Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun. 2019;10:5029. [PMID: 31695033 PMCID: PMC6834636 DOI: 10.1038/s41467-019-13036-1]

Anoxic desulfurization of biogas rich in hydrogen sulfide through feedback control using biotrickling filters: Operational limits and multi-omics analysis

Biodesulfurization is crucial for sustainable biogas purification from hydrogen sulfide (H2S). This study investigates the operational limits of anoxic biotrickling filters (BTFs) for treating biogas with high H2S concentrations (up to 20,000 ppmv) using nitrite, along with simulated interruptions in H2S supply. The BTF achieved a maximum elimination capacity of 312 g S-H2S m-3 h-1 with an H2S removal efficiency of 98 % at an empty bed residence time of 284 s. A proportional-integral-derivative (PID) feedback control system was successfully employed to maintain an H2S outlet concentration close to the requisite setpoint (100 and 500 ppmv) by adjusting the nitrite flow rate, thereby minimizing its accumulation. Continuous nitrite feeding after interruptions in H2S supply was essential to avoid H2S release due to sulfate-reducing bacteria. Multi-omics analyses, combining metagenomics and proteomics, revealed Sulfurimonas as the dominant sulfur-oxidizing bacteria, which downregulates most enzyme genes involved in nitrogen and sulfur metabolism in response to substrate starvation. These findings underscore the resilience of BTFs under extreme conditions and the value of multi-omics approaches in understanding microbial population dynamics, positioning BTFs as a robust solution for large-scale biogas purification.

Taxonomic reassessment of genomes from a divergent population of Streptococcus suis by average nucleotide identity analysis

Streptococcus spp., including the emerging zoonotic pathogen S. suis, represent a dominant bacterial population in the porcine nasopharynx. Species identification within the Streptococcus genus remains challenging and frequently ambiguous, resulting in indistinct species boundaries. By employing comparative genomic analyses, a previous study categorized S. suis into a central population and divergent lineages, based on the single nucleotide polymorphisms (SNPs) within core genes and the presence or absence of accessory genes, indicating evolutionary divergence. The divergent lineages were designated as the "out population" in this study for clarity. The 16S rRNA gene sequences of seven putative novel Streptococcus strains isolated from the throats of healthy pigs in China exhibited 100 % similarity to that of the 684_17B strain of S. suis, which clustered in the out population. This study established a threshold average nucleotide identity (ANI) value of 93.17 % for the identification of authentic S. suis. All the 645 genomes from the out population fell below this threshold, indicating that they did not belong to S. suis. Further taxonomic assessment of the 645 genomes from the out population revealed 18 clusters based on pairwise ANI comparisons, using a 92.33 % threshold, determined by pairwise ANI comparisons among the 2422 genomes from the central population of S. suis. These clusters were identified as 12 novel Streptococcus spp. (Streptococcus sp. nov-1-12) and six known Streptococcus spp. by ANI comparisons with type or reference genomes of 98 known Streptococcus spp. The study provides a useful framework for the identification of authentic S. suis and the determination of Streptococcus sp. nov.

Nanoplastic exposure affects the intestinal microbiota of adult Drosophila flies

Micro- and nanoplastics (MNPLs) are emerging environmental pollutants that have garnered significant attention over the past few decades due to their detrimental effects on human health through various exposure pathways. This study investigates the impact of MNPLs on gut microbiota, utilizing Drosophila melanogaster as a model organism. Drosophila was selected for its microbiota's similarities to humans and its established role as an accessible and well-characterized model system. To analyze microbiota, full-length 16S rRNA gene sequencing was performed using the Nanopore sequencing platform, enabling comprehensive profiling of the microbial populations present in the samples. As models of MNPLs, two commercial polystyrene nanoplastics (PS-NPLs, 61.20 and 415.22 nm) and one lab-made polylactic acid nanoplastic (PLA-NPLs, 463.90 nm) were selected. As a positive control, zinc oxide nanoparticles (ZnO-NPs) were used. The observed findings revealed that exposure to MNPLs induced notable alterations in gut microbiota, including a reduction in bacterial abundance and shifts in species composition. These results suggest that MNPLs exposure can lead to microbial dysbiosis and potential gut health disruptions through its interaction, either with the gut epithelial barrier or directly with the resident microorganisms.

Full-length 16S rRNA-based exploration of body site-specific bacterial signatures for origin determination and individual identification

When the available human-derived information at a crime scene is limited, it poses challenges in determining the origin of the biological materials and identifying their donors. In this context, microorganisms have gradually emerged as a valuable complementary tool. Nowadays, the application of third-generation sequencing technology for full-length 16S rRNA sequencing to explore the specific bacterial biomarkers in various biological materials holds significant research and practical value. In this study, we performed full-length 16S rRNA gene sequencing on sterile swabs from palmar skin, oral mucosa, and nasal cavity using the PacBio single-molecule real-time sequencing (SMRT) platform. Alongside identifying specific bacterial biomarkers for these biological materials from different body sites, the study also preliminarily explored the specific bacterial taxa in 19 individuals at the phylum, genus, and species levels. The results showed that the palmar skin bacteria primarily consist of Cutibacterium, Staphylococcus, and Streptococcus, the oral mucosal bacteria are dominated by Streptococcus, Neisseria, and Haemophilus, while the dominant bacteria in nasal cavity are Staphylococcus and Cutibacterium. Beta diversity analysis revealed significant differences in the bacterial community composition across the three origins of biological materials. Furthermore, classification models based on the bacterial species were constructed using the Random Forest, XGBoost, and KNN algorithms. The results showed that both Random Forest and XGBoost models achieved an accuracy of 97 %, significantly outperforming the KNN model (79 %). The prediction accuracy at the OTU level was comparable to that at the species level. In addition, bacterial community differences between individuals were observed at both the genus and species levels. Overall, this study further explores the potential of classification prediction methods based on bacterial features for distinguishing the body site origins of different biological materials and enabling individual traceability, thereby providing valuable data to support the application of microbiological techniques in forensic practice.

Characterization of the vaginal microbiota in women of childbearing age with different Nugent scores

The present study investigated the richness and diversity of vaginal microbiota among a cohort of 60 childbearing-age women. The samples were classified into three groups: healthy control (HC), bacterial vaginosis (BV), and BV intermediate (BVI). The number of Operational Taxonomic Units (OTUs) per sample ranged from 50 to 212, with three groups having 469 (HC), 482 (BVI), and 456 (BV) OTUs. Alpha diversity analysis (p < 0.05) showed that HC had lower diversity than the BV and BVI groups, whereas richness indices did not differ significantly across the groups. Beta diversity analysis (p < 0.05) indicated significant differences in species composition between groups, and specific biomarker taxa were identified for each group. Compared to HC, the BVI and BV groups showed an increase in Actinobacteria and Bacteroidetes, and a relative decrease in Bacillota. Overall, the vaginal microbiota of healthy women of childbearing age was in a state of absolute predominance of Lactobacillus, dominated by Lactobacillus crispatus or Lactobacillus iners alone, or both equally, and coexisted with a wide range of bacteria. However, patients in BVI group, Lactobacillus is reduced, dominated by L. iners, with an increased proportion of anaerobic bacteria (e.g., Gardnerella). While BV patients have predominantly Gardnerella with commensal bacteria, such as Prevotella and Fannyhessea, which collectively contribute to the development of BV. This study's findings provide insight into the dynamics of vaginal microbiota in women of childbearing age.

Understanding the implicit effects of 16S rRNA gene databases on microbial bioindicator studies

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.

Microbiome-based surveillance of zoonotic tick-borne pathogens from urban wild boars in Barcelona, 2022-2023

Incursions of wild animals into urban areas amplify the potential risks of zoonotic disease transmission by increasing contact between humans and animal reservoirs. Monitoring the presence of pathogens in these animals is crucial for assessing zoonotic risks but remains challenging due to the vast array of known and unknown pathogens harboured by animals. Microbiome-based approaches provide an efficient and comprehensive alternative for monitoring microbial communities and scanning the whole spectrum of bacterial pathogens. In this study, we applied this innovative conceptual framework to implement a sentinel monitoring system for investigating zoonotic tick-borne bacteria in three tick species sampled from wild boars in the Metropolitan Area of Barcelona (MAB). Using Nanopore sequencing of the full length 16 s rRNA gene, we demonstrated a fast and cost-effective approach for microbiome analysis. Our findings revealed the presence of two pathogenic genera widely documented in ticks, encompassing five species: Rickettsia massiliae and R. slovaca, both previously detected in the area, and for the first time, Francisella tularensis -the causative agent of tularemia- as well as F. hispaniensis and Diplorickettsia massiliensis, potentially emerging patogens. Finally, our results showed distinct bacterial compositions across the tick species examined. This study highlights the sensitivity and comprehensiveness of microbiome-based surveillance of tick-borne pathogens, enabling the early detection of emerging and low-abundance bacterial species that might otherwise go unnoticed with less sensitive techniques. Such proactive detection efforts are crucial for facilitating early identification and implementing prevention strategies to mitigate zoonotic risks.

