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Bibliography on: Biodiversity and Metagenomics

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Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 19 Feb 2025 at 01:30 Created: 

Biodiversity and Metagenomics

If evolution is the only light in which biology makes sense, and if variation is the raw material upon which selection works, then variety is not merely the spice of life, it is the essence of life — the sine qua non without which life could not exist. To understand biology, one must understand its diversity. Historically, studies of biodiversity were directed primarily at the realm of multicellular eukaryotes, since few tools existed to allow the study of non-eukaryotes. Because metagenomics allows the study of intact microbial communities, without requiring individual cultures, it provides a tool for understanding this huge, hitherto invisible pool of biodiversity, whether it occurs in free-living communities or in commensal microbiomes associated with larger organisms.

Created with PubMed® Query: biodiversity metagenomics NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

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RevDate: 2025-02-18
CmpDate: 2025-02-17

Kuźmycz O, Kowalczyk A, Bolanowska A, et al (2025)

A comprehensive analysis of the uterine microbiome in endometrial cancer patients - identification of Anaerococcus as a potential biomarker and carcinogenic cofactor.

Frontiers in cellular and infection microbiology, 15:1511625.

INTRODUCTION: Endometrial cancer (EC) is a significant gynecological malignancy with increasing incidence worldwide. Emerging evidence highlights the role of the uterine microbiome in the pathogenesis of EC. This study aims to characterize the uterine microbiome in EC patients and identify potential microbial biomarkers, with a focus on Anaerococcus as a differentiating taxon.

METHODS: The endocervical canal swabs from patients with EC (n=16) and non-cancerous patients (EM, n=13) were collected. The V3-V4 region of the 16S rRNA gene was sequenced using the Illumina platform. Bioinformatic analyses were performed with QIIME2, and statistical comparisons were conducted to assess differences in microbial composition and diversity. In vitro experiments were conducted to assess the functional impact of Anaerococcus on human uterine fibroblasts, including its ability to adhere to the human cells and induce oxidative stress.

RESULTS: The α-diversity metrics, including Shannon entropy and observed amplicon sequence variants (ASVs), revealed significantly higher microbial diversity in EC samples compared to EM. Anaerococcus was identified as a key taxon differentiating EC from EM groups, showing a higher relative abundance in EC samples. Functional predictions and in vitro assays indicated that Anaerococcus may contribute to carcinogenesis by inducing reactive oxygen species (ROS) production, and has the high ability to adhere to the human endometrial fibroblasts.

DISCUSSION: The study provides evidence of distinct microbial signatures in EC, with Anaerococcus emerging as a potential biomarker. The in vitro findings suggest its role in endometrial carcinogenesis, underscoring its potential as a target for future diagnostic and therapeutic applications.

RevDate: 2025-02-16
CmpDate: 2025-02-16

Echeveste Medrano MJ, Smith GJ, Sánchez-Andrea I, et al (2025)

Contrasting Methane, Sulfide and Nitrogen-Loading Regimes in Bioreactors Shape Microbial Communities Originating From Methane-Rich Coastal Sediment of the Stockholm Archipelago.

Environmental microbiology, 27(2):e70056.

Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane-rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane-saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by Methylobacter and Methylomonas in eutrophic conditions, whereas a more diverse methane-oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOs) were identified in MBAE14 and co-enriched Rugosibacter genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.

RevDate: 2025-02-18
CmpDate: 2025-02-18

Pu G, Hou L, Zhao Q, et al (2025)

Interactions between gut microbes and host promote degradation of various fiber components in Meishan pigs.

mSystems, 10(2):e0150024.

