additional prebiotic benefits.

Methods

This study evaluated the effects of a nutraceutical supplement, Slim, on the modulation of gut microbiota in obese mice induced by a high-fat diet.

Results

Our results demonstrated that Slim supplementation significantly improved lipid metabolism, reshaped colon histomorphology, and decreased levels of Mucispirillum schaedleri, which were correlated with VLDL-c and triglycerides.

Discussion

We suggest these effects are driven by a duplibiotic effect, resulting from the synergistic action of the bioactive compounds.

Functional versus compositional tests in the risk assessment of the impacts of pesticides on the soil microbiome

The Organisation of Economic Co-operation and Development (OECD) 216 nitrogen transformation test is used to understand the impacts of plant protection products (PPPs) on the soil microbiome. However, there is significant interest in developing the European PPP risk assessment to include new technologies such as amplicon sequencing to assess impacts on soil microbial community composition and diversity. We have little understanding of how to generate endpoints from amplicon sequencing data sets, their robustness, and whether they provide an appropriate level of protection to the soil microbiome. Our study addresses this key knowledge gap. We conducted a dose-response OECD 216 study with two chemicals, nitrapyrin and streptomycin, and calculated traditional functional endpoints, in accordance with the OECD 216 guideline, and used amplicon sequencing techniques to generate a range of endpoints based on soil bacterial diversity, richness, dissimilarity from the control, species sensitivity distributions, and threshold indicator analysis. We show it is possible to generate a range of endpoints from amplicon sequencing data sets; however, these endpoints varied significantly based on the calculation method, with up to a 101-fold difference between the least and most sensitive endpoints. Additionally, the relative sensitivity of these endpoints compared to the currently used functional OECD 216 metrics was compound dependent, with many endpoint calculation methods unable to detect the impacts of nitrapyrin on the soil microbiome at concentrations deemed ecotoxicologically relevant by OECD 216. Our study shows amplicon sequencing methods to study soil microbial ecotoxicology did not perform consistently and reliably when considering both nitrapyrin and streptomycin treatments and in many cases did not consistently provide an enhanced degree of protection over the functional OECD 216 assessments already integrated into the PPP risk assessment.

Increased temperature enhances microbial-mediated lignin decomposition in river sediment

BACKGROUND

Lignin, as the most abundant recalcitrant organic carbon in terrestrial ecosystems, plays a crucial role in the Earth's carbon cycle. After lignin entering aquatic environments, portion of it tends to accumulate in sediments, forming a stable carbon relatively reservoir. However, the increasing temperature caused by human activities may impact microbial-mediated lignin decomposition, thereby affecting sedimentary carbon reservoirs. Therefore, revealing how temperature affects microbial-mediated lignin decomposition in river sediment, a topic that remains elusive, is essential for comprehending the feedbacks between river carbon reservoirs and climate. To address this, we conducted stable isotope probing of river surface sediment using 13C-lignin and 13C-vanillin, and utilized a series of techniques, including CO2 production analysis, 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics, to identify the lignin-decomposing microbes and the effects of temperature on microbial-mediated lignin decomposition.

RESULTS

We found that elevated temperatures not only increased the total sediment respiration (total CO2) and the CO2 emissions from lignin/vanillin decomposition, but also enhanced priming effects. The 13C-labled taxa, including Burkholderiales, Sphingomonadales, and Pseudomonadales, were identified as the main potential lignin/vanillin decomposers, and their abundances and activity significantly increased as temperature increased. Furthermore, we observed that increasing temperature significantly increased the activity of lignin decomposing pathways, including β-aryl ether fragments and 4,5-PDOG pathway. Additionally, as temperature increases, the transcriptional abundances of other carbon cycling related genes, such as pulA (starch decomposition) and xyla (hemicellulose decomposition), also exhibited increasing trends. Overall, our study elucidated the potential lignin-decomposing microbes and pathways in river sediment and their responses to temperature increasing.

CONCLUSIONS

Our study demonstrated that the temperature increasing can increase the rate of lignin/vanillin decomposition via affecting the activity of lignin-decomposing microbes. This finding indicates that the ongoing intensification of global warming may enhance the decomposition of recalcitrant organic carbon in river sediment, thereby impacting global carbon cycling. Video Abstract.

Analysis of the quality and bacterial composition of spicy cabbage between Liaoning and Yanbian in northeastern China based on flavoromics and amplicon sequencing

BACKGROUND

Chinese spicy cabbage (CSC) is a famous traditional fermented vegetable widely consumed in northeast China. However, the differences in characteristics between Liaoning spicy cabbage (LNSC) and Yanbian spicy cabbage (YBSC), as well as the correlation between flavor attributes and microbiota remain unclear. This study clearly delineated the characteristics and correlations of ingredients, aroma characteristics and microbial communities between LNSC and YBSC.