The early-life fecal microbiota is associated with litter of origin but not with susceptibility to ETEC F4ab-mediated post-weaning diarrhea in CHCF1 genotyped pigs

INTRODUCTION

Universal biomarkers in the fecal microbiota that predict susceptibility to post-weaning diarrhea (PWD) would be valuable for future intervention strategies. Genetic susceptibility to enterotoxigenic E. coli (ETEC) infection in pigs is a major determinant of PWD and may unfavourably alter early-life gut microbiota composition. We investigated whether pigs genetically susceptible to ETEC F4ab/ac had different fecal microbiota composition and diversity pre- and post-weaning compared to genetically resistant pigs.

METHOD

Fecal microbiotas were characterized using long-read sequencing of the 16S rRNA gene in 24 CHCF1 heterozygous susceptible (RS) and 24 CHCF1 homozygous resistant (RR) pigs. These pigs were tested at early lactation (post-natal day (PND) 8) and late lactation (PND 22), which are critical periods for microbiota development and immune maturation. Twelve pigs from each group were weaned and transported to an experimental facility at PND 23, and were tested again at PND 24, prior to an ETEC F4ab challenge. This enabled studying immediate fecal microbiota changes after weaning and investigating whether CHCF1 RS pigs had compromised microbiotas compared to CHCF1 RR pigs preceding infection.

RESULTS

Across time, CHCF1 RS pigs had a higher number of observed OTUs (coef: 103, 95% CI [18.90; 192.76], p = 0.01) compared to CHCF1 RR pigs. There were no significant differences in the overall bacterial communities or differentially abundant taxa between genotypes. Littermates had bacterial communities more similar to each other compared to non-littermates during lactation (PND 8: R2 = 0.2, p = 0.001 and PND 22: R2 = 0.23, p = 0.001) and the litter effect persisted after weaning (PND 24: R2 = 0.4, p = 0.001).

CONCLUSION

We did not find major differences in the fecal microbiota between CHCF1 genotypes, pre- or post-weaning, that could help explain subsequent susceptibility to ETEC F4ab-mediated PWD. Litter explained a major part of the variation in the overall fecal bacterial community between pigs in the study.

Exploring the role of microbiome in cystic fibrosis clinical outcomes through a mediation analysis

Human microbiome plays a crucial role in host health and disease by mediating the impact of environmental factors on clinical outcomes. Mediation analysis is a valuable tool for dissecting these complex relationships. However, existing approaches are primarily designed for cross-sectional studies. Modern clinical research increasingly utilizes long follow-up periods, leading to complex data structures, particularly in metagenomic studies. To address this limitation, we introduce a novel mediation framework based on structural equation modeling that leverages linear mixed-effects models using penalized quasi-likelihood estimation with a debiased lasso. We applied this framework to a 16S rRNA sputum microbiome data set collected from patients with cystic fibrosis over 10 years to investigate the mediating role of the microbiome in the relationship between clinical states, disease aggressiveness phenotypes, and lung function. We identified richness as a key mediator of lung function. Specifically, Streptococcus was found to be significantly associated with mediating the decline in lung function on treatment compared to exacerbation, while Gemella was associated with the decline in lung function on recovery. This approach offers a powerful new tool for understanding the complex interplay between microbiome and clinical outcomes in longitudinal studies, facilitating targeted microbiome-based interventions.

IMPORTANCE

Understanding the mechanisms by which the microbiome influences clinical outcomes is paramount for realizing the full potential of microbiome-based medicine, including diagnostics and therapeutics. Identifying specific microbial mediators not only reveals potential targets for novel therapies and drug repurposing but also offers a more precise approach to patient stratification and personalized interventions. While traditional mediation analyses are ill-equipped to address the complexities of longitudinal metagenomic data, our framework directly addresses this gap, enabling robust investigation of these increasingly common study designs. By applying this framework to a decade-long cystic fibrosis study, we have begun to unravel the intricate relationships between the sputum microbiome and lung function decline across different clinical states, yielding insights that were previously unknown.

Distal gut colonization by oral bacteria during intensive chemotherapy: direct evidence from strain-level analysis of paired samples

Oral bacteria have been found in the colon in pathologies such as inflammatory bowel disease. To ascertain niche coalescence, 2 elements are essential: (i) paired oral/fecal samples and (ii) strain-level resolution. We profiled the microbiota in 283 samples from 39 patients undergoing intensive chemotherapy at baseline (saliva: 49, plaque: 51, stool: 43), week 2 (saliva: 18, plaque: 17, stool: 17), week 3 (saliva: 18, plaque: 21, stool: 21), and week 4 (saliva: 8, plaque: 10, stool: 10) of chemotherapy. Through strain-level analysis of paired samples, we demonstrate strong evidence for a breakdown of niche separation in most patients. The extent of overlap increased with time, particularly in patients with intestinal mucositis. Our findings provide definitive evidence for ectopic colonization of the distal gut by oral bacteria in a disease state, likely facilitated by intestinal mucositis. Microbiota contribution by the mouth to the colon may have consequences for the host.

Genealogically bewildered individuals and forensic identification: a review of current and emerging solutions

The increasing use of assisted reproductive technologies (ART) with donor gametes is driven by rising infertility rates, delayed parenthood, and the need to prevent hereditary diseases. Greater social acceptance of diverse family structures, advancements in reproductive medicine, and improving success rates also contribute. Accessibility, affordability, and cross-border reproductive care further expand ART's reach, making donor gametes a preferred option for many individuals and couples worldwide. The widespread application of ART has led to an increasing number of donor-conceived individuals, many of whom are now reaching reproductive maturity. This demographic shift introduces significant challenges for traditional forensic genetic identification methods, which rely on biological reference samples from genetically related individuals. The absence of such samples complicates the identification process, particularly for individuals conceived via gamete donation or adoption, where biological and legal parentage are incongruent. Conventional forensic genetic analyses, including short tandem repeat (STR) and single nucleotide polymorphism (SNP) profiling of autosomal, Y-chromosome, X-chromosome, and mitochondrial DNA, exhibit limited efficacy in these scenarios. While these methods can sometimes identify individuals conceived using a single donor gamete, they are insufficient for cases involving dual donor gametes or mitochondrial replacement therapy. Emerging methodologies such as forensic genetic genealogy, DNA methylation profiling, and human microbiome analysis offer innovative approaches but necessitate further clinical validation and standardization.

Antibiotic resistance in Helicobacter pylori: a genetic and physiological perspective

The identification of Helicobacter pylori (H. pylori) infection as the primary etiology of gastroduodenal diseases represents a significant advancement in the field of gastroenterology. The management of these diseases has undergone a substantial transformation, and antibiotic treatment is now universally applicable. H. pylori has been the subject of numerous investigations to determine the prevalence of antibiotic resistance. However, many of these studies are limited, particularly regarding the number and representativeness of the strains assessed. Genetic and physiological modifications, such as gene mutations, efflux pump alterations, biofilm formation, and coccoid formation, contribute to the observed resistance. Our review focuses on the emergence of antibiotic-resistant strains, particularly emphasizing the various modifications of H. pylori that confer this resistance. In conclusion, we elucidate the challenges, potential solutions, and prospects in this field, providing researchers with the knowledge necessary to overcome the resistance exhibited by H. pylori.

Contrasting Effects of Atmospheric Particulate Matter Deposition on Free-Living and Particle-Associated Bacteria in the South China Sea

Atmospheric particulate matter (PM) deposition has become an important nutrient source in marine ecosystems, increasing particulate organic carbon and resource heterogeneity. However, their effects on marine bacterial communities remain unclear. In this study, by conducting on-board microcosm experiments with anthropogenic East Asian PM in the oligotrophic South China Sea, the response of particle-associated (PA) bacteria was investigated and compared with its free-living (FL) counterparts. Results showed that PM input increased nutrient heterogeneity, shifting bacterial community composition and lifestyle. Copiotrophic PA bacteria became more abundant and contributed a disproportionately higher percentage to total bacterial production despite a decline in total bacterial abundance. FL bacteria showed increased diversity, shifting from oligotrophs to copiotrophs, while PA bacteria displayed reduced diversity and nondirectional compositional changes, suggesting their distinct assembly mechanisms in response to external nutrient inputs. Metagenomic analysis further revealed that PM drives a shift toward a copiotrophic, particle-attached lifestyle with upregulated pathways for chemotaxis, motility, and biofilm formation. Notably, PM addition also increased the relative abundance of oil-degrading taxa. These findings reveal the complexity of microbial responses to environmental perturbations and underscore the need to consider unique ecological niches and bacterial lifestyles.