UNLABELLED: Although metagenomic investigations into microbial fiber-degrading capabilities are currently prevalent, there is a notable gap in research concerning the regulatory mechanisms underpinning host-microbiota interactions that confer tolerance to high-fiber diets in pigs. In this study, 28 Meishan (MS) and 28 Large White (LW) pigs were subjected to feeding experiments involving various fiber levels. Subsequently, multi-omics was employed to investigate the influence of host-microbiota interactions on the fiber degradation of pigs. MS exhibited superior fiber digestibility compared with LW, particularly evident when fed a high-fiber diet. In MS, positive interactions among Treponema bryantii, Treponema sp., Rikenellaceae bacterium, and Bacteroidales bacterium WCE2004 facilitated the degradation of both cellulose and pectin. The reduced polymerization of polysaccharides and oligosaccharides observed in MS provides compelling evidence for their superior microbial fiber-degrading capability. The concentrations of propionate and butyrate retained in cecal lumen of MS was unchanged, whereas it was significantly increased in LW, indicating a strong absorption of short-chain fatty acids (SCFAs) in MS intestines. Correlation analysis using RNA-seq data revealed distinct patterns in LW and MS. In LW, microbial profiles along with GPR183 and GPR174 exhibited negative correlations with butyrate and propionate, respectively. Conversely, in MS, GPR174 and SLC2A4 were positively correlated with butyrate. Our findings underscore the dynamic collaboration among microbial species in degrading cellulose and pectin, coupled with the synergistic effects of SCFA transport-related genes, as crucial underpinnings for the heightened fiber digestibility observed in MS. These discoveries offer fresh perspectives into the intricate mechanisms governing host-microbiota interactions that influence fiber digestion in pigs.

IMPORTANCE: Studies on porcine intestinal microbiota have been widely conducted, and some microbial taxa with fiber degradation functions have been identified. However, the mechanisms of division among gut microbes in the degradation of complex fiber components are still unclear. In addition, the regulation of fiber digestion by host through absorption of short-chain fatty acids (SCFAs) needs to be further investigated. Our study used apparent total tract digestibility of dietary fiber to assess the utilization efficiency of dietary fiber between Meishan and Large White pigs. Subsequently, through metagenome sequencing and determination of fiber-degrading products, we found that in Meishan pigs, positive interactions among Treponema bryantii, Treponema sp., Rikenellaceae bacterium, and Bacteroidales bacterium WCE2004 facilitated the degradation of both cellulose and pectin. RNA-seq analysis elucidated breed-specific genes associated with SCFA absorption in cecum. By integrating multi-omics data, we constructed a framework outlining host-microbiota interactions that control dietary fiber utilization in pigs. Our data provide novel insights into host-microbiota interactions regulating fiber degradation and lay some theoretical foundations for improving the utilization efficiency of high-fiber cereal feed in pigs through targeted modulation of gut microbial function.

RevDate: 2025-02-18
CmpDate: 2025-02-18

Sáenz JS, Rios-Galicia B, J Seifert (2025)

Antiviral defense systems in the rumen microbiome.

mSystems, 10(2):e0152124.

The continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanisms. However, the diversity and prevalence of antiviral defense systems in complex communities are still unknown. We therefore investigated the diversity and abundance of viral defense systems in 3,038 high-quality bacterial and archaeal genomes from the rumen. In total, 14,241 defense systems and 31,948 antiviral-related genes were identified. Those genes represented 114 unique system types grouped into 49 families. We observed a high prevalence of defense systems in the genomes. However, the number of defense systems, defense system families, and system density varied widely from genome to genome. Additionally, the number of defense system per genome correlated positively with the number of defense system families and the genome size. Restriction modification, Abi, and cas system families were the most common, but many rare systems were present in only 1% of the genomes. Antiviral defense systems are prevalent and diverse in the rumen, but only a few are dominant, indicating that most systems are rarely present. However, the collection of systems throughout the rumen may represent a pool of mechanisms that can be shared by different members of the community and modulate the phage-host interaction.IMPORTANCEPhages may act antagonistically at the cell level but have a mutualistic interaction at the microbiome level. This interaction shapes the structure of microbial communities and is mainly driven by the defense mechanism. However, the diversity of such mechanism is larger than previously thought. Because of that, we described the abundance and diversity of the antiviral defense system of a collection of genomes, metagenome-assembled genomes (MAGs) and isolates, from the rumen. While defense mechanisms seem to be prevalent among bacteria and archaea, only a few were common. This suggests that most of these defense mechanisms are not present in many rumen microbes but could be shared among different members of the microbial community. This is consistent with the "pan-immune system" model, which appears to be common across different environments.

