Locally advanced rectal cancer (LARC) is treated with neoadjuvant chemo-radiotherapy (nCRT) followed by surgery. A minority of patients show complete response (CR) to nCRT and may avoid surgery and its functional consequences. Instead, most patients show non-complete response (non-CR) and may benefit from additional treatments to increase CR rates. Reliable predictive markers are lacking. Aim of this study was to identify novel signatures predicting nCRT responsiveness. We performed a combined analysis of tumor-associated microbiome and immune gene expression profiling of diagnostic biopsies from 70 patients undergoing nCRT followed by rectal resection, including 16 with CR and 54 with non-CR. Findings were validated by an independent cohort of 49 patients, including 7 with CR and 42 with non-CR. Intratumoral microbiota significantly differed between CR and non-CR groups at genus and species level. Colonization by bacterial species of Ruminococcus genera was consistently associated with CR, whereas abundance of Fusobacterium, Porhpyromonas, and Oscillibacter species predicted non-CR. Immune gene profiling revealed a panel of 59 differentially expressed genes and significant upregulation of IFN-gamma and -alpha response in patients with CR. Integrated microbiome and immune gene profiling analysis unraveled clustering of microbial taxa with each other and with immune cell-related genes and allowed the identification of a combined signature correctly identifying non-CRS in both cohorts. Thus, combined intratumoral microbiome-immune profiling improves the prediction of response to nCRT. Correct identification of unresponsive patients and of bacteria promoting responsiveness might lead to innovative therapeutic approaches based on gut microbiota pre-conditioning to increase nCRT effectiveness in LARC.

Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL-1) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO2, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.

Raising farm animals imparts various exposures that may shape the human microbiome. The oral microbiome has been increasingly implicated in disease development. Animal farming has also been associated with certain chronic diseases such as cancer; however, underlying biological mechanisms are unclear. We investigated associations between raising farm animals and the oral microbiome in the Agricultural Health Study.

This analysis included 1,245 participants (865 farmers and 380 spouses) who provided oral wash specimens and information on types and numbers of specific animals raised on their farms within 2 years before sample collection. The oral microbiome was measured by sequencing the V4 region of the 16S ribosomal RNA gene. We evaluated associations of farm animal exposures with alpha and beta diversity metrics (within- and between-sample diversity, respectively), as well as presence and relative abundance of specific bacterial genera. All analyses adjusted for potential confounders (e.g., age, sex, smoking, alcohol consumption).

Overall, 63 % of participants raised farm animals, most commonly cattle (46 %) and hogs (20 %). Those who raised a large number of hogs (≥2,000 vs. no hogs) had higher alpha diversity. Conversely, raising sheep/goats and raising larger numbers of poultry were associated with lower alpha diversity. Beta diversity was not significantly different between participants with and without any farm animals. Participants raising any farm animals had higher relative abundance of Porphyromonas and lower relative abundances of Prevotella and Ruminococcaceae UCG-014. Several genera were more likely to be absent with specific animal exposures (e.g., Capnocytophaga for cattle and sheep/goats; Corynebacterium, Dialister, Stomatobaculum, and Solobacterium for sheep/goats and poultry).

This was the largest study of farm animal exposures and the human microbiome to date. Findings suggest that raising specific farm animals may influence the oral microbiome, supporting the need to further investigate the potential role of animal farming in disease etiology.

Bladder cancer is a common malignancy of the genitourinary system. Recent studies have confirmed the existence of microorganisms in urine. This study aimed to characterize changes in the urinary microbiota of Chinese bladder cancer patients and determine differences between patients with muscle-invasive bladder cancer (MIBC) and those with non-muscle-invasive bladder cancer (NMIBC).

Urine samples were collected from 64 patients with bladder cancer and 94 disease-free controls using the clean catch method and sequenced by 16S rRNA gene sequencing. Sequencing reads were filtered by VSEARCH and clustered by UPARSE.

Significant associations were found between urinary microbiota and factors such as sex, age, and disease status. After age adjustment, differences in beta diversity were observed between healthy men and women, cancer patients and healthy controls, and NMIBC and MIBC patients. The cancer patients had an increased abundance of 14 bacterial genera, including Stenotrophomonas, Propionibacterium, and Acinetobacter. Notably, Peptoniphilus spp. were enriched in high-risk MIBC patients, indicating their potential as a risk marker. Functional prediction via PICRUSt analysis suggested enriched metabolic pathways in specific disease groups. Furthermore, molecular ecological network analysis revealed differences based on sex and disease type.

This significant microbial diversity indicates a potential correlation between urinary microbiota dysbiosis and bladder cancer, with implications for risk stratification and disease management. The identified urinary microbiota may serve as noninvasive markers for bladder cancer, warranting further validation in larger cohorts. This study provides a foundation for further research on the mechanisms of bladder cancer progression.

Analysis of the presence and the abundance of microorganisms related to diseases can be used to monitor marine environmental health. Our study evaluated the interference of taxonomic databases (SILVA, Greengenes v13.8, Greengenes2, and RDP) to monitor the distribution of bacterial genera potentially related to diseases in marine organisms (BGPRDs) from low- (Dois Rios Beach-DR), medium- (Abraão Beach-AB) and high (Guanabara Bay-GB) impacted marine environments. The frequency, richness, diversity, and composition of BGPRDs present in DR, AB and GB were significantly influenced by the different databases (p < 0.05). Consequently, the analyses revealed that the use of different databases resulted in controversial results regarding the distribution of BGPRDs in the DR, AB and GB. While Greengenes v13.8 and RDP showed that GB had the highest frequency of BGPRDs (p < 0.05), analysis based on Greengenes2 and SILVA revealed a greater frequency of BGPRDs in AB (p < 0.05). Additionally, there was no congruence of BGPRDs detected by each taxonomic database in DR, AB and GB. In highly-impacted GB, Arcobacter was the main BGPRD obtained with the Greengenes2 and RDP databases, whereas Synechococcus and Alteromonas represented the main BGPRD according to the Greengenes v13.8 and SILVA databases, respectively. Our results showed we cannot determine the exact composition and abundance of BGPRDs in low-, medium- and highly-impacted marine environments. These findings emphasize the critical influence of database choice on microbial community characterization and its implications for effective environmental monitoring and management strategies. Interestingly, alpha diversity indices of BGPRDs obtained from DR, AB and GB were consistent among the different databases and showed greater congruence than did the frequency, richness, distribution and abundance of BGPRDs. The use of diversity indices of BGPRDs can be an alternative to overcome the limitations caused by the bias of taxonomic annotations for biomonitoring marine environments.