Standardizing a microbiome pipeline for body fluid identification from complex crime scene stains

Recent advances in next-generation sequencing have opened up new possibilities for applying the human microbiome in various fields, including forensics. Researchers have capitalized on the site-specific microbial communities found in different parts of the body to identify body fluids from biological evidence. Despite promising results, microbiome-based methods have not been integrated into forensic practice due to the lack of standardized protocols and systematic testing of methods on forensically relevant samples. Our study addresses critical decisions in establishing these protocols, focusing on bioinformatics choices and the use of machine learning to present microbiome results in case reports for forensically relevant and challenging samples. In our study, we propose using operational taxonomic units (OTUs) for read data processing and generating heterogeneous training data sets for training a random forest classifier. We incorporated six forensically relevant classes: saliva, semen, skin from hand, penile skin, urine, and vaginal/menstrual fluid, and our classifier achieved a high weighted average F1 score of 0.89. Systematic testing on mock forensic samples, including mixed-source samples and underwear, revealed reliable detection of at least one component of the mixture and the identification of vaginal fluid from underwear substrates. Additionally, when investigating the sexually shared microbiome (sexome) of heterosexual couples, our classifier could potentially infer the nature of sexual activity. We therefore highlight the value of the sexome for assessing the nature of sexual activities in forensic investigations while delineating areas that warrant further research.IMPORTANCEMicrobiome-based analyses combined with machine learning offer potential avenues for use in forensic science and other applied fields, yet standardized protocols remain lacking. Moreover, machine learning classifiers have shown promise for predicting body sites in forensics, but they have not been systematically evaluated on complex mixed-source samples. Our study addresses key decisions for establishing standardized protocols and, to our knowledge, is the first to report classification results from uncontrolled mixed-source samples, including sexome (sexually shared microbiome) samples. In our study, we explore both the strengths and limitations of classifying the mixed-source samples while also providing options for tackling the limitations.

Exploring sub-species variation in food microbiomes: a roadmap to reveal hidden diversity and functional potential

Within-species diversity of microorganisms in food systems significantly shapes community function. While next-generation sequencing (NGS) methods have advanced our understanding of microbiomes at the community level, it is essential to recognize the importance of within-species variation for understanding and predicting the functional activities of these communities. This review highlights the substantial variation observed among microbial species in food systems and its implications for their functionality. We discuss a selection of key species in fermented foods and food systems, highlighting examples of strain-level variation and its influence on quality and safety. We present a comprehensive roadmap of methodologies aimed at uncovering this often overlooked underlying diversity. Technologies like long-read marker-gene or shotgun metagenome sequencing offer enhanced resolution of microbial communities and insights into the functional potential of individual strains and should be integrated with techniques such as metabolomics, metatranscriptomics, and metaproteomics to link strain-level microbial community structure to functional activities. Furthermore, the interactions between viruses and microbes that contribute to strain diversity and community stability are also critical to consider. This article highlights existing research and emphasizes the importance of incorporating within-species diversity in microbial community studies to harness their full potential, advance fundamental science, and foster innovation.

Metagenomic Analysis of Wild Apple (Malus sieversii) Trees from Natural Habitats of Kazakhstan

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.

Assessing the impact of diet formulation and age on targeted bacterial establishment in laboratory and mass-reared Mediterranean fruit fly using full-length 16S rRNA sequencing

Insect gut microbiota play important roles in host health and interactions with the environment. In laboratory and mass-reared insects, gut microbiomes can differ in composition and function compared to wild conspecifics. For fruit flies, such as the Mediterranean fruit fly (medfly; Ceratitis capitata), these changes can influence male performance and behavior. Overall, understanding factors that influence the ability of bacteria to establish in hosts is important for the establishment of lost or novel microbiota in mass-reared insects. The goal of this study was to evaluate how host age and diet-inoculation method influenced bacterial establishment in laboratory and mass-reared medflies. We used an Enterobacter strain with antibiotic resistance and coupled it with full-length PacBio Kinnex 16S rRNA sequencing to track the establishment of the specific isolates under different adult dietary conditions. We also used two longstanding reared lines of medfly in our study. Our results identified that diet had a strong interaction with age. The target bacterial isolate was detected in medfly when inoculated with liquid diet regardless of age, but those fed a slurry-based diet and a separate water source had less establishment. This was consistent for both fly rearing lines used in the study. 16S rRNA sequencing corroborated the establishment of the specific strain but also revealed some species/strain-level variation of Enterobacter sequences associated with the flies. Additionally, our study illustrates that long-read 16S rRNA sequencing may afford improved characterization of species- and strain-level distribution of Enterobacteriaceae in insects.

IMPORTANCE

Insects form intimate relationships with gut microorganisms that can help facilitate several important roles. The goal of our study was to evaluate factors that influence microbial establishment in lines of the Mediterranean fruit fly (medfly), an important pest species worldwide. Mass-reared insects for the sterile insect technique often possess gut microbiomes that substantially differ from wild flies, which can impact their performance in pest control contexts. Here, we show that liquid-based formulations can be utilized to manipulate the gut microbiota of mass-reared medflies. Furthermore, using near full-length 16S rRNA metabarcoding sequencing, we uncovered strain-level diversity that was not immediately obvious using other approaches. This is a notable finding, as it suggests that full-length 16S rRNA approaches can have marked improvements for some taxa compared to fewer hypervariable regions at approximately the same cost. Our results provide new avenues for exploring and interrogating medfly-microbiome interactions.

Persistent reduction of Bifidobacterium longum in the infant gut microbiome in the first year of age following intrapartum penicillin prophylaxis for maternal GBS colonization

Introduction

Group B Streptococcus is a significant cause of early-onset disease in term newborns, with a global incidence of 0.41/1000 live births. Intrapartum antibiotic prophylaxis (IAP) has reduced EOD incidence by over 80%, but concerns exist about its impact on the neonatal gut microbiome and potential long-term health effects.

Methods

This single center study examines the effects of IAP on the fecal infant microbiome in the first year of age and on the T cell phenotype in the first days after birth among 22 infants receiving IAP with penicillin due to maternal GBS colonization and 26 infants not exposed to IAP. The fecal microbiome was analyzed at birth, one month and one year of age through 16S rRNA gene sequencing. Additionally, a T cell phenotyping of peripheral blood was performed between the second and fifth day of age.

Results

At one month, IAP exposed infants had a significantly lower relative abundance of Bifidobacterium longum in fecal samples, an effect which was sustained at one year. In IAP exposed infants we found a proinflammatory T-helper cell profile, characterized by higher IL-17A, RORgt, and TGF-b expression.

Discussion

This study proposes a sustained impact of IAP on the neonatal microbiome and T cell repertoire.

2bRAD-M Reveals the Characteristics of Urinary Microbiota in Overweight Patients with Urinary Tract Stones

Background: Urinary tract stone (UTS) is a common disease significantly impacting human health. Obesity influences stone formation and increases UTS incidence, yet the differences in the urinary microbiota and pathways between overweight and healthy-weight UTS patients remain unclear. Methods: In this study, 16 patients were analyzed: 8 overweight and 8 healthy-weight UTS patients. Bladder urine samples were collected during surgery, and DNA was extracted for microbial analysis using 2bRAD markers. Microbial diversity and KEGG pathway differences were studied. Results: The results showed that overweight UTS patients had a significantly higher urinary microbial diversity than healthy-weight patients. The analysis identified differences in microbiota at various taxonomic levels. LEfSe analysis revealed Sphingomonas_paucimobilis as abundant in overweight patients, while Bifidobacterium_piotii dominated in healthy-weight patients. Key species, including Ralstonia_sp000620465, Sphingomonas_paucimobilis, and Campylobacter_D_coli, were identified. KEGG analysis highlighted enriched pathways in overweight UTS patients, including the porphyrin and chlorophyll metabolism, fatty acid metabolism, amino acid degradation, and renin-angiotensin and mineral absorption pathways. Conclusions: This study is the first to use 2bRAD-M microbiome analysis to compare the urinary microbiota between overweight and healthy-weight UTS patients. It identified significant microbiota and pathway differences, suggesting a link between microbiota imbalance, obesity, and stone formation. These findings provide potential targets for further research on obesity-related stone susceptibility mechanisms.