RevDate: 2025-02-18
CmpDate: 2025-02-18

Geers AU, Michoud G, Busi SB, et al (2025)

Deciphering the biosynthetic landscape of biofilms in glacier-fed streams.

mSystems, 10(2):e0113724.

UNLABELLED: Glacier-fed streams are permanently cold, ultra-oligotrophic, and physically unstable environments, yet microbial life thrives in benthic biofilm communities. Within biofilms, microorganisms rely on secondary metabolites for communication and competition. However, the diversity and genetic potential of secondary metabolites in glacier-fed stream biofilms remain poorly understood. In this study, we present the first large-scale exploration of biosynthetic gene clusters (BGCs) from benthic glacier-fed stream biofilms sampled by the Vanishing Glaciers project from the world's major mountain ranges. We found a remarkable diversity of BGCs, with more than 8,000 of them identified within 2,868 prokaryotic metagenome-assembled genomes, some of them potentially conferring ecological advantages, such as UV protection and quorum sensing. The BGCs were distinct from those sourced from other aquatic microbiomes, with over 40% of them being novel. The glacier-fed stream BGCs exhibited the highest similarity to BGCs from glacier microbiomes. BGC composition displayed geographic patterns and correlated with prokaryotic alpha diversity. We also found that BGC diversity was positively associated with benthic chlorophyll a and prokaryotic diversity, indicative of more biotic interactions in more extensive biofilms. Our study provides new insights into a hitherto poorly explored microbial ecosystem, which is now changing at a rapid pace as glaciers are shrinking due to climate change.

IMPORTANCE: Glacier-fed streams are characterized by low temperatures, high turbidity, and high flow. They host a unique microbiome within biofilms, which form the foundation of the food web and contribute significantly to biogeochemical cycles. Our investigation into secondary metabolites, which likely play an important role in these complex ecosystems, found a unique genetic potential distinct from other aquatic environments. We found the potential to synthesize several secondary metabolites, which may confer ecological advantages, such as UV protection and quorum sensing. This biosynthetic diversity was positively associated with the abundance and complexity of the microbial community, as well as concentrations of chlorophyll a. In the face of climate change, our study offers new insights into a vanishing ecosystem.

RevDate: 2025-02-18
CmpDate: 2025-02-18

Zhang M, Zhang L, Suo B, et al (2025)

Distribution Characteristics and Impacting Factors of Drug CYP Enzymes and Transporters in the Gastrointestinal Tract of Chinese Healthy Subjects.

Clinical pharmacology and therapeutics, 117(3):676-689.

The abundance of drug metabolic enzymes (DMEs) and transporters (DTs) in the human gastrointestinal tract significantly affects xenobiotic exposure in the circulating system, the basis of these compounds acting on humans. However, accurately predicting individual exposure in healthy subjects remains challenging due to limited data on protein levels throughout the gastrointestinal tract within the same individuals and inadequate assessment of factors influencing these levels. Therefore, we conducted a clinical study to obtain biopsy samples from 8 different gastrointestinal segments in 24 healthy Chinese volunteers. Concurrently, blood and fecal samples were collected for genotypic analysis and fecal microbiota metagenomic sequencing. Using an optimized LC-MS/MS method, we quantified the absolute protein abundance of CYP2C9, CYP2C19, CYP2D6, CYP3A4, P-gp, and BCRP from the stomach to the colon. Our results revealed significant regional differences in protein expression: CYP3A4 was the most abundant in the small intestine, whereas CYP2C9 was predominantly found in the colon. CYP2D6 was primarily located in the ileum, while other DMEs/DTs showed higher concentrations in the jejunum. Meanwhile, the enzyme abundance in the small intestine and colon and the relative ratio of transporters in different regions to the jejunum were accurately calculated, providing valuable data for refining the physiological parameters in the virtual gastrointestinal tract of Chinese healthy population in PBBMs. Additionally, BMI, IBW, sex, age, genotype, and fecal microbiota were identified as critical factors influencing the protein levels of these DMEs/DTs throughout the gastrointestinal tract, with notable regional differences. Consequently, this study provides a unique foundation for understanding xenobiotic absorption in humans.