Amplicon sequencing is a widely used method for surveying biological diversity. However, the technique is disturbed by PCR bias leading to errors in community composition analyses. In this study, microbial community composition was evaluated in twenty-eight locations of hot spring water with temperatures between 87-48°C at Nakabusa Hot Springs, Japan, using amplicon sequencing analysis with the V4 region of the 16S rRNA gene. In discrepancy with the greenish color and the absorption spectra of the microbial samples, the relative abundance of amplicon sequence variants (ASVs) in the major photosynthetic organisms, Chloroflexus spp., were scarce in any sample when using the annealing temperature of 50°C in amplicon PCR. Changing the annealing temperature to 68ºC significantly improved the detection efficiency of Chloroflexus ASVs, and the obtained numbers were consistent with the presence of the photosynthetic pigments. The abundance of many other microbial ASVs was also dependent on the annealing temperature. The log ratio in the abundance of major ASVs between two annealing temperatures was correlated with the GC content of the 16S rRNA gene, suggesting that even some other major ASVs in the community are seriously affected by PCR bias due to the GC content. Combined usage of results from two different annealing temperatures, rather than a result using a single annealing temperature, seems to be a better way to obtain community structure information with less PCR bias in thermophilic organisms of high 16S rRNA GC content.

Cultural heritage objects provide valuable historical information, but can also harbour biological threats. Still, little is said about the potential risks that may await unaware researchers, conservators, and archaeologists. Our work discusses the study results from the crypts in Krakow, which were opened for the first time. The human and coffin remains were examined. The number of actinomycetes, other mesophilic bacteria, bacterial spores, and xerophilic and non-xerophilic fungi was determined. In general, a low number of microbes was observed. However, scanning electron microscope (SEM) images showed many bacterial conglomerates and confirmed that microbial activity affected the fibres covering cadavers in the crypts. The most abundant were mesophilic bacteria, followed by bacterial spores and actinomycetes. They reached up to 107 CFU/g in fabric remains, 5.2 × 106 CFU/g in burial remains, and 1.6 × 106 CFU/g found under the coffin, and above 7.5 × 105 CFU/g for xerophilic and non-xerophilic fungi. NGS (Next-Generation Sequencing) results suggested that the low presence of microorganisms may be due to the dominance of unculturable or long-growing bacteria belonging to Mycobacterium, such as M. coloregonium, M. arupense, and M. pinnipedii. Moreover, other obligatory/non-obligatory pathogens, Bacteroides fragilis, Clostridium botulinum, Coxiella burnetii, Clostridium tetani, Corynebacterium diphtheriae, Enterobacter cloacae, Escherichia coli, Legionella pneumophila, Mycobacterium leprae, Rhodococcus equi, and Staphylococcus aureus have been recorded in examined samples, with the dominance in bone samples. Results indicate the risk of dangerous pathogens present in historical objects, the impact on health may be severe, and the need to use personal protective equipment and proper measures to control the physical conditions of crypts.

Objective: The aim of this work is to investigate the impact of exercise on gut microbiome composition, serum metabolites, and their correlation with osteoarthritis (OA) severity. Methods: Thirty-six Sprague-Dawley (SD) rats were randomly divided into four groups: Sham rats without treadmill walking (Sham/Sed group, n = 9), Sham rats with treadmill walking 2 months (Sham/TW2M group, n = 9), PTOA rats without treadmill walking (PTOA/Sed group, n = 9), and PTOA rats with treadmill walking 2 months (PTOA/TW2M group, n = 9). The PTOA model was induced by transection of the anterior cruciate ligament (ACLT) and destabilization of the medial meniscus (DMM). Histological evaluation and micro-CT analysis were performed to observe the pathological changes in cartilage and subchondral bone, respectively. Additionally, we conducted 16S rDNA sequencing of fecal samples and untargeted metabolomic analysis using liquid chromatography-mass spectrometry (LC-MS) of serum samples to detect the alteration of gut microbiota composition and metabolites. Results: Exercise effectively mitigated OA-related pathological changes, including articular cartilage degeneration and subchondral bone loss. Moreover, 16S rDNA sequencing analysis of gut microbiome revealed a decreased abundance of Bacteroidetes (p < 0.01), Bacteroidia (p < 0.01), Rikenellaceae (p < 0.01), [Paraprevotellaceae] (p < 0.01), and Paraprevotella (p < 0.01) but an increase in Firmicutes (p < 0.01) in PTOA/TW2M group rats compared with PTOA/Sed group as a response to exercise. In addition, the results of metabolomics analysis showed that exercise treatment contributed to the upregulation of Daidzein and Anthranilic acid and downregulation of 1-Palmitoyllysophosphatidylcholine. Moreover, the correlation analysis showed that Rikenellaceae significantly positively correlated with both OARSI (r = 0.81, p < 0.01) and Mankin score (r = 0.83, p < 0.01) and negatively correlated with the serum level of Anthranilic acid (r = -0.56, p < 0.01) and Daidzein (r = -0.46, p < 0.01). Conclusions: Exercise can effectively mitigate OA through slowing down articular cartilage degeneration and subchondral bone loss, modulating gut microbiota composition, and increasing beneficial metabolites.