RESULTS

Metabolomic analysis revealed distinct compositional differences in both volatile and non-volatile metabolites between LNSC and YBSC. Through relative odor activity value analysis, 17 and 14 key flavor compounds were identified as characteristic components in LNSC and YBSC, respectively. Amplicon sequencing demonstrated significant regional variations in the bacterial community structure of CSC. Spearman correlation analysis demonstrated strong correlations between 20 bacteria and 11 free amino acids, 22 volatile flavor compounds.

CONCLUSION

This study systematically compared the quality characteristics between LNSC and YBSC, providing fundamental data for the evaluation of spicy cabbage and fermented food products. © 2025 Society of Chemical Industry.

Microecology in vitro model replicates the human skin microbiome interactions

Skin microecology involves a dynamic equilibrium among the host, microbiome, and internal/external environments. This equilibrium, shaped by multifactorial interactions, reflects individual specificity and diversity. Creating a replicable in vitro skin microecological model is highly challenging. Here, we introduce a mimicked stratum corneum microecology model (SCmic). It uses light cured crosslinked hydrogels as a scaffold and moisture source, and nonviable epidermal cells as the main nutrient. This setup establishes a suitable, stable, and reproducible microecology for microbiome colonization. Notably, it replicates the normal/oily skin microbiota with no significant differences from the original native microbiota at the genus level. Simultaneously, we have developed a standardized human skin microbiota model (Hcm), featuring seven dominant strains that form a representative microbial community. The models provide highly convenient approaches for exploring the intricate mutual interactions among skin microecology, influence of microbiota on skin health, and metabolism of chemical substances by microbiota.

Inclusion of Multi-Strained Probiotics Improves the Fecal Microbiota and Carcass Quality of Pigs

Limited studies have addressed the effects of multi-strain probiotics on gut microbiota and their influence on meat traits in pigs. Thus, this study investigated the impact of including a commercialized multi-strain probiotic product (SYN) (SYNLAC-LeanAd) into the dietary regimen of crossbred Landrace × Yorkshire × Duroc (LYD) pigs. The study spanned a duration of 22 weeks, from weaning until slaughtering, during which the carcass traits, meat quality, and fecal microbiota profile were compared to those of pigs fed diets with or without an antibiotic growth promoter (AGP). The results demonstrated that the inclusion of SYN significantly improved meat quality parameters, including marbling score, tenderness, and intramuscular fat (p < 0.05) in comparison to pigs fed with AGP. The analysis of fecal microbiota revealed that SYN inclusion increased the populations of Clostridiaceae, Coriobacteriaceae, and Erysipelotrichaceae compared to the control and AGP groups. Additionally, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis predicted that the amino acid and lipid metabolism pathways were facilitated in pigs from the SYN group. These findings suggest that the inclusion of SYNLAC-LeanAd has the potential to positively impact the fecal microbiota profile, which in turn may lead to improved carcass traits and meat quality in commercial crossbred pigs.

Different active exogenous carbons improve the yield and quality of roses by shaping different bacterial communities

The application of exogenous organic carbon represents a significant strategy for enhancing soil fertility and promoting sustainable agricultural development. This approach modifies the physicochemical properties of soil and influences microbial community structures, consequently improving crop yield and quality. Nevertheless, the mechanisms underlying microbial community responses to various forms of active exogenous organic carbon remain poorly understood and require further investigation. A 1-year follow-up experiment was conducted to examine the effects of different carbon sources on the yield and quality of cut roses, along with the characteristics of the soil bacterial community. The results indicated that applying organic fertiliser and biochar significantly enhanced the productivity of cut roses, demonstrating a sustained growth-promoting effect. Organic fertiliser provides more active, readily oxidisable organic carbon to the soil compared to biochar. In contrast, biochar supplies stable organic carbon, including inert organic carbon that is difficult to oxidise, firm organic carbon (FOC), and total inert organic carbon, which has a high degree of humification that significantly exceeds that of organic fertiliser. The application of biochar and organic fertiliser not only altered the abundance, diversity, and composition of the rhizosphere microbial community but also enriched beneficial microorganisms. Redundancy analysis results indicated that FOC, available phosphorus, and soil organic matter were the primary factors influencing the bacterial community. The results of this study demonstrated that exogenous organic carbon exerted positive and indirect effects on crop yield by influencing soil properties and bacterial communities. These findings provide novel evidence supporting the rational application of biochar and organic fertilisers as a means to promote agricultural sustainability in red soil regions.