RevDate: 2025-02-15
CmpDate: 2025-02-15

O' Donovan CM, Nori SRC, Shanahan F, et al (2025)

Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.

Scientific reports, 15(1):5619.

Human gut microbiome composition and function is influenced by environmental and lifestyle factors, including exercise and fitness. We studied the composition and functionality of the faecal microbiome of recreational (non-elite) runners (n = 62) with serial shotgun metagenomics, at 4 time points over a 7-week period. Gut microbiome composition and function was stable over time. Grouping of samples on the basis of their fitness level (fair, good, excellent, and superior) or habitual training (low (4-6 h/week), medium (7-9 h/week), high (10-12 h/week), and extreme (13 + hours/week)) revealed no significant microbiome-related differences. Overall, the species Faecalibacterium prausnitzii, Blautia wexlerae, and Prevotella copri were the most abundant members of the gut microbiome. Analysis of co-abundance groups (CAGs) revealed no significant relationship between CAGs and fitness levels or training subgroups. Functional pathways were similar across all samples and timepoints with no clustering based on associated metadata. The most abundant genes identified within samples corresponded to pathways for nucleoside and nucleotide biosynthesis, amino acid biosynthesis, and cell wall biosynthesis. Collectively, these results describe the microbiome of active recreational runners and note temporal stability amongst participants.

RevDate: 2025-02-17
CmpDate: 2025-02-17

Wang H, Liu Q, Abouelfetouh MM, et al (2025)

The role of the hypothalamus-gut microbiota in the pathogenesis of periparturient fatty liver disease in dairy cows.

Veterinary journal (London, England : 1997), 309:106290.

During the periparturient period, dairy cows experience negative energy balance due to reduced feed intake, leading to adipose tissue breakdown, liver damage, and fat accumulation. This study examined the gut-liver-brain axis to explore the link between fatty liver disease, changes in hypothalamic appetite-related neurons, and microbiome shifts in dairy cows. Thirty cows were monitored, with daily DMI recordings and blood sampling. Postpartum brain, liver, and ileal contents were collected from 10 selected cows, divided into two groups: H-DMI (slight DMI decrease) and L-DMI (severe DMI decrease). The L-DMI group of cows exhibited higher plasma NEFA, BHBA, ALT, and AST levels, along with severe hepatic steatosis and lipid accumulation. Transcriptome sequencing of the hypothalamic arcuate nucleus (ARC) revealed decreased expression of Hypocretin Neuropeptide Precursor (HCRT), orexin-A (OX-A), Orexin Receptor Type 1 (OX1R), and Cannabinoid Receptor 1 (CB1) in the L-DMI group, while Pro-opiomelanocortin (POMC) and Melanocortin 4 Receptor (MC4R) expression increased. Metagenomic analysis of ileal contents showed reduced abundance of Ruminococcus spp. in the L-DMI group, which may be associated with fatty liver disease (FL). Integrated omics analysis showed that increased MC4R expression was correlated with the elevated abundance of bacteria such as Akkermansia glycaniphila, and reduced abundance of species such as Methanobrevubacter thaueri and Ruminococcus spp. Decreased HCRT expression was also linked to Akkermansia glycaniphila. In conclusion, these changes may affect DMI through the OX-A/POMC pathway, with neurological and gut microbiome alterations potentially leading to appetite suppression, negative energy balance, and the development of fatty liver disease.

RevDate: 2025-02-17
CmpDate: 2025-02-17

Quraishi MN, Cheesbrough J, Rimmer P, et al (2025)

Open Label Vancomycin in Primary Sclerosing Cholangitis-Inflammatory Bowel Disease: Improved Colonic Disease Activity and Associations With Changes in Host-Microbiome-Metabolomic Signatures.