Stroke is the second leading cause of death worldwide. Acute ischemic stroke (AIS) patients often exhibit hypercoagulable state and gut microbiota dysbiosis. However, the association between coagulation abnormalities and gut microbiota dysbiosis in AIS patients and their predictive value for poor functional outcomes in AIS has not been investigated. Our study enrolled 95 AIS patients and 81 healthy controls, using 16S rRNA sequencing to analyze gut microbiota composition. Baseline fibrinogen level was found to be an independent risk factor for poor functional outcomes at 90-day follow-up (odds ratio = 2.16, 95% confidence interval: 1.02-4.59, P = 0.044). AIS patients showed significant gut microbiota dysbiosis, with significantly increased Parabacteroides and Alistipes, and decreased Prevotella and Roseburia, associated with coagulation indices. Furthermore, compared with AIS patients with normal coagulation function, those in a hypercoagulable state exhibited a significant increase in Alistipes and a decrease in Prevotella. We identified gut microbial biomarkers consisting of 15 bacteria that predicted poor functional outcome in AIS patients at 90-day follow-up. Coagulation indices improved the predictive performance of these biomarkers. In training and validation cohorts, area under the curve (AUC) values were 0.930 and 0.890 for microbial biomarkers alone, 0.691 and 0.751 for coagulation indices alone, and 0.943 and 0.944 for coagulation indices combined with gut microbial biomarkers. Our study showed that AIS patients with hypercoagulable state had gut microbiota dysbiosis, with Alistipes and Prevotella significantly associated with coagulation indices. A classification model based on coagulation indices and gut microbial biomarkers accurately predicted poor functional outcome in AIS patients at 90-day follow-up.

Acute ischemic stroke (AIS) patients often exhibit hypercoagulable state and gut microbiota dysbiosis. However, the relationship between hypercoagulable state and gut microbiota dysbiosis in AIS patients and their predictive value for poor functional outcomes has not been fully explored. Our study of 95 AIS patients showed that baseline fibrinogen level was an independent risk factor for poor functional outcome at 90-day follow-up in AIS patients. Hypercoagulable state in AIS patients correlates with gut microbiota dysbiosis. AIS patients with hypercoagulable state had increased Alistipes abundance and decreased Prevotella abundance. A classification model based on coagulation indices and gut microbial biomarkers accurately predicted poor functional outcome in AIS patients at 90-day follow-up.

Kazakhstan's rich biodiversity includes diverse apple populations, notably the wild apple tree (Malus sieversii) prized for traits like disease resistance and adaptability, potentially aiding breeding programs. Analyzing their microbiomes offers insights into bacterial diversity and how it influences apple tree development, making it a reliable method for understanding ecological interactions. In this research, 334 apple tree samples were collected from different mountain ranges in southeastern Kazakhstan. An analysis using nanopore-based 16S rRNA sequencing showed a distinct similarity in the microbiome compositions of samples from the Zhongar and Ile Alatau mountain ranges, with a predominance of Pseudomonadaceae, Enterobacteriaceae, and Microbacteriaceae. In contrast, samples from Ketmen ridge showed a higher prevalence of Enterobacteriaceae. Alongside the less represented Pseudomonadaceae family, in the Ketmen ridge region, bacteria of the Xanthomonadaceae, Alcaligenaceae, and Brucellaceae families were also present. Across all regions, beneficial plant-associated bacteria were identified, such as Pseudomonas veronii, Stenotrophomonas geniculata, and Kocuria rhizophila, potentially enhancing plant resilience. However, opportunistic phytopathogens were also detected, including Pseudomonas viridiflava and Serratia marcescens, particularly in the Ile Alatau region. These findings highlight the complex microbial interactions in M. sieversii, thus offering key insights into host-microbe relationships that can inform apple breeding and ecological preservation efforts.

Biofilters are widely utilized for treating odorous gases. Understanding the biosafety of biofilters in real-world applications necessitates a comprehensive investigation into their bioaerosol emission characteristics. In this study, bioaerosols captured from the inlet and outlet, along with packing material microbiome were investigated over a 12-month period from three full-scale biofilters. Their characteristics, size distribution, and sources were investigated and analyzed. Notably, over 96 % of the bioaerosols originated from the inlet air rather than from the packing materials. Full-scale biofilters not only reduced bacterial emissions by 5-17 % but also lowered the potential pathogenicity. Although biofilters effectively diminished bioaerosol emissions, there are still potential pathogenicity primarily originated from the inlet air. This study emphasizes the significance of considering upstream processes when evaluating the risks associated with bioaerosols in real-world applications.

The rising use of artificial sweeteners, favored for their zero-calorie content and superior sweetness, necessitates understanding their impact on the gut microbiome. This study examines the effects of five common artificial sweeteners-Acesulfame K, Rebaudioside A, Saccharin, Sucralose, and Xylitol-on gut microbiome diversity using minibioreactor arrays. Fecal samples from three healthy individuals were used to inoculate bioreactors that were subsequently supplemented with each sweetener. Over 35 days, microbial diversity and network composition were analyzed. Results revealed synthetic sweeteners like Sucralose and Saccharin significantly reduced microbial diversity, while non-synthetic sweeteners, particularly Rebaudioside A and Xylitol, were less disruptive. Acesulfame K increased diversity but disrupted network structure, suggesting potential long-term negative impacts on microbiome resilience. Sucralose enriched pathogenic families such as Enterobacteriaceae, whereas natural sweeteners promoted beneficial taxa like Lachnospiraceae. Random Matrix Theory (RMT) based analysis highlighted distinct microbial interaction patterns, with Acesulfame K causing persistent structural changes. Findings suggest non-synthetic sweeteners may be more favorable for gut health than synthetic ones, emphasizing cautious use, particularly for those with gut health concerns. This study enhances our understanding of artificial sweeteners' effects on the gut microbiome, highlighting the need for further research into their long-term health implications.

Kelp (Laminaria japonica) is renowned for its rich content of flavor-enhancing amino acids and nucleotides; however, approximately 40% of kelp, including the thin edges and root areas, is discarded during its processing due to its inferior taste. To recycle these kelp byproducts, we have cultivated a functional microbial consortium through continuous enrichment. Analysis via 16S rRNA sequencing has shown that during the three fed-batch fermentation stages of kelp waste, the microbial community was predominantly and consistently composed of three phyla: Halanaerobiaeota, Bacteroidota, and Proteobacteria. At the genus level, Halanaerobium emerged as the dominant player, exhibiting a trend of initial increase followed by a decline throughout the fermentation process. Enzymes such as alginate lyases and both acidic and neutral proteases were found to play crucial roles in the degradation of kelp residues into sauces. Notably, electronic tongue analysis revealed that the fermented kelp sauce demonstrated strong umami characteristics. Furthermore, four novel umami peptides, EIL, STEV, GEEE, and SMEAVEA, from kelp were identified for the first time, with their umami effect largely attributed to strong hydrogen bond interactions with the T1R1-T1R3 umami receptors. In conclusion, this study proposed a sustainable method for kelp by-product utilization, with implications for other seaweed processing.