Cross-laboratory replication of pseudomyxoma peritonei tumor microbiome reveals reproducible microbial signatures

Recent work has demonstrated that cancer-specific microbial communities often colonize tumor tissues. However, untangling low-biomass signals from environmental contamination makes this research technically challenging. We utilize pseudomyxoma peritonei (PMP), a cancer characterized by the spread of mucus-secreting cells throughout the peritoneal cavity, to develop a robust workflow for identifying reproducible tumor microbiomes. Typically originating from the rupture of an appendiceal tumor into the peritoneal cavity, metastasized tumors have been previously shown to harbor a core set of microbes. However, that work did not control for the potential contamination of these low microbial biomass samples. We expand upon these prior findings by characterizing the microbiome of 70 additional PMP tumors and six normal peritoneal control tissues along with appropriate laboratory controls. Additionally, DNA from a subset of 25 tissues was extracted and sequenced at an independent laboratory. We found evidence of reproducible microbial signatures between the replicates of six different PMP tumors that include a set of core taxa that may be introduced from surgical contamination, as well as patient-specific taxa that are also commonly implicated in colorectal cancer. In addition, preoperative chemotherapy treatment was found to reduce tumor microbiome diversity. Our findings demonstrate how independent sample replication can be a powerful approach to investigate low-biomass microbial communities associated with tumor tissues that will improve low microbial biomass research.IMPORTANCERecent work has demonstrated that microbial communities colonize over 30 different types of tumor tissues. The origin of these communities and their possible involvement in carcinogenesis or cancer treatment outcomes remains an unclear, yet important area of research. A current major challenge in characterizing low-biomass, tumor-associated microbiomes is the introduction of environmental contamination during collection, handling, DNA extraction, PCR, and sequencing. Here, we provide a framework for replicating low-biomass tumor microbiome samples to help identify tumors with robust microbial signals and low background contamination. Using this replication approach, we show that pseudomyxoma peritonei (PMP) tumors host reproducible microbial communities, including organisms that have previously been associated with colorectal cancer. Incorporating sample replication into future tumor microbiome studies is a promising approach that will help identify robust signals and increase reproducibility in the field.

Fecal microbiota landscape of commercial poultry farms in Faisalabad, Pakistan: A 16S rRNA gene-based metagenomics study

This study explores the microbiota of broiler and layer farms, aiming to understand how genetic breed, age, and farm type influence microbial communities in commercial settings. Fecal samples from 18 poultry farms (twelve layers and six broilers) in Faisalabad, Pakistan were analyzed using 16S rRNA gene sequencing of the V3-V4 region to evaluate bacterial composition. The dominant phylum, Firmicutes, accounted for 58.72 % of the microbial population, with Lactobacillus being the most abundant genus in both broilers and layers. The total abundance of potentially pathogenic genera was also assessed with Enterococcus and Corynebacterium being the most prevalent across all farms, regardless of bird type. Layers exhibited greater microbial richness and diversity than broilers, while the Karachi cage system (KCS) farm type showed higher richness than Floor system (FS). Although the breed significantly influenced microbial diversity, age was not a determining factor. Co-occurrence analyses revealed close interactions among phyla (Actinobacteriota, Proteobacteria, Firmicutes, Fusobacteriota, and Bacteroidota) and genera (Lactobacillus, Brevibacterium, Enterococcus), suggesting their pivotal roles within the microbial community. Additionally, functional analysis detected important metabolic pathways and traced microbial signatures of key pathogenic bacteria, enhancing our understanding of microbial contributions to poultry health. Despite limitations such as the need for broader geographic sampling and accounting for diet and medication, this study advances microbiome research in Pakistan's poultry sector, emphasizing consistent taxa and opening avenues for future investigations into microbiome manipulations for improved food safety and achieve better sustainable practices.

Microbial Ecosystem Therapeutics 4 (MET4) elicits treatment-specific IgG responses associated with changes in gut microbiota in immune checkpoint inhibitor recipients with advanced solid tumors

BACKGROUND

Gut microbiome modulation has shown promise in its potential to treat cancer in combination with immunotherapy. Mechanistically, the pathways and routes by which gut microbiota may influence systemic and antitumor immunity remain uncertain. Here, we used blood and stool samples from Microbial Ecosystem Therapeutic 4 (MET4)-IO, an early-phase trial testing the safety and engraftment of the MET4 bacterial consortium in immune checkpoint inhibitor recipients, to assess how MET4 may affect systemic immunity.

METHODS

Circulating antibody responses induced by MET4 were assessed using an antimicrobial antibody flow cytometry assay on pretreatment and post-treatment plasma. Antibody responses were associated with taxonomic changes in stool identified by metagenomic sequencing. Mass cytometry was performed on peripheral blood mononuclear cells to identify shifts in circulating immune subsets associated with antibody responses.