Journal of Crohn's & colitis, 19(2):.

BACKGROUND: We conducted a single-arm interventional study, to explore mucosal changes associated with clinical remission under oral vancomycin (OV) treatment, in primary sclerosing cholangitis-associated inflammatory bowel disease (PSC-IBD); NCT05376228.

METHODS: Fifteen patients with PSC and active colitis (median fecal calprotectin 459 µg/g; median total Mayo score 5) were treated with OV (125 mg QID) for 4 weeks and followed-up for a further 4 weeks of treatment withdrawal (8 weeks, end-of-study). Colonic biopsies were obtained at baseline and Week 4. Clinical assessments, and serum and stool samples (metagenomics, metatranscriptomics, and metabolomics) were collected at Weeks 0, 2, 4, and 8. The primary efficacy outcome measure was the induction of clinical remission.

RESULTS: Oral vancomycin resulted in clinical remission in 12/15 patients and significant reductions in fecal calprotectin. Oral vancomycin was associated with reduced abundances of Lachnospiraceae, genera Blautia and Bacteroides; and enrichment of Enterobacteriaceae, and genera Veillonella, Akkermansia, and Escherichia. Oral vancomycin treatment was associated with the downregulation of multiple metatranscriptomic pathways (including short-chain fatty acid [SCFA] metabolism and bile acid [BA] biotransformation), along with host genes and multiple pathways involved in inflammatory responses and antimicrobial defence; and an upregulation of genes associated with extracellular matrix repair. Oral vancomycin use resulted in the loss of specific fecal SCFAs and secondary BAs, including lithocholic acid derivatives. Colitis activity relapsed following OV withdrawal, with host mucosal and microbial changes trending toward baseline.

CONCLUSIONS: Four weeks of OV induces remission in PSC-IBD activity, associated with a reduction in gut bacterial diversity and compositional changes relating to BA and SCFA homeostasis.

RevDate: 2025-02-18
CmpDate: 2025-02-17

Arumugam U, Sudarsanan GB, Karuppannan AK, et al (2025)

Metagenomic Studies Reveal the Evidence of Akkermansia muciniphila and Other Probiotic Bacteria in the Gut of Healthy and Enterocytozoon hepatopenaei (EHP)-Infected Farmed Penaeus vannamei.

Probiotics and antimicrobial proteins, 17(1):432-439.

Penaeus vannamei (whiteleg shrimp) is the most widely cultured shrimp globally. Enterocytozoon hepatopenaei (EHP), a microsporidian parasite, infects P. vannamei and causes severe growth retardation, subsequent production, and economic losses in the shrimp culture. The influence of EHP infection in the shrimp gut microbiota is poorly studied, and this would be an interesting area to investigate since the gut microbiome of shrimp influences a number of key host processes such as digestion and immunity. In this study, a metagenomic approach was followed to compare the overall species richness of the gut microbiota of EHP-infected and healthy P. vannamei. Bacterial genomic DNA from the healthy and EHP-infected gut sample were profiled for the bacterial 16S rRNA gene, targeting the V3-V4 conserved region. Operational taxonomic units (OTUs), an approximation of definitive taxonomic identity, were identified based on the sequence similarity within the sample reads and clustered together using a cut-off of 97% identity using UCLUST. The OTUs were then used for the computation of alpha diversity and beta diversity for each sample. EHP-infected gut sample showed lower bacterial abundance throughout the family, class, order, genus, and species levels when compared to healthy gut sample. This study shows that the shrimp gut microbiota is sensitive and exhibits a high level of plasticity during a microsporidian infection like EHP. Furthermore, Akkermansia muciniphila, a novel probiotic bacterium, has been reported in the shrimp gut for the first time.

RevDate: 2025-02-14
CmpDate: 2025-02-14

Cantuti Gendre J, Le Marrec C, Chaillou S, et al (2025)

Exploring viral diversity in fermented vegetables through viral metagenomics.

Food microbiology, 128:104733.

Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.