Tick-borne diseases (TBDs) pose a significant public health challenge, as their incidence is increasing due to the effects of climate change and ecological shifts. The interplay between tick-borne pathogens and the host microbiome is an emerging area of research that may elucidate the mechanisms underlying disease susceptibility and severity. To investigate the diversity of microbial communities in ticks infected with vertebrate pathogens, we analyzed the microbiomes of 142 tick specimens. The presence of Rickettsia and Anaplasma pathogens in individual samples was detected through PCR. Our study aimed to elucidate the composition and variation of microbial communities associated with three tick species, which are known vectors for various pathogens affecting both wildlife and humans. We employed high-throughput sequencing techniques to characterize the microbial diversity and conducted statistical analyses to assess the correlation between the presence of specific pathogens and the overall microbial community structure. Pathogen screening revealed an overall positivity rate of 51.9% for Anaplasma and 44.6% for spotted fever group rickettsia (SFGR). Among the three tick species (Dermacentor silvarum, Haemaphysalis concinna, and Haemaphysalis japonica) analyzed, D. silvarum (the predominant species) exhibited the highest pathogen prevalence. The results indicate significant variation in microbial diversity between tick samples, with the presence of Anaplasma and SFGR associated with distinct changes in the microbial community composition. These findings underscore the complex interactions between ticks and their microbial inhabitants, enriching our understanding of tick-borne diseases.

Mounting evidence suggests that sustained microbial dysbiosis is associated with the development of multiple cancers, while the species-level bacterial taxa and metabolic dysfunction of oral microbiome in patients with head and neck squamous cell carcinoma (HNSCC) remains unclear. In this cross-sectional study, comprehensive metagenomic and 16S rRNA amplicon sequencing analyses of oral swab samples from 172 patients were performed. Unsupervised clustering algorithms of relative microbial abundance profiles revealed three distinctive microbiome clusters. Based on the metagenomic and 16S rRNA amplicon sequencing data, machine learning-based methods were used to construct the HNSCC diagnostic classifier, which exhibited high area under the curve values of 0.78-0.89. Our study provided the first exhaustive metagenomic and 16S rRNA amplicon sequencing analyses to date, revealing that microbial-metabolic dysbiosis is a potential risk factor for HNSCC progression and therefore providing a robust theoretical basis for potential diagnostic and therapeutic strategies for HNSCC patients.

Soil bacterial and fungal communities play fundamental roles in biogeochemical cycles and ecosystem stability. Urbanization alters soil properties and microbial habitats, driving shifts in community composition, yet the divergent responses of bacteria and fungi and their ecological consequences remain inadequately understood. To elucidate these differential responses, we investigated soil bacterial and fungal communities along an urbanization gradient, ranging from undisturbed reference forests to urban parks, across three distinct climatic regions. To capture different disturbance intensities, urban parks were classified by tree age into old parks (>60-year-old trees) and young parks (10-20-year-old trees). Climate had a strong influence on soil microbiota, yet urbanization still significantly altered both bacterial and fungal communities in all regions. Urban disturbances homogenized soil microbial communities: average similarity among bacterial communities increased from ∼79 % in forests to ∼85 % in young urban parks, indicating substantial homogenization, whereas fungal communities showed little homogenization. Urbanization also homogenized microbial functional traits, with a greater reduction in trait dissimilarity for bacteria than for fungi. Bacterial communities exhibited high adjustability to urban conditions, dominated by generalist taxa (∼90 %), whereas fungal communities consisted mostly of specialists (∼83 %). Despite these asynchronous responses-bacteria adjusting and homogenizing more than fungi-overlapping functional traits between bacteria and fungi help maintain functional resilience in urban ecosystems.

The assembly of the rhizosphere microbiome determines its functionality for plant fitness. Although the interactions between arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) play important roles in plant growth and disease resistance, research on the division of labor among the members of the symbionts formed among plants, AMF, and PGPR, as well as the flow of carbon sources, is still insufficient. To address the above questions, we used soybean (Glycine max), Funneliformis mosseae, and Pseudomonas putida KT2440 as research subjects to establish rhizobiont interactions and to elucidate the signal exchange and division of labor among these components. Funneliformis mosseae can attract P. putida KT2440 by secreting cysteine as a signaling molecule and can promote the colonization of P. putida KT2440 in the soybean rhizosphere. Colonized P. putida KT2440 can stimulate the l-tryptophan secretion of the host plant and can lead to the upregulation of genes involved in converting methyl-indole-3-acetic acid (Me-IAA) into IAA in response to l-tryptophan stimulation. Collectively, we decipher the tripartite mechanism of rhizosphere microbial community assembly via cross-kingdom interactions.

Global warming is expected to significantly impact the soil fungal and bacterial microbiomes, yet the predominant ecological response of microbial taxa-whether an increase, decrease, or no change-remains unclear. It is also unknown whether microbial taxa from different evolutionary lineages exhibit common patterns and what factors drive these changes. Here, we analyzed three mid-term (> 5 years) warming experiments across contrasting dryland and temperate-boreal ecosystems, encompassing over 500 topsoil samples collected across multiple time points. We found that warming altered the relative abundance of microbial taxa, with both increases and decreases over time. For instance, the relative abundance of bacterial and fungal taxa responding to warming (increase or decrease) accounted for 35.9% and 42.9% in the dryland ecosystem, respectively. Notably, taxa within the same phylum exhibited divergent responses to warming. These ecological shifts were linked to factors such as photosynthetic cover and fungal lifestyle, both of which influence soil functions. Overall, our findings indicate that soil warming can reshape a significant fraction of the microbial community across ecosystems, potentially driving changes in soil functions.