RESULTS

Increases in circulating anti-MET4 immunoglobulin G (IgG) responses were measured by flow cytometry post-consortium treatment in MET4 recipients, but not untreated control participants, with five individuals displaying notably higher antibody responses. Stronger IgG responses were associated with greater increases in multiple taxa, including MET4 microbe Collinsella aerofaciens, which was previously linked with immune checkpoint response. However, these taxa were not enriched in the IgG-bound fraction post-MET4 treatment. Greater increases in circulating B cells and FoxP3+ CD4+ T cells post-MET4 treatment were observed in the blood of high IgG responders, while CD14+ and CD16+ monocyte populations were decreased in these individuals.

CONCLUSION

These results demonstrate the induction of treatment-specific circulating humoral immunity by a bacterial consortium and suggest potential mechanisms by which gut microbes may contribute to antitumor immunity.

Hand-to-surface bacterial transfer and healthcare-associated infections prevention: a pilot study on skin microbiome in a molecular biology laboratory

Background

Healthcare-associated infections (HAIs) are a major global public health problem, contributing significantly to patient morbidity and mortality. This study analyses differences in type and amounts of bacteria transferred from volunteers' dominant palm to two healthcare-relevant surfaces (glass and laminate table), both before and after hand washing with water and antibacterial soap. The aim was to understand hand-to-surface microbial contamination and support the development of HAI prevention strategies.

Methods

Microbial DNA was extracted and sequenced to identify bacteria species. Taxonomic and statistical analyses were performed to evaluate bacterial diversity and abundance across the experimental groups.

Results

The results confirmed greater bacteria abundance and species richness on palm compared to surfaces, with a significant reduction after hand washing, especially on glass. Taxa analysis highlighted the increased persistence of Gram-negative HAIs-related bacteria on laminate surface, while Gram-positive opportunistic bacteria were more abundant on palms and glass surface. Beta diversity confirmed significant differences in microbial composition between the groups, highlighting the importance of bacteria-surface characteristics in designing preventive measures.

Conclusion

Despite some limitations, our study emphasizes the importance of microbiological surveillance for all opportunistic bacteria with pathogenic potential. These findings can contribute to more effective guidelines for surface disinfection and hand washing, key elements in preventing HAIs.

FACdb: a comprehensive resource for genes, gut microbiota, and metabolites in farm animals

Farm animals, including livestock and poultry, play essential economic, social, and cultural roles and are indispensable in human welfare. Farm Animal Connectome database (FACdb) is a comprehensive resource that includes the association networks among gene expression, gut microbiota, and metabolites in farm animals. Although some databases present the relationship between gut microbes, metabolites, and gene expression, these databases are limited to human and mouse species, with limited data for farm animals. In this database, we calculate the associations and summarize the connections among gene expression, gut microbiota, and metabolites in farm animals using six correlation or distance calculation (including Pearson, Spearman, Cosine, Euclidean, Bray-Curtis, and Mahalanobis). FACdb contains over 55 million potential interactions of 73,571 genes, 11,046 gut microbiota, and 4,540 metabolites. It provides an easy-to-use interface for browsing and searching the association information. Additionally, FACdb offers interactive visualization tools to effectively investigate the relationship among the genes, gut microbiota, and metabolites in farm animals. Overall, FACdb is a valuable resource for understanding interactions among gut microbiota, metabolites, and gene expression. It contributes to the further utilization of microbes in animal products and welfare promotion. Compared to mice, pigs or other farm animals share more similarities with humans in molecular, cellular, and organ-level responses, indicating that our database may offer new insights into the relationship among gut microbiota, metabolites, and gene expression in humans.

Protocol to study the impact of breast cancer on colonization resistance of mouse microbiota using network node manipulation

Network analysis is a powerful tool for investigating complex interactions between different microbial taxa within a community. We present a protocol to study the gut microbial community in a mouse model of breast cancer using a network-based approach. Here, we describe the procedures for tumor cell production and inoculation and 16S rRNA data processing. We then detail steps for constructing co-occurrence networks based on correlations between microbial abundances. For complete details on the use and execution of this protocol, please refer to Wu-Chuang et al.1.

Gut microbial signatures associated with uremic pruritus in hemodialysis patients

BACKGROUND

The gut microbiota influences the gut-skin-kidney axis, but its role in uremic pruritus remains poorly understood. This study aimed to explore differences in gut microbial profiles between hemodialysis (HD) patients with and without uremic pruritus and identify potential microbial signatures associated with uremic pruritus.

METHODS

We conducted a cross-sectional study of HD patients with and without uremic pruritus. Stool samples were collected from all participants, and the gut microbiota composition was analyzed using 16S rRNA gene sequencing. Alpha and beta diversity metrics were calculated to assess microbial diversity. LEfSe analysis was performed to identify differentially abundant taxa associated with uremic pruritus.