RevDate: 2025-02-16
CmpDate: 2025-02-16

Eckermann H, Lustermans H, Parnanen K, et al (2025)

Maternal pre- and postnatal stress and maternal and infant gut microbiota features.

Psychoneuroendocrinology, 172:107273.

BACKGROUND: Maternal stress can have short and long term adverse (mental) health effects for the mother and her child. Previous evidence suggests that the gut microbiota may be a potential mediator and moderator for the effects of stress via various pathways. This study explored the maternal microbiota trajectory during pregnancy as well as the association between pre- and postnatal maternal stress and features of the maternal and infant gut microbiota during and after pregnancy. In line with previous research, we hypothesized that maternal stress would be positively related to maternal and infant microbiota volatility and that infants of highly stressed mothers would show a relative increase in Proteobacteria and a relative decrease in Bifidobacterium.

METHODS: We collected maternal stool samples at 18 and 32 weeks of pregnancy and 8 months postpartum. Infant stools samples were obtained at 2, 6 and 12 weeks and 8 months postpartum. All samples were analyzed using shotgun metagenome sequencing. We also collected several measures of maternal stress (self-reported depression, anxiety, and stress, and hair cortisol and cortisone), most at the same time points as the microbiota samples.

RESULTS: Our data indicated that the maternal microbiota does not undergo drastic changes from the second to the third trimester of pregnancy but that the postpartum microbiota differs significantly from the prenatal microbiota. Furthermore, we identified associations between several stress measures and maternal and infant gut microbiota features at different time points including positive and negative associations with alpha diversity, beta diversity and individual microbial phyla and species relative abundances. Also, the maternal stress composite score, the perceived stress score and the log-ratio of hair cortisol and cortisone were all positively associated with infant microbiota volatility.

CONCLUSION: Our study provides evidence that maternal prenatal and postnatal stress is related to both the maternal and the infant microbiota. Collectively, this and previous studies indicate that maternal stress does not uniformly associate with most gut microbial features. Instead, the associations are highly time point specific. Regarding infant microbiota volatility, we have consistently found a positive association between stress and infant microbiota volatility. This warrants future research investigating this link in more depth.

RevDate: 2025-02-16
CmpDate: 2025-02-16

Yuan X, Zhang Y, Pang L, et al (2025)

Insulin resistance links dysbiosis of gut microbiota with cognitive impairment in first-episode drug-naïve schizophrenia.

Psychoneuroendocrinology, 172:107255.

This study aimed to explore the relationship among gut microbiota imbalance, the homeostasis model of assessment of insulin resistance (HOMA-IR) and cognitive impairments in patients with schizophrenia (SCZ). We conducted a case-control study involving 189 first-episode, drug-naïve SCZ patients and 115 healthy controls (HCs). Main methods adopted included metagenomics analysis, glucose metabolism assessment, and cognitive function evaluation using the MATRICS Consensus Cognitive Battery (MCCB). Fecal microbiota composition was analyzed via high-throughput sequencing of 16S ribosomal RNA. Patients with SCZ showed a higher likelihood of developing IR (23 %), compared to HCs (12 %). The IR group exhibited significantly higher levels of fasting blood glucose (FBG), fasting insulin (FINS), HOMA-IR, and homeostasis model assessment-β (HOMA-β), while showing lower insulin sensitivity index (ISI) levels (all p < 0.05). Patients with IR demonstrated lower scores in working memories (WM), verbal learning (HVLT) and reasoning and problem solving (RPS), compared to those without IR. Additionally, microbiota analysis revealed that IR patients had higher abundance of Negativicutes, Streptococcaceae, Enterobacteriaceae, Lachnoclostridium, Dialister, Klebsiella, and Enterobacter, and lower abundance of Flavonifractor and Rikenellaceae. Notably, Negativicutes, Streptococcaceae, Lachnoclostridium, Flavonifractor, and Rikenellaceae were shared between SCZ and IR conditions. Mediation analysis indicated that the relative abundance of Streptococcaceae have an indirect effect on WM through HOMA-IR (β=-0.148, SE=0.067, 95 %CI=-0.280 to -0.020). The study suggests that IR may play a mediating role in the relationship between gut microbiota dysbiosis and cognitive impairments in patients with SCZ, which could point to potential new avenues for therapeutic interventions.