The effect of founders (the potential influence of initially colonizing species on the composition, functionality, and stability of communities) plays a crucial role in community assembly; many experimental studies on priority effects or artificially assembled species have suggested the existence of this effect, but direct experimental evidence at the community level remains limited. This study used sterilized and nonsterilized paocai soup (a traditional Chinese fermented vegetable soup) from the same source to simulate initial environments with and without founders. These were placed in beakers with varying opening sizes on an open rooftop for 15 days to explore the impact of founders on community assembly under different dispersal intensities. The 16S rRNA sequencing analysis revealed that communities with founders exhibited lower species richness (320) compared to communities without founders (645). Additionally, communities with founders showed reduced species turnover and richness variation (53.7%) compared to communities without founders (60.9%). Furthermore, the average variability degree (AVD) in communities with founders (0.446 ± 0.044) was significantly lower than in communities without founders (0.927 ± 0.466), indicating higher community stability. Finally, deterministic processes dominated communities with founders (with heterogeneous selection contributing 70%), whereas stochastic processes primarily governed communities without founders (homogeneous dispersal 10% and undominated processes 70%). These findings demonstrate that founders presence reduces dispersal impacts, decreases community diversity, enhances stability, and deterministic processes. The effect of founders fundamentally shapes the direction of community assembly. This study helps further understanding of how founders influence biodiversity maintenance and community assembly processes.

Passive treatment using microorganisms is a promising method for removing toxic metals from acid mine drainage (AMD). To provide a better understanding of the compositions of mine microbial communities and their relationship with pH and metal concentrations in mine water, we analyzed both physicochemical data and 16S rRNA gene amplicon sequences from 40 untreated drainages from 30 abandoned mines across all regions of Japan. In the 40 mine drainages, higher concentrations of metals (iron, lead, cadmium, copper, and manganese) were detected in mine drainages with acidic pH (< 4.5; 24 samples) than in those with circumneutral pH (> 6.0; 16 samples), except for arsenic. Comparison of principal coordinate analysis scatter plots between mine drainages of acidic and circumneutral pH revealed a relatively clear separation of microbial compositions except for one mine drainage sample. In the 24 AMDs, the dominant operational taxonomic units (OTUs) found at relative abundance levels >3 % were generally one of three related to Caballeronia arationis, Ferrovum myxofaciens, or Gallionella capsiferriformans, except for two mine drainage samples. Although the microbial communities of the 40 mine drainages were obtained from a single sampling time (triplicate analysis), they may reflect the typical microbial communities of each mine drainage, because analysis of drainage samples taken from the same sampling point over three different seasons (summer, autumn, and winter) revealed similar communities regardless of the season. Among mine drainages analyzed in this study, the OTU showing 96.8 % identity to C. arationis was the most prevalent bacterial OTU, which was found in 23 drainages (the top OTU in 15 mine drainages) with >3 % relative abundance.

Bacteria are the major component of poultry gastrointestinal tract (GIT) microbiota and play an important role in host health, nutrition, physiology regulation, intestinal development, and growth. Bacterial community profiling based on the 16S ribosomal RNA (rRNA) gene amplicon sequencing approach has become the most popular method to determine the taxonomic composition and diversity of the poultry microbiota. The 16S rRNA gene profiling involves numerous steps, including sample collection and storage, DNA isolation, 16S rRNA gene primer selection, Polymerase Chain Reaction (PCR), library preparation, sequencing, raw sequencing reads processing, taxonomic classification, α- and β-diversity calculations, and statistical analysis. However, there is currently no standardized protocol for 16S rRNA gene analysis profiling and data deposition for poultry microbiota studies. Variations in DNA storage and isolation, primer design, and library preparation are known to introduce biases, affecting community structure and microbial population analysis leading to over- or under-representation of individual bacteria within communities. Additionally, different sequencing platforms, bioinformatics pipeline, and taxonomic database selection can affect classification and determination of the microbial taxa. Moreover, detailed experimental design and DNA processing and sequencing methods are often inadequately reported in poultry 16S rRNA gene sequencing studies. Consequently, poultry microbiota results are often difficult to reproduce and compare across studies. This manuscript reviews current practices in profiling poultry microbiota using 16S rRNA gene amplicon sequencing and proposes the development of guidelines for protocol for 16S rRNA gene sequencing that spans from sample collection through data deposition to achieve more reliable data comparisons across studies and allow for comparisons and/or interpretations of poultry studies conducted worldwide.

Antibiotic resistance has become a global health concern, driving the need for sustainable alternatives in animal husbandry. This study explores the potential of natural feed additives as a viable solution to enhance poultry growth and health while reducing reliance on antibiotics. Chinese herbal medicines and probiotics have been widely studied as green, healthy, and safe antibiotic alternatives in livestock and poultry production. A total of 120 chickens were randomly divided into four groups: a control group and three treatment groups supplemented with 1% Pulsatilla chinensis powder, 3% fresh Acer truncatum, or 1% Clostridium butyricum. The results showed that Pulsatilla chinensis powder significantly increased gamma-glutamylcysteine (p < 0.05), UDP-N-acetylglucosamine (p < 0.05), tyramine (p < 0.01), and leucine (p < 0.05). Acer truncatum notably altered cecal metabolites, including L-tyrosine (p < 0.05), α-ketoisovaleric acid (p < 0.01), myristoleic acid (p < 0.01), glutathione (p < 0.05), and PGA1 (p < 0.05). Clostridium butyricum modified cecal metabolites such as L-glutamine (p < 0.05), riboflavin (p < 0.05), L-Carnitine (p < 0.05), ergocalciferol (p < 0.01), and α-tocotrienol (p < 0.05).

Antibiotic resistance poses a significant threat to human health, and wastewater treatment plants (WWTPs) are important reservoirs of antibiotic resistance genes (ARGs). Here, we analyze the antibiotic resistomes of 226 activated sludge samples from 142 WWTPs across six continents, using a consistent pipeline for sample collection, DNA sequencing and analysis. We find that ARGs are diverse and similarly abundant, with a core set of 20 ARGs present in all WWTPs. ARG composition differs across continents and is distinct from that of the human gut and the oceans. ARG composition strongly correlates with bacterial taxonomic composition, with Chloroflexi, Acidobacteria and Deltaproteobacteria being the major carriers. ARG abundance positively correlates with the presence of mobile genetic elements, and 57% of the 1112 recovered high-quality genomes possess putatively mobile ARGs. Resistome variations appear to be driven by a complex combination of stochastic processes and deterministic abiotic factors.