RESULTS

Among 93 HD patients (mean age: 61.9 years, 31.2 % female), uremic pruritus occurred in 61.3 % of patients, with a median visual analog scale (VAS) score of 4.0. While alpha diversity did not differ significantly between groups, beta diversity analysis revealed significant compositional differences (unweighted UniFrac metric, P = 0.004; weighted UniFrac metric, P < 0.001). LEfSe analysis revealed significant enrichment of the order Pasteurellales, family Pasteurellaceae and genus Dialister in patients with uremic pruritus, whereas the order Corynebacteriales was more abundant in patients without pruritus (P < 0.05, LDA score > 3).

CONCLUSION

In this study, we found significant differences in gut microbiota composition between HD patients with and without uremic pruritus and identified potential microbial biomarkers for uremic pruritus. Further studies are needed to elucidate the underlying mechanisms and explore microbiota-targeted therapeutic interventions.

The impact of wild-boar-derived microbiota transplantation on piglet microbiota, metabolite profile, and gut proinflammatory cytokine production differs from sow-derived microbiota

Colonization of co-evolved, species-specific microbes in early life plays a crucial role in gastrointestinal development and immune function. This study hypothesized that modern pig production practices have resulted in the loss of co-evolved species and critical symbiotic host-microbe interactions. To test this, we reintroduced microbes from wild boars (WB) into conventional piglets to explore their colonization dynamics and effects on gut microbial communities, metabolite profiles, and immune responses. At postnatal day (PND) 21, 48 piglets were assigned to four treatment groups: (i) WB-derived mixed microbial community (MMC), (ii) sow-derived MMC, (iii) a combination of WB and sow MMC (Mix), or (iv) Control (PBS). Post-transplantation analyses at PND 48 revealed distinct microbial communities in WB-inoculated piglets compared with Controls, with trends toward differentiation from Sow but not Mix groups. WB-derived microbes were more successful in colonizing piglets, particularly in the Mix group, where they competed with Sow-derived microbes. WB group cecal digesta enriched with Lactobacillus helveticus, Lactobacillus mucosae, and Lactobacillus pontis. Cecal metabolite analysis showed that WB piglets were enriched in histamine, acetyl-ornithine, ornithine, citrulline, and other metabolites, with higher histamine levels linked to Lactobacillus abundance. WB piglets exhibited lower cecal IL-1β and IL-6 levels compared with Control and Sow groups, whereas the Mix group showed reduced IFN-γ, IL-2, and IL-6 compared with the Sow group. No differences in weight gain, fecal scores, or plasma cytokines were observed, indicating no adverse effects. These findings support that missing WB microbes effectively colonize domestic piglets and may positively impact metabolite production and immune responses.IMPORTANCEThis study addresses the growing concern over losing co-evolved, species-specific microbes in modern agricultural practices, particularly in pig production. The implementation of strict biosecurity measures and widespread antibiotic use in conventional farming systems may disrupt crucial host-microbe interactions that are essential for gastrointestinal development and immune function. Our research demonstrates that by reintroducing wild boar-derived microbes into domestic piglets, these microbes can successfully colonize the gut, influence microbial community composition, and alter metabolite profiles and immune responses without causing adverse effects. These findings also suggest that these native microbes can fill an intestinal niche, positively impacting immune activation. This research lays the groundwork for future strategies to enhance livestock health and performance by restoring natural microbial populations that produce immune-modulating metabolites.

Social organization and physical environment shape the microbiome of harvester ants

All animals harbor microbiomes, which are obtained from the surrounding environment and are impacted by host behavior and life stage. To determine how two non-mutually exclusive drivers - physical environment and social organization - affect an organism's microbiome, we examined the bacterial communities within and around nests of harvester ants (Veromessor andrei). We collected soil and nest content samples from five different ant nests. We used 16S rRNA gene sequencing and calculated alpha and beta diversity to compare bacterial diversity and community composition across samples. To test the hypotheses that physical environment and/or social organization impact ant colonies' community of microbes we compared our samples across (i) sample types (ants, brood, seeds and reproductives (winged alates), and soil), (ii) soil inside and outside the nest, and (iii) soil from different chamber types. Interestingly, we found that both the environment and social organization impact the bacterial communities of the microbiome of V. andrei colonies. Soil from the five nests differed from one another in a way that mapped onto their geographical distance. Furthermore, soil from inside the nests resembled the surrounding soil, supporting the physical environment hypothesis. However, the bacterial communities associated with the contents within the nest chambers, i.e., ants, brood, seeds, and reproductives, differed from one another and from the surrounding soil, supporting the social organization hypotheses. This study highlights the importance of considering environmental and social factors in understanding microbiome dynamics.