RevDate: 2025-02-14
CmpDate: 2025-02-14

Li Z, Liao Y, Huang C, et al (2025)

Analyzing fungal community succession and its correlation to flavor compounds in the Cupei fermentation process of Sichuan shai vinegar.

Food microbiology, 128:104718.

Sichuan Shai vinegar, a distinctive condiment from Southwest China, is produced through open-air solid-state fermentation, employing a unique Chinese herbal medicine mixture (Yaoqu) as the fermentation starter. Despite its culinary significance, the dynamics and roles of fungal communities within the Cupei fermentation phase remain understudied. This study employed high-performance liquid chromatography (HPLC) to quantify 11 organic acids and 17 amino acids, revealing a significant increase in organic acid content from 2.56 g/100 g-17.47 g/100 g dry weight and a gradual elevation in free amino acid content from 0.53 g/100 g-5.59 g/100 g throughout the fermentation process. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS) identified 85 volatile flavor compounds, predominantly consisting of 2 alcohols, 10 acids, 29 esters, 4 ketones, 6 aldehydes, and 14 other types. High-throughput sequencing facilitated the identification of key microorganisms, with Lichtheimia, Brettanomyces, Pichia, Saccharomyces, Kazachstania, and Syncephalastrum emerging as the most abundant fungal genera. Correlation analysis revealed significant positive correlations between 20 fungi and 11 organic acids, 24 fungi and 16 amino acids, and 50 fungi and 76 volatile flavor compounds. Notably, Lichtheimia, Pichia, and Brettanomyces were identified as the most influential in flavor metabolism. These findings elucidate the microbial metabolic mechanisms during Sichuan Shai vinegar fermentation, laying a foundation for further research and potential applications in vinegar production.

RevDate: 2025-02-14
CmpDate: 2025-02-14

Sequino G, Cobo-Diaz JF, Valentino V, et al (2025)

Environmental microbiome mapping in poultry processing chain and assessment of microbial dynamics in response to different storage conditions.

Food microbiology, 128:104734.

Poultry production chain comprises a complex network involving various stages from rearing to the final distribution of poultry products. This study explores the intricate dynamics within this chain, using shotgun metagenomics, particularly focusing on taxonomic and functional composition of the microbiome, antibiotic resistance and virulence potential. Moreover, the study of the impact of different packaging and storage conditions provides insights into how diverse packaging strategies and storage temperature can impact the shelf-life of chicken meat. Microbiome mapping in poultry processing facility revealed the dominance of Brochothrix thermosphacta, Pseudomonas fragi and Psychrobacter immobilis on poultry-based products and industrial surfaces. Indeed, surfaces of equipment and tools have a significant impact on the microbial composition of the final food products. Furthermore, the study of the microbiome dynamics in chicken meat stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) revealed temperature-dependent microbiota shifts in chicken meat, highlighting specific spoilage organisms (SSOs) in the different packaging methods. Additionally, our results showed that poultry-based products and industrial surfaces belonging to carcasses processing area hosted elevated levels of Antibiotic Resistance Genes, mainly associated with resistance to aminoglycosides, β-lactams, MLSPs (which includes macrolides, lincosamides, streptogramins and pleuromutilins) amphenicols and tetracyclines classes and several Virulence-associated genes related to adherence, biofilm, effector delivery system, motility, nutritional/metabolic factors and regulation. Finally, our findings underscored a notably mobile resistome, showing multiple AR class correlated with mobile elements. This poses a considerable risk, emphasizing the urgent need for proactive measures in addressing potential antibiotic resistance genes dissemination in the poultry chain.

RevDate: 2025-02-14
CmpDate: 2025-02-14

Li Q, Wu X, Niu X, et al (2025)

Integrated metagenomic and metabolomic analyses of the effects of total flavonoids of Rhizoma Drynariae on reducing ovariectomized-induced osteoporosis by regulating gut microbiota and related metabolites.