Assessment of spoilage microbial communities in modified atmosphere-packed ready-to-eat salad during cold storage: A comparative study using MALDI-TOF MS identification and PacBio full-length 16S rRNA and ITS sequencing

Effect of storage temperatures and modified atmosphere packaging (MAP) on the shelf-life and spoilage microbial dynamics of industrially produced mayonnaise-based potato salad was studied over two years (Spring 2021, Autumn 2021, Spring 2022). Three salad batches, stored at chilling and abuse temperatures ranging from 0 °C to 12 °C, were analyzed. Microbial communities were evaluated using ISO-standard microbiological methods, MALDI-TOF MS identification, and PacBio full-length 16S rRNA gene and fungal ITS amplicon sequencing. The results showed that sensory and microbiological quality strongly depended on storage temperature, MAP packaging, and salad batch. The recommended upper temperature limit of 6 °C did not preserve salad quality at the end of its shelf-life, while storage below 4 °C extended the seven-day shelf-life to 10 days. Distinct spoilage communities were identified across batches, dominated by Dellaglioa algida, Leuconostoc carnosum, and Latilactobacillus sakei (Spring 2021); Leuconostoc inhae and Leuconostoc gelidum (Autumn 2021); and Lactococcus carnosus (Spring 2022). The microbial communities of ingredients and processing facilities influenced salad microbiota. Comparative analysis showed that full-length 16S rRNA sequencing provided higher resolution, detecting species missed by culturing methods, including psychrotrophic and fastidious lactic acid bacteria. However, fungal community analysis, using full-length ITS amplicons, requires the selection of specific fungal primers. This study provides a comprehensive evaluation of microbial profiles in RTE salads under different storage conditions, highlighting the critical role of temperature and microbial management in preserving MAP salad safety and quality during extended shelf-life.

Intestinal microbiota profiles of captive-bred cynomolgus macaques reveal influence of biogeography and age

BACKGROUND

Age-associated changes to the intestinal microbiome may be linked to inflammageing and the development of age-related chronic diseases. Cynomolgus macaques, a common animal model in biomedical research, have strong genetic physiological similarities to humans and may serve as beneficial models for the effect of age on the human microbiome. However, age-associated changes to their intestinal microbiome have previously only been investigated in faecal samples. Here, we have characterised and investigated the effects of age in the cynomolgus macaque intestinal tract in luminal samples from both the small and large intestine.

RESULTS

Whole metagenomic shotgun sequencing was used to analyse the microbial communities in intestinal content obtained from six different intestinal regions, covering the duodenum to distal colon, of 24 healthy, captive-bred cynomolgus macaques, ranging in age from 4 to 20 years. Both reference-based and assembly-based computational profiling approaches were used to analyse changes to intestinal microbiota composition and metabolic potential associated with intestinal biogeography and age. Reference-based computational profiling revealed a significant and progressive increase in both species richness and evenness along the intestinal tract. The microbial community composition also significantly differed between the small intestine, caecum, and colon. Notably, no significant changes in the taxonomic abundance of individual taxa with age were found except when sex was included as a covariate. Additionally, using an assembly-based computational profiling approach, 156 putative novel bacterial and archaeal species were identified.

CONCLUSIONS

We observed limited effects of age on the composition of the luminal microbiota in the profiled regions of the intestinal tract except when sex was included as a covariate. The enteric microbial communities of the small and the large intestine were, however, distinct, highlighting the limitations of frequently used faecal microbial profiling as a proxy for the intestinal microbiota. The identification of a number of putative novel microbial taxa contributes to knowledge of the full diversity of the cynomolgus macaque intestinal microbiome.

Effect of PGPR on growth and nutrient utilization of Elymus nutans Griseb at different temperatures

Plant growth-promoting rhizobacteria (PGPR) are beneficial bacteria that facilitate plant growth and can be used in the restoration of ecosystems. However, PGPR vary in their temperature tolerance, and few studies have investigated the effect of temperature on PGPR-mediated growth promotion or PGPR inoculum colonization. Therefore, we isolated and purified rhizosphere bacteria from the rhizosphere soil of Elymus nutans Griseb (EnG), collected from the Qinghai-Tibet Plateau. Selective culture media were used to assess whether these strains possess plant growth-promoting abilities and to measure the magnitude of their plant growth-promoting ability. Then screen out the strains (S1, S2, S3, S4, and S5) with strong plant growth-promoting ability for identification. To demonstrate the growth-promoting effects of the selected PGPR, we conducted a study. In this study, we simulated three temperature gradients (10°C, 15°C, and 20°C) during the growing season of EnG on the Tibetan Plateau. Furthermore, we established four incubation substrate treatments: T1(addition of PGPR but no addition of NPK fertilizers), T2 (neither PGPR nor NPK fertilizers addition), T3 (addition of PGPR both and NPK fertilizers), and T4 (addition of NPK fertilizers but not PGPR), to explore the effects of PGPR on the growth and nutrient (NPK) utilization efficiency of EnG at different temperatures. The results revealed that compared with those under T2, the plant height (PT) and dry weight under, T1 increased by 51.72% - 70.67% and 24.99-51.25%, respectively. The soluble sugar (SS) and soluble protein (SP) content significantly increased by 59.37% and 369.66%, respctively, at 10 °C (p < 0.05) and by 100.17% and 94.5%, respectively, at 15 °C (p < 0.05). Compared with those under T4, the physiological efficiencies of N (NPE) at 15 °C and 20 °C significantly decreased by 40.43% and 72.11%, respectively, under T3. In summary, these showed that this PGPR (S1, S2, S3, S4, and S5) promoted the growth of EnG on the Tibetan plateau and improved its nutrient utilization efficiency.

Design and validation of universal and taxon-specific 16S rRNA qPCR primers for detection of freshwater harmful algal bloom-forming cyanobacteria

Freshwater harmful algal bloom-forming cyanobacteria have become an increasingly prominent global concern from both environmental and human health perspectives. To enable and facilitate timely decision making in taking preventative and mitigative measures, rapid, accurate, sensitive and quantitative tools are needed for the detection and monitoring of toxin-producing cyanobacteria. Here we report the development of taxon-specific quantitative polymerase chain reaction (qPCR) primers capable of distinguishing 10 cyanobacterial genera or clade from non-target groups as well as a new set of universal primers capable of amplifying all cyanobacteria species. When evaluated by 4 stringent metrics and primer-template mismatches, these de novo designed qPCR primers outperformed published primers in amplifying the 16S rRNA gene of their target strains among the collection of 16 in-house cyanobacterial strains belonging to 10 genera. The 10 best-performing designed primers were validated using field samples from three field locations with historically documented HAB events. The field validation results corroborated with both microscopic observations and Nanopore sequencing of full-length 16S amplicons. Our study demonstrated the effectiveness of our design-screen-evaluation-validation pipeline in developing taxon-specific qPCR primers for detecting and quantifying group-specific target populations and their promising application to field HABs samples. With the advancement of massive parallel sequencing technologies and bioinformatic tools, a community-wide 16S full-length sequencing run can provide a panoramic view of the genetic diversity and site-specific variant info about the target taxa of interest, enabling the fast development of new taxon-specific qPCR assays and their refinement or modification to adapt to site-specific genetic variations in field samples.

Tracheal and cloacal bacterial diversity of red listed Eastern Imperial Eagle (Aquila heliaca)

This study aimed to improve knowledge of raptor microbiomes by providing the first description of tracheal and cloacal bacterial diversity of Eastern Imperial Eagles (Aquila heliaca). To date, only few studies are available and they are carried out mainly on captive birds. The Eastern Imperial Eagle is species of significant conservation concern and, therefore, characterization microbiota contributes valuable information to the field of avian microbiology and aids in conservation efforts for this threatened species, moreover, identification of avian and human pathogens within microbial communities and evaluation of potential threats to birds, humans, and other species are crucial for sustainably balancing the wellbeing of ecosystems, 3,500 OTUs were identified from each sample supported by ∼2.8 Million sequence reads. The tracheal and cloacal microbiomes were dominated by Gammaproteobacteria (67.5%), Bacilli (43.8%), and Negativicutes (22.0%). We detected dissimilarities between cloacal (unique 440 OTUs) and tracheal (337 unique OTUs) samples, and significant evidence of moderate positive monotonic relationship between cloacal and tracheal bacterial communities. No significant differences between individuals from different nests. Aquila heliaca can serve as an indicator of presence of bacterial species in its respective habitats. Efforts aiming at protection of red-listed birds may not presently prioritize microbiome considerations but integrating microbiome research into conservation strategies could yield significant benefits.

Insights into the balance of safety, flavor, and texture in fermented fish: A study based on full-length sequencing of fermented largemouth bass (Micropterus salmoides)

In this study, the effect of fermentation on the safety, flavor, and texture of largemouth bass (Micropterus salmoides) was investigated. Compared to fresh fish, the proteins formed a network structure that enhanced bound water proportion, texture hardness, and water holding capacity, while it reduced cooking losses. TVB-N and TBARS levels increased gradually but stayed within safe limits. However, histamine accumulation surpassed the recommended limit at 56.84 ± 0.17 mg/100 g in late stages. A total of 67 volatile compounds were detected, with 13 identified as key flavor compounds (OAV > 1). 3rd-generation full-length 16S rRNA gene sequencing revealed a microbial community shift from high diversity to dominance by strains like Vibrio anguillarum, Vagococcus fessus, and Vagococcus coleopterorum. Among these, 10 species were highly correlated with flavor formation. This study reveals quality patterns in fermented largemouth bass, providing insights into achieving a balance among safety, flavor, and texture in fermented fish.