Integrating sequence composition information into microbial diversity analyses with k-mer frequency counting

k-mer frequency information in biological sequences is used for a wide range of applications, including taxonomy classification, sequence similarity estimation, and supervised learning. However, in spite of its widespread utility, k-mer counting has been largely neglected for diversity estimation. This work examines the application of k-mer counting for alpha and beta diversity as well as supervised classification from microbiome marker-gene sequencing data sets (16S rRNA gene and full-length fungal internal transcribed spacer [ITS] sequences). Results demonstrate a close correspondence with phylogenetically aware diversity metrics, and advantages for using k-mer-based metrics for measuring microbial biodiversity in microbiome sequencing surveys. k-mer counting appears to be a suitable and efficient strategy for feature processing prior to diversity estimation as well as supervised learning in microbiome surveys. This allows the incorporation of subsequence-level information into diversity estimation without the computational cost of pairwise sequence alignment. k-mer counting is proposed as a complementary approach for feature processing prior to diversity estimation and supervised learning analyses, enabling large-scale reference-free profiling of microbiomes in biogeography, ecology, and biomedical data. A method for k-mer counting from marker-gene sequence data is implemented in the QIIME 2 plugin q2-kmerizer (https://github.com/bokulich-lab/q2-kmerizer).

IMPORTANCE

k-mers are all of the subsequences of length k that comprise a sequence. Comparing the frequency of k-mers in DNA sequences yields valuable information about the composition of these sequences and their similarity. This work demonstrates that k-mer frequencies from marker-gene sequence surveys can be used to inform diversity estimates and machine learning predictions that incorporate sequence composition information. Alpha and beta diversity estimates based on k-mer frequencies closely correspond to phylogenetically aware diversity metrics, suggesting that k-mer-based diversity estimates are useful proxy measurements especially when reliable phylogenies are not available, as is often the case for some DNA sequence targets such as for internal transcribed spacer sequences.

Information storage across a microbial community using universal RNA barcoding

Gene transfer can be studied using genetically encoded reporters or metagenomic sequencing but these methods are limited by sensitivity when used to monitor the mobile DNA host range in microbial communities. To record information about gene transfer across a wastewater microbiome, a synthetic catalytic RNA was used to barcode a highly conserved segment of ribosomal RNA (rRNA). By writing information into rRNA using a ribozyme and reading out native and modified rRNA using amplicon sequencing, we find that microbial community members from 20 taxonomic orders participate in plasmid conjugation with an Escherichia coli donor strain and observe differences in 16S rRNA barcode signal across amplicon sequence variants. Multiplexed rRNA barcoding using plasmids with pBBR1 or ColE1 origins of replication reveals differences in host range. This autonomous RNA-addressable modification provides information about gene transfer without requiring translation and will enable microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.

Insights into long term glass corrosion mechanisms from the Ballidon experiment

At the Ballidon experiment, one of the longest running glass durability studies, modern and simulant archaeological glasses were buried in mildly alkaline, under-saturated, conditions for 52 years. Glass surfaces were analysed to determine the extent and mechanisms of alteration. Alteration layer chemistry was complex and included Ca from the surrounding limestone sediment and P from porewater resulting in Ca, Pb and Fe-phosphate rich phases interspersed with Si and Al rich regions. There was evidence for ongoing evolution of the alteration layer structure due to continued fluid ingress. Lamellae in the silica-rich regions approximately numbering the years of burial and indicating a possible link between their formation and seasonal climate cycling. Comparison of field samples with laboratory dissolution tests highlighted the impact of surface finish on initial alteration rate and the limitations of using alteration layer thickness to estimate the amount of glass that has dissolved.

Impact of Fermented Soy Beverages Containing Selected Vaginal Probiotics on the In Vitro Fecal Microbiota of Post-Menopausal Women

The gut microbiome of women can change after menopause, and during this phase women can also be more susceptible to vaginal dysbiosis. Recent studies have explored the probiotic potential of Lactobacillus crispatus BC4 and Lactobacillus gasseri BC9 against various pathogens and their use as co-starters in foods. However, their effects on the gut microbiota of post-menopausal women, who are more prone to dysbiosis, have not been examined. This study investigated the effects of predigested soy beverages (INFOGEST) containing BC4 and BC9 (encapsulated or not) on the composition and metabolic activity of the gut microbiota in post-menopausal women, using a fecal batch culture model. Parameters such as pH, gas, SCFAs, and microbiota composition (targeted qPCR and 16S rRNA gene sequencing) were assessed. The study, while highlighting a strong variability among donors, showed differences in gut microbiota response to the tested products. For instance, donor 2 showed a significant increase in bifidobacteria with BC4 + BC9 and E-BC9, while BC4 increased Ruminococcaceae in donors 1 and 3, and E-BC4 and E-BC9 enhanced Akkermansia in donor 1. BC4, E-BC4, E-BC9, and E-BC4 + BC9 significantly impacted metabolic activity, as measured by SCFAs, compared to other samples. However, no significant differences in gas production were observed.