Slow-onset neurodegenerative disease in a low-expresser 2N4R P301L transgenic (Tg) mouse model is marked by neuroinflammation and by differing patterns of CNS deposition and accumulation of tau conformers, with such heterogeneities present even within inbred backgrounds. Gut microbial genotypes were notably divergent within C57BL6/Tac or 129SvEv/Tac congenic (Cg) sublines of TgTauP301L mice, and these sublines differed when challenged with antibiotic treatment and fecal microbial transplantation. Whereas aged, transplanted Cg 129SvEv/Tac TgTauP301L mice had neuroanatomical deposition of tau resembling controls, transplanted Cg C57BL6/Tac TgTauP301L mice had different proportions of rostral versus caudal tau accumulation (p = 0.0001). These data indicate the potential for environmental influences on tau neuropathology in this model. Furthermore, Cg C57BL6/Tac TgTauP301L cohorts differed from 129SvEv/Tac counterparts by showing 28% versus 9% net intercurrent loss (p = 0.0027). While the origin of this phenomenon is not established, it offers a parallel to differing patterns of frailty observed in C57BL6 versus 129 SvEv Tg mice expressing the 695 amino acid isoform of human amyloid precursor protein. We infer that generalized responses to protein aggregation might account for similar reductions in viability even when expressing different human proteins in the same inbred strain background.

The persistence and specificity of fish host-microbial interaction during evolution is an important part of exploring the host-microbial symbiosis mechanism. However, it remains unclear how the environmental and host factors shape fish host-microbe symbiotic relationships in subtropical rivers with complex natural environments. Freshwater fish are important consumers in rivers and lakes and are considered keystone species in maintaining the stability of food webs there. In this study, patterns and mechanisms shaping gut microbiota community in 42 fish species from the Pearl River, in the subtropical zone of China, were investigated. The results showed that fish host specificity is a key driver of gut microbiota evolution and diversification. Different taxonomic levels of the host showed different degrees of contribution to gut microbiota variation. Geographical location and habitat type were the next most important factors in shaping gut microbiota across the 42 fishes, followed by diet and gut trait. Our results emphasized the contribution of stochastic processes (drift and homogenizing dispersal) in the gut microbial community assembly of freshwater fishes in the middle and lower reaches of the Pearl River. Phylosymbiosis is evident at both global and local levels, which are jointly shaped by complex factors including ecological or host physiological filtration and evolutionary processes. The core microbiota showed co-evolutionary relationships of varying degrees with different taxonomic groups. We speculate that host genetic isolation or habitat variation facilitates the heterogeneous selection (deterministic process), which occurs and results in different host-core bacterium specificity.

Freshwater fish are regarded as the dominant consumers in rivers and lakes. Due to their diverse feeding modes, fish significantly enhance the trophic link and nutrient recycling/retention in aquatic habitats. For this, they are often considered keystone species in maintaining the stability of food webs in rivers and lakes. A significant part of fish nutrition is essentially mediated by their gut microbiota, which can enhance fish tolerance to fluctuations in external resources and improve the efficiency of nutrients extracted from various food sources. As gut bacterial symbionts have a profound impact on the nutrition and development of their hosts, as well as their overall fitness, it is critical to answer the question of how hosts maintain these benefits by procuring or inheriting these vital symbionts, which is still largely unanswered, especially for freshwater fish. Our study provides new insights into the co-evolutionary relationship between wild fish and their symbiotic microbiome, the hidden diversity of gut microbiome, and the ecological adaptation potential of wild freshwater fish.

Cyanobacterial harmful algal blooms pose significant threats to global water supplies, ecosystems, and economies. Among the harmful cyanobacteria, Planktothrix, a resilient and toxin-producing filamentous cyanobacterium, has garnered increasing attention. However, an understanding of the entire microbiome, particularly the phycosphere surrounding Planktothrix blooms, remains largely unexplored. To the best of our knowledge, this is the first comprehensive study combining 16S rDNA and fungal internal transcribed spacer amplicon sequencing and shotgun metagenomics to elucidate Planktothrix bloom microbiomes and identify potential microbial or functional biomarkers for CyanoHABs. Our observations revealed that a summer bloom in Grand Lake St. Marys was initiated with Dolichospermum and then shifted to Planktothrix dominance. This transition was associated with nitrogen metabolism genes, suggesting that nitrogen plays a key role in bloom persistence through interactions among nitrogen-fixing bacteria, ammonia-oxidizing archaea, anammox bacteria, and denitrifiers. Additionally, metagenomic data revealed a strong positive correlation of toxin concentration with carbohydrate-nitrogen-sulfur-fatty acid associated metabolic pathways and a strong negative correlation with pollutant degradation pathways. Intriguingly, diazotrophic methane-related microbes were detected, which opens discussion on potential symbiosis that couples nitrogen and carbon metabolism. Toxin-degrading bacteria, such as Polynucleobacter and Acidovorax, were positively correlated with fungi like Vishniacozyma, proposing their cooperative roles during bloom events. Notably, Rhodobacter, a photosynthetic purple non-sulfur bacterium, showed strong negative correlations with both Planktothrix and the toxin-producing gene mcyE, positioning it as a promising biomarker for early bloom detection. Overall, this study advances the understanding of Planktothrix-dominated bloom ecology and highlights microbial signatures for proactive CyanoHAB management in freshwater systems.