Influence of orthodontic appliances and nitrate on the oral microbiota

In this pilot study, we investigated the bacterial changes introduced on the subgingival, tongue, and saliva microbiota during fixed orthodontic treatment, with or without daily administration of nitrate-containing beet juice for 2 weeks in 22 individuals with good general health. We followed clinical parameters in combination with microbiota changes before, after 2 weeks, and after 6 months of treatment with fixed orthodontic appliances. In accordance with variations in community composition at the sampling sites, effects to orthodontic treatment differed. Subgingival communities responded promptly to orthodontic treatment with no additional structural changes over time, whereas saliva and tongue communities were affected only after extended treatment. Periodontal pathogens such as Selenomonas sputigena were enriched in subgingival communities, whereas Streptococcus mutans was enriched in saliva. Specifically, Rothia mucilaginosa increased tremendously in relative abundance in both tongue and saliva communities. The effect of beet juice on microbial composition was significant in subgingival samples even though the differences were not mirrored in single differentially distributed genera or species. This indicates changes in the complete subgingival microbial net of interacting species. However, the prevention of Corynebacterium matruchotii enrichment by beet juice may be important for prevention of biofilm formation. Enrichment of Neisseria flavescens group bacteria and Abiotrophia and depletion of different Actinomyces and Stomatobaculum were observed on tongue communities. We conclude that subgingival microbiota are rapidly affected by fixed orthodontic appliances and can be positively influenced by regular administration of nitrate-containing juice. KEY POINTS: • The subgingival site, tongue, and saliva contain different microbiota • The microbiota react differently to orthodontic treatment and beet juice • Key genera and species affected by treatments were identified.

Complementary foods in infants: an in vitro study of the faecal microbial composition and organic acid production

The transition from breastmilk to complementary foods is critical for maturing the colonic microbiota of infants. Dietary choices at weaning can lead to long-lasting microbial changes, potentially influencing health later in life. However, the weaning phase remains underexplored in colonic microbiome research, and the current understanding of how complementary foods impact the infant's colonic microbiota is limited. To address this knowledge gap, this study assessed the influence of 13 food ingredients on the in vitro microbial composition and production of organic acids by the faecal microbiota in New Zealand infants aged 5 to 11 months. To better represent real feeding practices, ingredients were combined with infant formula, other complementary foods, or both infant formula and other foods. Among the individual food ingredients, fermentation with peeled kūmara (sweet potato) increased the production of lactate and the relative abundance of the genus Enterococcus. Fermentation with blackcurrants, strawberries, or raspberries enhanced acetate and propionate production. Additionally, fermentation with blackcurrants increased the relative abundance of the genus Parabacteroides, while raspberry fermentation increased the relative abundance of the genera Parabacteroides and Eubacterium. When combined with infant formula or with blackcurrants, fermenting black beans increased butyrate production and stimulated the relative abundance of Clostridium sensu stricto 1. These foods are promising candidates for future clinical trials.

Gut Microbiota and Hepatocellular Carcinoma: Metabolic Products and Immunotherapy Modulation

BACKGROUND

The relationship between hepatocellular carcinoma (HCC) and gut microbiota has gained attention for its impact on HCC immunotherapy.

METHODS

Key gut microbial metabolites, including bile acids, toll-like receptor 4, short-chain fatty acids, and bacterial toxins, contribute to HCC progression and influence immune responses through the gut-liver axis. As immune checkpoint inhibitors (ICIs) become common in HCC treatment, modulating the gut microbiota offers new strategies to enhance ICIs efficacy. However, individual differences in microbial composition introduce challenges, with some HCC patients showing resistance to ICIs.

RESULTS

This review summarizes the latest findings on the role of gut microbiota in HCC and explores emerging therapeutic approaches, including fecal microbiota transplantation, probiotics, antibiotics, and natural compounds.

CONCLUSIONS

The focus is on translating these insights into personalized medicine to optimize ICIs responses and improve HCC treatment outcomes.

Chinese herbal medicine improves antioxidant capacity of chicken liver at high stocking density involved gut-liver microbiota axis based on multi-omics technologies

Traditional Chinese Medicine (TCM), such as artemisinin, berberine and proanthocyanidin, has been considered an effective additive for broiler production. High density farming (HDF), which is the primary modern mode of chicken production, is associated with animal health problems. This work aimed to evaluate the effects of dietary TCMs (dihydroartemisinin, hydrochloride, and oligomeric proanthocyanidins) on improving the antioxidant capacity of chickens under HDF and their underlying mechanisms. A total of 360 Wuding chickens (134-day-old) were divided into five experimental groups: one normal stocking density (8 birds/m2, control group) and four high stocking density (16 birds/m2), with six replicates for each group. For four HDF groups, one group was fed the basal diet, and the other three groups were fed the basal diet supplemented with 80 mg/kg dihydroartemisinin, 600 mg/kg berberine hydrochloride, and 250 mg/kg grape oligomeric proanthocyanidins, respectively. HDF increased malondialadehyde level, but decreased superoxide dismutase, glutathione and glutathione peroxidase levels in the liver of broiler; however, dietary TCMs apparently alleviated this attenuation. Dietary TCMs significantly decreased the expression of genes involved in cholesterol synthesis in the liver and the levels of tripepides in the intestine of the HDF chickens. Meanwhile, dietary TCMs significantly altered the composition of the liver microbiome in the HDF chickens, expressing by reduced Pseudomonas but enriched Bradyrhizobium. The gut microbiota of the HDF chickens was also altered following dietary TCM administration, with a decreased abundance of Microbacter margulisiae and an increased abundance of acetate synthesis genes. Association analysis of the multi-omics results revealed negative correlations between liver cholesterol synthesis and antioxidant factors that could be regulated by gut microbiota-produced short-chain fatty acids. Furthermore, alleviating of oxidative stress by dietary TCMs also showed significant correlations with the liver microbiome, which could be mediated by tripeptides produced by the gut microbiota. These results indicated that dietary TCM is beneficial in improving antioxidant defenses in HDF chickens and interpreted the mechanisms of action of TCM from the perspective of modern science.

Backtracking identification techniques for predicting unclear bacterial taxonomy at species level: molecular diagnosis-based bacterial classification

Bacterial 16S rRNA genes are widely used to classify bacterial communities within interesting environments (e.g., plants, water, human body) because they contain nine hyper-variable regions (V1-V9) reflecting a large number of sequence variation sites between species. Short-read sequencing platform (targeting partial region of 16S rRNA gene; approximately 150-500 bp) commonly used in the 16S-based microbiome study is favored by many researchers because it is economical and can generate highthroughput sequencing data faster than long-read sequencing platforms. However, this sequencing platform has technical limitations in that it cannot clarify bacterial classification at the species level compared to long-read sequencing technology, which can cover the unclassification issue due to sequence similarity between species by targeting the 16S full-length region. In recent microbiome research-related industries, species-level high-resolution microbial classification is considered a key challenge to secure microbial resources among institutions in the field. However, the long-read sequencing platforms currently offered are still under price adjustment (demanding higher cost than short-read sequencing platforms) and have the disadvantage of low base-calling accuracy compared to short-read sequencing platforms. Therefore, this brief communication introduces the'Molecular diagnosis-based bacterial classification' technology to predict candidate species by backtracking for unclassified bacterial taxonomy at the species level in the NGS-based 16S microbiome study.

Metagenomics education in a modular CURE format positively affects students' scientific discovery perception and data analytical skills

Targeted metagenomics is a rapidly expanding technology to analyze complex biological samples and genetic monitoring of environmental samples. In this research field, data analytical aspects play a crucial role. In order to teach targeted metagenomics data analysis, we developed a 4-week inquiry-driven modular course-based undergraduate research experience (mCURE) using publicly available Australian coral microbiome DNA sequencing data and associated metadata. Since an enormous amount of metadata was provided alongside the DNA sequencing data, groups of students were able to develop their own authentic research questions. Throughout the course, the student groups worked on these research questions and were supported with bioinformatics and statistics lessons. Additionally, practical aspects of data collection and analysis were addressed during hands-on field work on a nearby Dutch beach. Evaluation of the course indicated that the majority of students (1) achieved the intended metagenomics-based learning outcomes and (2) experienced scientific discovery while working on their research projects. In conclusion, the huge amount of data and metadata available in the coral microbiome data set facilitated the development of a strongly inquiry-driven course. Different groups of students were able to develop and conduct their own distinct microbiome research projects and our current mCURE format positively affected students' metagenomics data analytical skills and scientific discovery perception.

Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research?

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.