Full-length 16S rRNA Sequencing Reveals Gut Microbiome Signatures Predictive of MASLD in children with obesity

BACKGROUND

The gut microbiota plays a crucial role in metabolic dysfunction-associated steatotic liver disease (MASLD). Next-generation sequencing technologies are essential for exploring the gut microbiome. While recent advancements in full-length 16S (FL16S) rRNA sequencing offer better taxonomic resolution, whether they establish stronger associations with the risk of MASLD remains to be determined.

METHOD

This study utilized long-read FL16S and short-read V3-V4 16S rRNA sequencing to profile gut microbiome compositions in age-, sex-, and BMI-matched case-control pairs of obese children with and without MASLD. A random forest predictive model was employed, using gut-microbiota features selected based on the top 35 most abundant taxa or a linear discriminant analysis score greater than 3. The model's performance was evaluated by comparing the area under the receiver operating characteristic curve (AUC) through a tenfold cross-validation method.

RESULTS

Subjects with MASLD exhibited significantly elevated serum alanine aminotransferase, triglycerides, and homeostasis model assessment of insulin resistance levels compared to controls. At the genus level, the gut microbiome compositions detected by both FL16S and V3-V4 sequencing were similar, predominantly comprising Phocaeicola and Bacteroides, followed by Prevotella, Bifidobacterium, Parabacteroides, and Blautia. The AUC for the model based on FL16S sequencing data (86.98%) was significantly higher than that based on V3-V4 sequencing data (70.27%), as determined by DeLong's test (p = 0.008).

CONCLUSION

FL16S rRNA sequencing data demonstrates stronger associations with the risk of MASLD in obese children, highlighting its potential for real-world clinical applications.

Comprehensive analysis of the metabolism of core microorganisms in polyphenolic compound formation during the acetic acid fermentation stage of millet vinegar

BACKGROUND

Polyphenolic compounds in millet vinegar are crucial functional substances, but the mechanisms underlying their formation and metabolism remain unclear. Acetic acid fermentation (AAF) represents the most active microbial metabolism stage and is pivotal for forming polyphenolic compounds. This study comprehensively analyzed the role of the microbiome in polyphenolic compound production and metabolism during AAF.

RESULTS

Changing patterns were observed in both the microbiome and polyphenolic monomer compounds during AAF of millet vinegar. Lactobacillus harbinensis (0.624-0.454%) was identified as the dominant species in the pre-AAF stage, exhibiting a significant positive correlation with caffeic acid, kaempferic acid and kaempferolide (P < 0.05). Lactobacillus harbinensis-mediated polyphenolic compound metabolism was further confirmed through genomic analysis and pure culture fermentation techniques. Lactobacillus harbinensis encodes enzymes such as carbohydrate hydrolases, glycosidases and cellulases, which promote the release and metabolism of polyphenolic compounds from grain hulls.

CONCLUSION

This study confirmed that L. harbinensis, as a core microorganism in millet vinegar fermentation, can significantly augment the content of total phenols and specific polyphenolic compounds. These findings provide valuable insights for optimizing millet vinegar production. © 2024 Society of Chemical Industry.

Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola

BACKGROUND

Plant health depends on beneficial interactions between the roots and their microbiomes. Despite recent progress on the role of the grapevine microbiome, the taxonomic identity and functional traits of microbial taxa specific to healthy or Plasmopara viticola-diseased plants, as well as to the susceptible or resistant cultivar are unknown. Using metabarcoding and shotgun metagenomics sequencing, we investigated the effect of downy mildew on the root-associated microbiome (rhizospheric soil, rhizoplane and endosphere) of 41B-grafted susceptible cultivar (Chardonnay) and resistant interspecific hybrid (Voltis) at flowering and veraison stages. The impact of conventional treatment on the rhizomicrobiome assembly of Chardonnay was also evaluated.

RESULTS

Analyses revealed a core bacteriome shared between both susceptible and resistant cultivars. This also highlighted common functional traits between the rhizosphere and rhizoplane bacteriomes in both cultivars. A dysbiosis state was also evidenced by a loss of beneficial communities in the rhizosphere of the P. viticola-infected cultivar. Microbial genome assemblies showed functional differences between healthy and diseased plants, with a loss of Pseudomonas and Phyllobacterium taxa at veraison. This state was mainly characterized by a loss of genes involved in polyamine transport and metabolism in the susceptible cultivar. It was also marked by an increase in population evenness and total bacterial diversity, and the presence of pathogenic species in susceptible plants.