Agarwood is a valuable resinous aromatic substance known to have healing properties. Only plants in the Thymelaeace family, specifically the genera Aquilaria and Gyrinops, produce it to defend themselves from insect, bacterial, and fungal attacks. Over-harvesting of natural agarwood has given rise to different artificial agarwood induction techniques. However, the contribution of endophytic microorganisms in this process remains largely unknown. Herein, we employed fire drills and fire drill + brine treatments and investigated their impact on metabolite constituents and endophytes over time. Gas chromatography-mass spectrometry was used to examine the metabolites, and 16 S and ITS amplicon sequencing were applied to check for endophytes. Metabolites from each treatment were related to 16 S and ITS amplicon sequencing results from different times to find out what effect the treatments had and what role endophytes played in making agarwood. Fire drills with 50-80 ml of 0.4 mmol brine treatment resulted in the highest production of essential oil from agarwood, whereas fire drills with 50-80 ml of 4.0 mmol brine treatment produced the highest number of metabolites. Agarwood fragrant compounds such as chromones, sesquiterpenes, and agarotetrol were prominent among the differentially expressed metabolites and were positively associated with the abundance of bacterial endophytes Acidobacteriota, Chlamydiae, Bacteroidota, and Actinobacteria; and the fungal endophytes Rozellomycota, Basidiomycota, Aphelidiomycota, and Mortierellomycota. Saprotrophs and pathogens were prevalent in the treatment groups; however, with time, their proportion declined as Symbiotroph's proportion inclined, indicating successive roles of these fungi in agarwood induction and propagation. Among them, Acidobacteriota, Chlamydiae, Bacteroidota, and Actinobacteria bacterial; and Rozellomycota, Basidiomycota, Aphelidiomycota, and Mortierellomycota fungal endophytes are correlated with enhanced levels of essential agarwood fragrances such as Chromones, Sesquiterpenes, and Agarospirol. Our results show how important bacterial and fungal endophytes are for making agarwood. They also show how these endophytes change when interacting with the host plant after a fire drill and a brine treatment. A moderate brine concentration (0.4 mmol) following a fire drill can thus be employed as a sustainable agarwood production practice.

This study investigates the influence of three regulators of human homeostasis-intestinal microbiota, immune profile, and circulating metabolites-on stroke severity. We conducted a study involving 33 patients with mild/moderate stroke (MS) and 32 with severe stroke (SS), all assessed during the acute phase (first 24 h). The analysis focused on microbiota composition (45 patients), serum metabolomics and inflammatory markers (20 patients). The patients with SS exhibited more pronounced insulin resistance associated with increased levels of branched-chain amino acids and their metabolites. SS patients showed an increase in inflammatory cytokines IL-6 and TNF-α, and surprisingly an increase in IL-10 and butyrate which are anti-inflammatory. SS patients also displayed a distinct microbiota profile, with statistically significant differences in β-diversity compared to the MS group, notably a higher prevalence of Pseudomonadota (formerly Proteobacteria). In summary, our data indicate that patients with SS, compared to those with MS, are characterized by a more inflammatory and insulin-resistant state, associated with three key regulators: microbiota, metabolites, and interleukins. These findings provide new insights into the regulatory components of the gut-brain axis, which could be developed into cost-effective and widely accessible therapies for SS.

The gut microbiome is recognized as a critical factor in advancing precision nutrition and medicine for health and in developing dietary recommendations and targeted therapies for gastrointestinal (GI) health and diseases. However, conventional sampling methods, such as fecal analysis and colonoscopy, often fail to capture microbial information from specific regions of the GI tract or require invasive procedures, thereby limiting accuracy and clinical utility. As a non-invasive alternative, passive sampling capsules have been developed for site-specific microbiome analysis by employing pH-sensitive enteric coatings that delay sampling until the capsule reaches the targeted intestinal region. Although this approach has been successful in the small intestine, colonic sampling remains challenging due to the high interpersonal variability in intestinal pH, which makes it difficult to rely solely on a pH-triggering mechanism. To overcome this challenge, a dual bacterially and pH triggered polymeric enteric coating was created by blending lactulose and N,N-dimethylaminoethyl methacrylate, enabling complete dissolution within the colonic region. Through systematic characterization of multiple polymer blend compositions using Fourier Transform Infrared Spectroscopy, Thermogravimetric Analysis, and Differential Scanning Calorimetry, an optimized design was identified that provides both suitable physical integrity and rapid (∼2 h) degradation in the presence of colonic bacteria, across a pH range of 5 to 8. The optimized blend was subsequently applied as a double-layer enteric coating on a sampling capsule, enabling the dissolution of the outer layer in the small intestine and complete dissolution of the inner layer in the colon. In-vitro and in-vivo pig model studies were conducted to validate the capsule's sampling performance and to ensure the preservation of the microbial environment. Furthermore, 16S rRNA sequencing revealed a taxonomic similarity between samples collected by the capsule and the colonic microbiome (residing between the ileum and fecal matter). Overall, this technology provides an effective approach to targeted microbial sampling and may pave the way for more comprehensive colonic microbiome analyses and improved diagnostic capabilities for GI diseases. STATEMENT OF SIGNIFICANCE: Precise monitoring of the gut microbiome is vital for understanding health and disease, yet current sampling techniques often lack precision or require invasive procedures. Our work introduces a novel, non-invasive capsule that targets the colon using a dual-trigger polymer system activated by both pH and colonic bacteria. This design enables localized sampling of gut microbiota, overcoming the limitations of fecal analysis, endoscopy, and earlier pH-triggered capsule designs. By capturing microbial communities directly from the colon, our technology provides deeper insights into colonic health and conditions such as inflammatory bowel disease and colorectal cancer. This breakthrough represents a significant advancement in precision nutrition and medicine for human health, and advanced diagnostics and targeted therapies to support dietary guidance, clinical practice and biomedical research.

Antibiotics in early life can promote adiposity via interactions with the gut microbiota, but they represent only one possible route of antimicrobial exposure. Dietary preservatives exhibit antimicrobial activity, contain chemical structures accessible to microbial enzymes, and may therefore similarly disrupt microbial contributions to metabolic development.

Here, we test the hypothesis that preservatives alter the gut microbiota with consequences for host metabolism.

We screened common dietary preservatives for in vitro and ex vivo activity against a panel of gut bacteria and whole fecal microbial communities, profiling outcomes via optical density measurements and 16S rDNA sequencing. We then exposed adult mice to diet-relevant doses of 4 preservatives [acetic acid, butylated hydroxyanisole (BHA), ethylenediaminetetraacetic acid (EDTA), and sodium sulfite] or ampicillin (positive control) for 7 d. Finally, we examined the effects of early-life EDTA and low-dose ampicillin exposure starting in gestation in a mouse model, tracking differences in growth and metabolism.