Characterization of keratinase from Chryseobacterium camelliae Dolsongi-HT1 and efficacy on skin exfoliation

Keratin is the outermost layer that protects our skin and has an appropriate turnover cycle. With age, the keratin turnover cycle begins to dysfunction. To overcome this issue, we artificially remove dead skin cells. In this study, we attempted to screen enzymes that could be useful in the cosmetics industry to develop enzymes suitable for the enzyme-based method, a mild exfoliation method that does not damage the skin. Chryseobacterium camelliae Dolsongi-HT1 with keratinolytic activity was isolated from green tea leaves (sourced from the Dolsongi tea garden, Jeju Island). The keratinolytic activity of C. camelliae Dolsongi-HT1 was detected in the culture media, indicating that the target keratinolytic enzyme is a secreted protein. Keratinolytic activity was demonstrated using forearm skin keratin and reconstituted human skin models. The enzyme from C. camelliae Dolsng-HT1 (HT1) could efficiently decompose human skin keratin. Moreover, experiments using the reconstituted human skin model demonstrated that HT1 is efficient in exfoliating the outermost stratum corneum. Compared with the popularly used chemical exfoliation method, enzymatic exfoliation using HT1 was less abrasive and did not damage the epidermal layer. Keratinolytic enzyme was identified using protein purification and mass spectrometry. The identified enzyme (iHT1) was expressed in the Bacillus subtilis RIK 1285 secretory protein expression system. The iHT1 enzyme showed high activity over a wide temperature range (30-60 °C), with the highest activity at 30 °C. The optimum pH for the activity of iHT was pH8.

Retrospective investigation of 43 necropsy cases of Tyzzer disease in foals and partial genome sequence of Clostridium piliforme by shotgun metagenomics

Clostridium piliforme is an obligate intracellular filamentous bacterium that causes Tyzzer disease (TD) in many animals. The disease manifests as severe, multifocal necrotizing hepatitis, with a high fatality rate in foals. Through retrospective investigation, we detected C. piliforme in 43 equine necropsy cases from 2012 to 2024. Positive cases were diagnosed from February to July, peaking in May. The age of affected foals ranged from 4 days to 2 months. Histologically, all cases had necrotizing hepatitis with multifocal, coalescing pinpoint, tan or reddish foci. Since only a partial 16S rRNA gene sequence was available for the horse strain of C. piliforme, we used shotgun metagenomics to obtain its genome sequence from the liver of a necropsied foal with TD. The sequences obtained were compared against the NCBI NT/NR database with the highest number of reads and contigs aligning to Clostridium species. A complete 16S rRNA gene was obtained, showing the highest identity to a 16S rRNA gene of the horse strain of C. piliforme (99.05 %), followed by 98.02-96.71 % identities to rabbit and rodent strains of C. piliforme, indicating cross-species variation. Additional identified genes included alveolysin, exo-α-sialidase, flagellar and spore formation/vegetation, providing the first genetic evidence of virulence factors for C. piliforme. Furthermore, presence of genes encoding multidrug export and multidrug resistance proteins suggested C. piliforme could develop resistance to beta-lactams and fluoroquinolones. This study provides the first partial genome sequence of C. piliforme using a shotgun metagenomics hepatic sampling approach on a foal with TD.

Multi-cohort analysis identifying core ocular surface microbiome and bacterial alterations in eye diseases

PURPOSE

Inconsistency exists among reported studies on the composition of human ocular surface microbiome (OSM). The roles of OSM in ocular diseases remain uncertain. In this study, we aimed to determine the composition of OSM and to evaluate its potential roles and functions from multiple cohorts.

METHODS

Raw 16 s sequencing data were obtainable from publicly available repositories, sourced from 17 published studies. Employing a standardized method, we processed the data and conducted a cross-cohort analysis. Through bioinformatics pipelines QIIME2 and PICRUSt2, we processed a total of 1875 ocular surface samples. Core microbiome analyses, genera comparisons, and MetaCyc pathway analyses were performed within each cohort independently. The results were then combined to identify shared patterns across different datasets.

RESULTS

The core OSM comprised seven genera: Corynebacterium, Staphylococcus, Acinetobacter, Streptococcus, Pseudomonas, Cutibacterium and Bacillus. Corynebacterium and Staphylococcus are the most abundant genera on ocular surface. Most ocular diseases showed OSM alterations and eight genera demonstrated a non-specific, shared response among two or more ocular diseases. Moreover, changes in various metabolic pathways were predicted following OSM alteration, indicating potential roles of OSM in biological processes.

CONCLUSION

We refined the core OSM candidates combining multiple cohorts. The common pattern shared by different cohorts is worth further investigation. Changes in metabolic pathways based on bioinformatic analysis indicated a role of OSM on ocular diseases. Our results help extend the knowledge and encourage further investigations on the associations between OSM and ocular diseases.

Shining Light on Oral Biofilm Fluorescence In Situ Hybridization (FISH): Probing the Accuracy of In Situ Biogeography Studies

The oral biofilm has been instrumental in advancing microbial research and enhancing our understanding of oral health and disease. Recent developments in next-generation sequencing have provided detailed insights into the microbial composition of the oral microbiome, enabling species-level analyses of biofilm interactions. Fluorescence in situ hybridization (FISH) has been especially valuable for studying the spatial organization of these microbes, revealing intricate arrangements such as "corncob" structures that highlight close bacterial interactions. As more genetic sequence data become available, the specificity and accuracy of existing FISH probes used in biogeographical studies require reevaluation. This study examines the performance of commonly used species-specific FISH probes, designed to differentiate oral microbes within in situ oral biofilms, when applied in vitro to an expanded set of bacterial strains. Our findings reveal that the specificity of several FISH probes is compromised, with cross-species hybridization being more common than previously assumed. Notably, we demonstrate that biogeographical associations within in situ oral biofilms, particularly involving Streptococcus and Corynebacterium, may need to be reassessed to align with the latest metagenomic data.

Characterization of gut microbiota in Apis cerana Across different altitudes in the Peninsular India

BACKGROUND

Honey bees are vital to global ecosystems and agriculture due to their role as key pollinators. The gut microbiota of honey bees is essential for their health, providing nutrition and protection against pathogens. While extensive research has been conducted on Western honey bees, Less is understood about the gut microbiota of Apis cerana, an economically important species in South Asia. This study aimed to identify and describe the gut microbiota of Apis cerana across different elevations in the Indian peninsula to understand how these bacterial communities adapt to various ecological niches.

RESULTS

High-throughput metagenome sequencing of the 16S rRNA gene (V1-V9 region) showed that the core microbiota genera in Apis cerana guts across elevations were Gilliamella, Lactobacillus, Snodgrassella, and Frischella. Gilliamella apicola and Lactobacillus kunkeei were identified as the most abundant species. Alpha diversity analysis showed a trend of decreasing species diversity as altitude increased from 200 to 1200 m, with a slight increase observed above 1400 m. Culturable bacterial species identified through 16S rRNA amplification belonged to the Proteobacteria, Firmicutes, and Actinobacteria phyla. Different elevations harboured distinct bacterial communities, with some species being unique to certain altitudes.

CONCLUSIONS

This study provides valuable insights into the diversity and adaptations of Apis cerana gut microbiota across various ecological niches in the Indian peninsula. The observed variations in microbial communities at different elevations suggest that environmental factors play a significant role in shaping the gut microbiota of honey bees. Understanding these microbial dynamics could help in developing strategies to improve bee health and address critical questions in host-microbe symbiosis. Furthermore, this research lays the groundwork for future studies on the functional roles of these bacterial communities in Apis cerana and their potential applications in beekeeping practices.

Human Gut Microbiome: A Connecting Organ Between Nutrition, Metabolism, and Health

The gut microbiome plays a vital role in human health, functioning as a metabolic organ that influences nutrient absorption and overall well-being. With growing evidence that dietary interventions can modulate the microbiome and improve health, this review examines whether healthcare systems should prioritize personalized microbiome-targeted therapies, such as probiotics, prebiotics, and microbiota transplants, over traditional pharmaceutical treatments for chronic diseases like obesity, diabetes, cardiovascular risk, and inflammatory conditions. A systematic review using Web of Science and Scopus databases was conducted, followed by a scientometric analysis. Key metabolic pathways, such as dietary fiber fermentation and short-chain fatty acid production, were explored, focusing on their impact on lipid and glucose metabolism. The interactions between microbial metabolites and the immune system were also investigated. Dietary interventions, including increased fiber and probiotic intake, show potential for addressing dysbiosis linked to conditions, such as type 2 diabetes, obesity, and autoimmune diseases. The review emphasizes the need to incorporate microbiome modulation strategies into clinical practice and research, calling for a multidisciplinary approach that integrates nutrition, microbiology, and biochemistry to better understand the gut microbiome's complex role in health.