CONCLUSIONS

This study reveals distinct and overlapping bacterial communities and functional genes in the rhizospheric soil, rhizoplane and root endosphere of both susceptible and resistant grapevine cultivars to downy mildew. Microbial diversity and abundant taxa of grapevine roots are influenced by downy mildew and cultivar susceptibility. Common bacterial functions are shared among rhizocompartments of susceptible and resistant cultivars, revealing a dysbiosis state and functional signatures related to plant immunity, especially in the infected-susceptible plants.

Bicarbonate-Rich Mineral Water Mitigates Hypoxia-Induced Osteoporosis in Mice via Gut Microbiota and Metabolic Pathway Regulation

Background: High-altitude hypoxia is known to adversely affect bone health, leading to accelerated bone loss and metabolic alterations. Recent studies suggest that factors such as bicarbonate and gut microbiota may play key roles in bone health. Mineral water, rich in bicarbonate, may influence bone health and the gut-bone axis under such conditions. Methods: Mice were exposed to hypoxia and treated with different concentrations of drinking water. Bone-related parameters were assessed using dual-energy X-ray absorptiometry (DXA) and Micro-CT. Bone health was assessed using the measurement of serum biomarkers. Additionally, Untargeted Metabolomics was employed to analyze differential metabolites between groups, while gut microbiota composition was analyzed using 16S rRNA sequencing. Results: BMW consumption increased bone mineral density (BMD) and helped alleviate the damage to the microstructure of bones caused by hypoxia and delayed the progression of osteoporosis. Additionally, BMW was shown to enhance probiotics such as Akkermansia and Dubosiella and regulate the longevity-regulating pathway as well as the PI3K/AKT/mTOR (PAM) signaling pathway. This study also discovered changes in metabolic products due to BMW intervention, predominantly in pathways such as the amino acid, prostaglandin, and purine metabolisms, with correlation analysis further exploring the relationships between gut microbiota and these differential metabolites. Conclusions: Long-term exposure to high-altitude hypoxic conditions affects the structure of gut microbiota and bone metabolism in mice. The consumption of BMW improves the structure of gut microbiota and regulates the metabolic pathways to maintain bone health under high-altitude hypoxia.

Cross-kingdom-mediated detection of intestinal protozoa through NLRP6

Intestinal protists are detected by the host innate immune system through mechanisms that remain poorly understood. Here, we demonstrate that Tritrichomonas protozoa induce thickening of the colonic mucus in an NLRP6-, ASC-, and caspase-11-dependent manner, consistent with the activation of sentinel goblet cells. Mucus growth is recapitulated with cecal extracts from Tritrichomonas-infected mice but not purified protozoa, suggesting that NLRP6 may detect infection-induced microbial dysbiosis. In agreement, Tritrichomonas infection causes a shift in the microbiota with the expansion of Bacteroides and Prevotella, and untargeted metabolomics reveals a dramatic increase in several classes of metabolites, including sphingolipids. Finally, using a combination of gnotobiotic mice and ex vivo mucus analysis, we demonstrate that wild-type, but not sphingolipid-deficient, B. thetaiotaomicron is sufficient to induce NLRP6-dependent sentinel goblet cell function, with the greatest effect observed in female mice. Thus, we propose that NLRP6 is a sensor of intestinal protozoa infection through monitoring microbial sphingolipids.

Diversity and Structure of the Prokaryotic Community in Tropical Monomictic Reservoir

Bacteria and Archaea are microorganisms that play key roles in the biogeochemical transformations that control water quality in freshwater ecosystems, such as in reservoirs. In this study, we characterize the prokaryotic community of a high-relevance tropical eutrophic reservoir using a 16S rRNA gene survey during a low-water level fluctuation period mainly used for storage, associating the distribution of these microorganisms with the hydrogeochemical conditions of the water column. Our findings revealed that diversity and structure of the prokaryotic community exhibited spatio-temporal variations driven by the annual circulation-stratification hydrodynamic cycle and are significantly correlated with the concentrations of dissolved oxygen (DO), soluble reactive phosphorus (SRP), and dissolved inorganic nitrogen (DIN). During the heterotrophic circulation, the breakdown of thermal gradient leads to a homogeneous distribution of the nutrients, where the presence of DO promotes the dominance of aerobic and facultative heterotrophic bacteria such as Bacteroidota, Actinobacteriota, and Verrucomicrobiota. Also, the autotrophic circulation was characterized by an increase of DO and NO3- concentrations, with abundant Cyanobacteria. Finally, during the stratification, the presence of prokaryotes associated with the metabolism of CH4 was detected, mainly in the hypolimnion, as well as others related to sulfate reduction and nitrification. This study shows the diversity of the prokaryotic community in tropical eutrophic reservoirs, and how the continuous monitoring with metabarcoding techniques can provide critical insights for a deeper understanding of the biogeochemical dynamics and improve the water resource management in the future.