Preservatives altered microbial growth and community structure in vitro, ex vivo, and in vivo, but with compound-specific changes in gut microbiota composition distinct from those of ampicillin. Long-term EDTA exposure from gestation reduced calorie absorption and cecal acetate, resulting in 32% lower gains in body fat in females for a given food intake (±12% standard error, linear mixed effects model). Females exposed to ampicillin exhibited a similar 42% (±11%) reduction in food-adjusted gains in adiposity, along with larger brains and smaller livers. By contrast, among males, EDTA had no detectable metabolic impacts whereas ampicillin exposure increased food-adjusted gain in body fat by 108% (±12%).

Our results highlight the potential for everyday doses of common preservatives to affect the gut microbiota and impact metabolism differently in males and females. Thus, despite their generally regarded as safe designation, preservatives could have unintended consequences for consumer health via their impact on the gut microbiota.

Studies on human gut microbiota have recently highlighted a significant decline in bacterial diversity associated with urbanization, driven by shifts toward processed diets, increased antibiotic usage, and improved sanitation practices. This phenomenon has been largely overlooked in the Colombian Amazon, despite rapid urbanization in the region. In this study, we investigate the composition of gut bacterial microbiota and intestinal protozoa and soil-transmitted helminths (STHs) in both urban and rural areas of Leticia, which is located in the southern Colombian Amazon. Despite their geographic proximity, the urban population is predominantly non-indigenous, while indigenous communities mostly inhabit the rural area, resulting in notable lifestyle differences between the two settings. Our analyses reveal a reduction in bacterial families linked to non-processed diets, such as Lachnospiraceae, Spirochaetaceae, and Succinivibrionaceae, in the urban environment compared to their rural counterparts. Interestingly, Prevotellaceae, typically associated with non-processed food consumption, shows a significantly higher abundance in urban Leticia. STH infections were primarily detected in rural Leticia, while intestinal protozoa were ubiquitous in both rural and urban areas. Both types of parasites were associated with higher gut bacterial richness and diversity. Additionally, microbial metabolic prediction analysis indicated differences in pathways related to unsaturated fatty acid production and aerobic respiration between rural and urban bacterial microbiomes. This finding suggests a tendency towards dysbiosis in the urban microbiota, possibly increasing susceptibility to non-communicable chronic diseases. These findings provide new insights into the impact of urbanization on gut microbiota dynamics in the Amazonian context and underscore the need for further research to elucidate any associated health outcomes.

The Zoige uranium mine is situated in the harsh, cold northern region of Sichuan, characterized by its high altitude and fragile ecosystem. Uncovering the organisms that thrive in such extreme climates, particularly microorganisms, is of paramount importance for advancing bioremediation efforts. Herein, the potential functional microbiota for uranium sequestration in Zoige uranium mine soil was explored using high-throughput sequencing combined with bioinformatics analysis. Analysis of the physicochemical properties of soils showed that the concentration of uranium ranged from 35.20 to 40.62 µg·g-1 around the uranium mine. Bacterial communities differed significantly in soils around the Zoige uranium mine, with the most abundant phyla being Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Gemmatimonadota, Verrucomicrobia, and Firmicutes. Notably, Actinobacteria was considered a biomarker for distinguishing soils with high uranium by linear discriminant analysis effect size. Meanwhile, the correlation analysis demonstrated that Firmicutes and Cyanobacteria were significantly and positively associated with uranium in soil samples, with the correlation coefficients being 0.8601 and 0.7832, respectively. Furthermore, the phylogenetic investigation of communities by reconstruction of unobserved states analysis revealed that the bacterial microbiota was mainly enriched in biosynthesis function in these soils. Interestingly, the abundance of functional genes involved in amino acid biosynthesis increased whereas that related to fatty acid biosynthesis decreased with an increase in uranium content. Taken together, Actinobacteria, Firmicutes, and Cyanobacteria were the potential functional microbiota for uranium sequestration via amino acid and fatty acid biosynthesis pathways in Zoige uranium mine soil. These findings are conducive to obtaining functional strains for developing microbial remediation technologies for uranium contamination.IMPORTANCEBased on the significance of the Zoige uranium mine and its unique ecological environment, this study emphasizes the necessity of in situ bioremediation. Herein, the potential functional microbiota for uranium sequestration in Zoige uranium mine soil was explored using high-throughput sequencing and bioinformatics analysis. Actinobacteria, Firmicutes, and Cyanobacteria were the potential functional microbiota in Zoige uranium mine soils. These microbes interacted and tolerated uranium via amino acid and fatty acid biosynthesis pathways. These findings provide insights into the functional microbiota of uranium sequestration, which are conducive to developing microbial resources and bioremediation technology for treating uranium contamination.

Sorghum bicolor, an important global crop, adapted to thrive in hotter and drier conditions than maize or rice, has deep roots that interact with a stratified soil microbiome that plays a crucial role in plant health, growth, and carbon storage. Microbiome studies on agricultural soils, particularly fields growing S. bicolor, have been mostly limited to surface soils (<30 cm). Here we investigated the abiotic factors of soil properties, field location, depth, and the biotic factors of sorghum type across 38 genotypes of the soil microbiome. Utilizing 16S rRNA gene amplicon sequencing, our analysis reveals significant changes in microbial composition and decreasing diversity at increasing soil depths within S. bicolor fields, regardless of genotype or field, with microbial richness and diversity declining to a minimum at the 60-90 cm layer and increasing beyond the 90 cm depth. Notably, specific microbial families, such as Thermogemmatisporaceae and an unclassified family within the ABS-6 order, were enriched in deeper soil layers beyond 30 cm. These findings highlight the importance of soil depth in agricultural soil microbiome studies.IMPORTANCESorghum bicolor is a valuable model for studying the microbiome in deep soils, which is crucial for enhancing carbon sequestration in agricultural systems. As we look to crops with deeper roots for improved carbon storage, it is essential to move beyond the traditional focus on surface soils in agricultural settings. This study shifts that focus by investigating microbial dynamics at greater soil depths, revealing significant changes in microbial composition and diversity with increasing depth, revealing the critical role of deep-soil microbiomes in nutrient cycling and carbon sequestration in agricultural fields with the deep-rooted crop S. bicolor. By exploring these processes beyond surface soils, this research supports the development of sustainable agricultural practices that can better harness the potential of deep-rooted crops for long-term carbon storage.