A Literature Review on the Impact of the Gut Microbiome on Cancer Treatment Efficacy, Disease Evolution and Toxicity: The Implications for Hematological Malignancies

The gut microbiome plays a crucial role in modulating the efficacy and toxicity of cancer therapies, particularly in hematological malignancies. This review examines the dynamic interplay between gut microbiota and cancer treatments, such as chemotherapy, immunotherapy, and hematopoietic stem cell transplantation (HSCT). Disruptions in the gut microbiome, known as dysbiosis, are associated with adverse effects like gastrointestinal toxicity, neutropenia and cardiotoxicity during chemotherapy. Conversely, the supplementation of probiotics has shown potential in mitigating these side effects by enhancing gut barrier function and regulating immune responses. In HSCT, a higher diversity of gut microbiota is linked to better patient outcomes, including reduced graft-versus-host disease (GVHD) and improved survival rates. The microbiome also influences the efficacy of immunotherapies, such as immune checkpoint inhibitors and CAR-T cell therapy, by modulating immune pathways. Research suggests that certain bacteria, including Bifidobacterium and Akkermansia muciniphila, enhance therapeutic responses by promoting immune activation. Given these findings, modulating the gut microbiome could represent a novel strategy for improving cancer treatment outcomes. The growing understanding of the microbiome's impact on cancer therapy underscores its potential as a target for personalized medicine and offers new opportunities to optimize treatment efficacy while minimizing toxic side effects.

Characteristics of upper and lower respiratory tract microbiota after lung transplantation

BACKGROUND

The composition and characteristics of airway microbiota offer critical insights for clinical decision-making. Current research on chronic lung diseases shows differences in the composition and characteristics of upper and lower respiratory tract microbiota compared with healthy individuals. However, the temporal changes of these microbial communities in lung transplant recipients remain poorly characterized.

METHODS

This is a longitudinal prospective study. Respiratory specimens were collected regularly from lung transplant recipients for testing and analysis. A total of 150 bronchoalveolar lavage fluid (BALF) samples, 150 throat swab samples, 51 sputum samples, and 36 lung tissue samples were collected from the recipients, at 7 days, 14 days, 1 month, 2 months, 3 months, and 6 months post-transplant for 16S rRNA gene sequencing and analysis.

RESULTS

Our study showed that there were significant differences in α-diversity and β-diversity among lung tissue, throat swab, and sputum samples, although α-diversity did not show a significant difference between lung tissue and BALF. Most amplicon sequence variants (ASVs) belonged to the families Enterobacteriaceae, Pseudomonadaceae, and Stenotrophomonas in BALF, while most ASVs belonged to the genera Streptococcus, Pseudomonadaceae, and Stenotrophomonas in sputum samples. Regarding dynamic changes, Corynebacterium and Staphylococcus were more prevalent in the early post-operative period but gradually decreased by 7 days post-operatively, while the common microbiota found in healthy populations based on literature became the most abundant ASVs at 6 months post-operatively in our study participants. Pseudomonadaceae and Stenotrophomonas contributed to the similarity in the composition of upper and lower respiratory microbiota.

CONCLUSIONS

This study demonstrates that lung transplant recipients exhibit unique characteristics in their upper and lower respiratory tract microbiota, which are distinct ecological profiles, and both undergo significant changes within 6 months post-operatively. The similarity between upper and lower respiratory tract microbiota is associated with microbial diversity and taxonomic dominance.

CLINICAL TRIAL

The clinical trial was registered at Chinese Clinical Trial Registry (ChiCTR2200056908) in February 2022.

Rapid Bacterial Identification through Multiplexed Nucleic Acid Detection on a Digital Microfluidic Platform for Enhanced Clinical Intervention against Infections

Bacterial infections often lead to severe health consequences owing to their ability to infiltrate multiple anatomical sites, including the bloodstream, respiratory tract, and digestive tract, posing substantial diagnostic and therapeutic challenges. Consequently, a rapid and versatile detection method capable of identifying a broad spectrum of bacterial pathogens is urgently required to facilitate precise antibiotic prescriptions. Addressing this need, we introduce MiND-DMF (Multibacterial Infection Nucleic Acid Detection on a Digital Microfluidic Platform), a cost-effective digital microfluidic platform tailored for multiplexed bacterial detection. This system integrates DNA extraction, recombinase polymerase amplification (RPA), and CRISPR-based detection technologies, enabling the efficient identification of six common infectious bacteria. Operating at a constant temperature of 37 °C, MiND-DMF completes the entire diagnostic process in just 55 min and is compatible with human reference genes. In spiked samples, the platform demonstrated a detection limit of 100 CFU/mL, highlighting its exceptional sensitivity and quantification capability. In clinical evaluations, MiND-DMF exhibited outstanding performance, achieving 100% sensitivity and 98%-100% specificity compared to conventional PCR methods across 50 samples derived from diverse tissue sources. This robust platform demonstrates strong anti-interference capabilities, making it suitable for analyzing various tissue fluids including blood, alveolar lavage fluid, urine, nasal secretions, appendiceal pus, and ear pus. The versatility and precision of MiND-DMF support the monitoring of hospital-acquired bacterial infection origins, empowering physicians to prescribe targeted antibiotics and enhancing overall infection prevention and control strategies. By accurately detecting bacteria from multiple sources, MiND-DMF can play a pivotal role in improving patient outcomes and public health.

Endothelial progenitor cells improve intestinal homeostasis after hematopoietic stem cell transplantation in mice

Transplant conditioning regimens disrupt the intestinal barriers, leading to delayed vascularity and impeded the regenerative process. However, our understanding of the specific mechanisms underlying the use of cellular therapy to accelerate revascularization for intestinal repair is currently limited. To address this knowledge gap, we conducted a longitudinal study to investigate the effects and potential benefits of endothelial progenitor cells (EPCs) infusion on the restoration of intestinal homeostasis in a murine model of bone marrow transplantation (BMT). Our results revealed that the EPCs infusion improved the structure status of the intestine, as demonstrated by a well-preserved crypt structure, longer villi, reduced infiltration of inflammatory cells, and increased expression of ZO-1 and MECA-32. Additionally, EPCs infusion resulted in significantly lower proportions of Tc1 and Th1 cells on day 10, as well as a delayed peak in Tc17 cells on day 20, with no differences compared with BMT group thereafter. Moreover, EPCs infusion enhanced the expression of immune regulatory molecules IL-10, IL-17, IL-18, and NLRP6 on day 15. Mechanistically, EPCs infusion up-regulated phos-ERK1/2 and down-regulated phos-p38 MAPK on day 5 (early transplantation). The richness of intestinal microbiota changed significantly, and Erysipelotrichaceae was identified as the main index to differentiate the BMT and EPC treatments, exhibiting a significant negative correlation with IL-10 and IL-18 in the EPC group. Taken together, this study highlights the protective role of EPCs in post-transplantation intestinal damage, and identifies critical immune cells, signaling pathways, and selectively enriched intestinal microbes contributing to the beneficial effects of EPCs during intestinal repair.

Multi-omics analyses of the gut microbiota and metabolites in children with metabolic dysfunction-associated steatotic liver disease

The development and severity of metabolic dysfunction-associated steatotic liver disease (MASLD) in children are closely related to alterations of gut microbiota. This study aims to investigate changes in the gut microbiota signature and microbial metabolites in children with MASLD. We collected fecal samples from children and adolescents aged 6-16 years, and the presence of MASLD was diagnosed by ultrasound. We performed 16S ribosomal DNA sequencing and targeted metabolomics in 36 and 25 subjects, consisting of healthy controls, children with obesity, and children with MASLD. The α-diversity was significantly lower in children with obesity and MASLD compared with healthy controls. Linear discriminant analysis of effect size analysis identified Anaerostipes and A. hadrus as the top biomarkers differentiating the obesity group from the MASLD group. In MASLD patients with high alanine aminotransferase values (≥50 U/L for boys and 44 U/L for girls), we observed a decrease in the gut microbiota health index. MASLD patients with high shear wave elastography (E) values (≥6.2 kPa) showed an increased abundance of Ruminococcus torques, which was positively correlated with the levels of deoxycholic acid (DCA) and E values. Importantly, the mediation analysis identified positive associations between R. torques and clinical indicators of MASLD that were mediated by DCA. Overall, our study suggests that gut microbiota and metabolites are significantly altered in children with MASLD, and targeting R. torques may offer potential benefits for disease management.IMPORTANCEThis study investigated alterations in the gut microbiota signature and microbial metabolites in children with metabolic dysfunction-associated steatotic liver disease (MASLD). We found that an increased abundance of Ruminococcus torques was associated with increased levels of deoxycholic acid and the progression of MASLD, suggesting that R. torques may serve as a novel clinical target in pediatric MASLD.

Lactobacillus salivary LSbg3 is a Potential Food Probiotic Having Excellent Anti-pathogen Effect That Might Improve Antibiotic-Resistant Diarrhea in Dogs

Antibiotics may disrupt the intestinal microbiota balance and induce antimicrobial resistance. Although probiotics should be a priority treatment for animal diarrhea, it still has chance to be used as same/or behind as antibiotics in the clinic. Among the probiotics, Lactobacillus (Lact.) was the most frequently utilized in clinical setting since its excellent ability of safety, anti-pathogen, stress resistance, and easy colonization in intestine. In this study, we screened 24 strains of Lact. in the presence of antibiotics from clinical common antibiotic-treated feces, identified L. salivarius LSbg3 exhibiting good stress resistance, potent antibacterial activity, and exceptional intestinal adhesion capability. Its genome showed a good function of regulating intestinal nutrition while lack of transmission antibiotic-resistance genes. Additionally, in a simulated canine diarrhea with failed antibiotic treatment, LSbg3 had a good efficacy in the releasing diarrhea, balancing the microbiome and suppressing typical pathogens, positioning a potential food probiotic have excellent effect on anti-pathogen that can effectively improve antibiotic-resistant diarrhea in dogs.

Probiotic treatment induces sex-dependent neuroprotection and gut microbiome shifts after traumatic brain injury

BACKGROUND

Recent studies have highlighted the potential influence of gut dysbiosis on traumatic brain injury (TBI) outcomes. Alterations in the abundance and diversity of Lactobacillus species may affect immune dysregulation, neuroinflammatory responses, anxiety- and depressive-like behaviors, and neuroprotective mechanisms activated in response to TBI.

OBJECTIVE

This study aims to evaluate the protective and preventive effects of Pan-probiotic (PP) treatment on the inflammatory response during both the acute and chronic phases of TBI.

METHODS

Males and female mice underwent controlled cortical impact (CCI) injury or sham. They received a PP mixture in drinking water containing strains of Lactobacillus plantarum, L. reuteri, L. helveticas, L. fermentum, L. rhamnosus, L. gasseri, and L. casei. In the acute group, mice received PP or vehicle (VH) treatment for 7 weeks before TBI, continuing until 3 days post-injury (dpi). In the chronic group, treatment began 2 weeks before TBI and was extended through 35 dpi. The taxonomic microbiome profiles of fecal samples were evaluated using 16S rRNA V1-V3 sequencing analysis, and Short-chain fatty acids (SCFAs) were measured. Immunohistochemical, in situ hybridization, and histological analyses were performed to assess neuroinflammation post-TBI, while behavioral assessments were conducted to evaluate sensorimotor and cognitive functions.

RESULTS

Our findings suggest that a 7-week PP administration induces specific microbial changes, including increased abundance of beneficial bacteria such as Lactobacillaceae, Limosilactobacillus, and Lactiplantibacillus. PP treatment reduces lesion volume and cell death at 3 dpi, elevates SCFA levels at 35 dpi, and decreases microglial activation at both time points, particularly in males. Additionally, PP treatment improved motor recovery in males and alleviated depressive-like behaviors in females.

CONCLUSION

Our findings indicate that PP administration modulates microbiome composition, reduces neuroinflammation, and improves motor deficits following TBI, with these effects being particularly pronounced in male mice.

Optimization of thermostable amylolytic enzyme production from Bacillus cereus isolated from a recreational warm spring via Box Behnken design and response surface methodology

This study aimed to find a source for local amylase-producing microbes. Sixteen isolates were obtained from the water samples from the warm spring and characterized based on morphological and biochemical tests. The 16S rRNA molecular identification technique confirmed the most potent isolate as Bacillus cereus. The thermophilic property of the bacterium demonstrated that it could withstand temperatures of up to 80 °C. One-factor-at-a-time (OFAT) and Box Behnken Design (BBD) coupled with response surface methodology (RSM) optimization techniques were used to improve amylase production. OFAT established optimal physical parameter conditions as the starch concentration of 5% w/v, inoculum volume of 2% v/v, pH of 8, incubation temperature of 45 °C, and 48 h of incubation, leading to amylase activity of 172.6 U/mL by the isolated B. cereus. A quadratic mathematical model with a coefficient of determination (R2) of 0.9957 was established for the amylase production process. Enhanced amylase activity of 196.02 U/mL was achieved with BBD-RSM under optimal growth conditions of pH of 7, incubation time of 48 h, substrate concentration of 5% w/v of starch, and at 45 °C, a 1.2-fold increase compared to the OFAT method. The B. cereus strain isolated from the warm spring was a mildly thermophilic bacterium with the potential for synthesizing amylolytic enzymes with characteristics beneficial for commercial utilization.

Genetic Diversity and Growth-Promoting Functions of Endophytic Nitrogen-Fixing Bacteria in Apple

Understanding the dominant populations and biological functions of endophytic nitrogen-fixing bacteria in apple plants is of great significance for the healthy growth management and sustainable development of apple cultivation. In this study, we investigated the community diversity and potential plant growth-promoting abilities of endophytic nitrogen-fixing bacteria in different tissues of apple trees by combining high-throughput sequencing of the nifH gene with traditional isolation and cultivation techniques. Sequencing results revealed that the endophytic bacteria were affiliated with 10 phyla, 14 classes, 30 orders, 42 families, and 72 genera. Rhizobium was the dominant genus in the roots and twigs, while Desulfovibrio dominated the leaf tissues. The diversity and richness of endophytic bacteria in the roots were significantly higher than those in the leaves. Using four types of nitrogen-free media, a total of 138 presumptive endophytic nitrogen-fixing bacterial strains were isolated from roots, leaves, and twigs. These isolates belonged to 32 taxonomic groups spanning 5 phyla, 8 classes, 11 orders, 13 families, and 18 genera. The nifH gene was successfully amplified from the representative strains of all 32 groups using specific primers. Nitrogenase activity among the isolates ranged from 26.86 to 982.28 nmol/(h·mL). Some strains also exhibited the ability to secrete indole-3-acetic acid (IAA), solubilize phosphate and potassium, and produce siderophores. Six individual strains and three microbial consortia were tested for their plant growth-promoting effects on apple tissue culture seedlings. All treatments showed growth-promoting effects to varying degrees, with the RD01+RC16 consortium showing the most significant results: plant height, number of leaves, and chlorophyll content were 2.4, 3.3, and 4.2 times higher than those of the control, respectively. These findings demonstrate the rich diversity of endophytic nitrogen-fixing bacteria in apple plants and their promising potential for application in promoting host plant growth.

Intratumoral microbiota for hepatocellular carcinoma: from preclinical mechanisms to clinical cancer treatment

Intratumoral microbiota has been found to be a crucial component of hepatocellular carcinoma (HCC). Due to insufficient recognition, technical limitations, and low biomass of intratumoral microbiota, it is poorly understood. Intratumoral microbiota exhibit significant diversity in HCC tissues. It is involved in the development of HCC through several mechanisms, such as remodeling the immunosuppressive microenvironment, metabolic reprogramming, and genetic alterations. Moreover, intratumoral microbiota is associated with the metastasis of HCC cells. Herein, we reviewed the history of intratumoral microbiota, applied biotechnology to depict the signatures of intratumoral microbiota, investigated the potential sources of intratumoral microbiota, and assessed their functions, mechanisms, and heterogeneity. Furthermore, in this review, we summarized the development of therapeutics that can be used in the treatment of HCC and proposed future perspectives for research in this field.

Comprehensive gut microbiota and metabolomics combined with network pharmacology reveal the effects of acupuncture treatment for chemotherapy-induced nausea and vomiting

Background

Chemotherapy-induced nausea and vomiting (CINV) significantly impact cancer patients' quality of life. Traditional pharmacological treatments often have limited effectiveness and can cause adverse effects. Acupuncture, a key practice in traditional Chinese medicine (TCM), shows promise as a complementary therapy for CINV. The purpose of this study was to explore the effects and underlying mechanisms of acupuncture in treating CINV.

Methods

We employed a multi-faceted approach to comprehensively explore the abnormal performances of CINV model and to elucidate the regulatory effects of acupuncture in treating CINV through the integration of 16S rRNA analysis, serum metabolomics, and network pharmacology.

Results

Acupuncture significantly reduced kaolin consumption, mitigated anorexia, and attenuated body weight loss compared to the model group. Acupuncture was found to modulate the gut microbiota composition, enhancing beneficial taxa and reducing harmful ones. Serum metabolomic analysis revealed significant alterations in metabolic profiles, with acupuncture impacting various metabolites involved in pathways related to fatty acid biosynthesis, urea cycle, and amino acid metabolism. Spearman correlation analysis indicated a significant association between gut microbial taxa and serum metabolites. Furthermore, network pharmacology analysis identified key genes (MAPK1, STAT3, EGFR, AKT1, SRC) and pathways (PI3K/Akt, neuroactive ligand-receptor interaction) associated with the anti-CINV effects of acupuncture. In conclusion, acupuncture holds promise in ameliorating CINV through its multifaceted impact on gut microbiota, serum metabolome, and molecular pathways.

Conclusions

Acupuncture was an adjunctive and important non-drug treatment for CINV, with the protective effects linked to the improvement of gut microbiota disruption and metabolic abnormalities.