PloS one, 20(2):e0317832.

TFRD has been widely used in China to treat osteoporosis (OP). However, the specific molecular mechanism of TFRD against OP has not been fully clarified. Our previous studies have also proved that TFRD could attenuate OP and the clinical equivalent dose of 67.5mg/kg/d is the effective dose for TFRD treating OP. Therefore, this study used 67.5mg/kg as the dosage of TFRD in combination with multi omics to investigate the mechanism of action of TFRD in the treatment of OP. The aim of this study was to further elucidate molecular mechanism of TFRD for treating OP based on metagenomic and metabolomic analyses. In this study, hematoxylin-eosin (H&E) staining, micro computed tomography (micro-CT) and bone mineral density (BMD) analysis were used to observe pharmacological effects of TFRD against ovariectomized (OVX)-induced OP. Subsequently, multiomics analysis including metagenomics, untargeted and short chain fatty acids (SCFAs) metabolomics were carried out to identify whether the anti-osteoporosis mechanism of TFRD correlated with gut microbiota and related metabolites. Our results indicate that TFRD could improve the microstructure and density of trabecular bone in OVX rats. 17 differential species, which mainly from Akkermansia, Bacteroides, and Phascolarctobacterium genus, 14 related differential metabolites and acetic acid in SCFAs were significantly altered by OVX and reversed by TFRD. Furthermore, according to results of untargeted metabolomics analysis, it was found that several metabolic pathways such as phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis and so on might play an important role in TFRD against OP. In order to further study the relationship between gut microbiota and related metabolites, spearman correlation analysis was used, and showed that gut microbiota such as Akkermansia muciniphila might be closely related to several metabolites and metabolic pathways. These findings suggest that TFRD treatment could reduce the effects of OVX-induced OP by altering community composition and abundance of gut microbiota, regulating metabolites and SCFAs. It was speculated that the gut microbiota especially Akkermansia muciniphila and related metabolites might play an important role in TFRD against OP, and deserve further study by follow-up experiment. This conclusion provides new theoretical support for mechanism research of TFRD against OP.

RevDate: 2025-02-14
CmpDate: 2025-02-14

Reiss RA, Guerra PA, Makhnin O, et al (2025)

Whole metagenome sequencing and 16S rRNA gene amplicon analyses reveal the complex microbiome responsible for the success of enhanced in-situ reductive dechlorination (ERD) of a tetrachloroethene-contaminated Superfund site.

PloS one, 20(2):e0306503.

The North Railroad Avenue Plume (NRAP) Superfund site in New Mexico, USA exemplifies successful chlorinated solvent bioremediation. NRAP was the result of leakage from a dry-cleaning that operated for 37 years. The presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera (OHRG), and reductive dehalogenase (rdh) genes detected in groundwater samples indicated that enhanced reductive dechlorination (ERD) was the remedy of choice. This was achieved through biostimulation by mixing emulsified vegetable oil into the contaminated aquifer. This report combines metagenomic techniques with site monitoring metadata to reveal new details of ERD. DNA extracts from groundwater samples collected prior to and at four, 23 and 39 months after remedy implementation were subjected to whole metagenome sequencing (WMS) and 16S rRNA gene amplicon (16S) analyses. The response of the indigenous NRAP microbiome to ERD protocols is consistent with results obtained from microcosms, dechlorinating consortia, and observations at other contaminated sites. WMS detects three times as many phyla and six times as many genera as 16S. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. Methane was not detected before biostimulation but appeared afterwards, corresponding to an increase in methanogenic Archaea. Assembly of WMS reads produced scaffolds containing rdh genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing in aquifer microenvironments or by microbes that produce O2 via microbial dismutation. The NRAP model for successful ERD is consistent with the established pathway and identifies new taxa and processes that support this syntrophic process. This project explores the potential of metagenomic tools (MGT) as the next advancement in bioremediation.

RevDate: 2025-02-15
CmpDate: 2025-02-15

Mondal A, Parvez SS, Majumder A, et al (2025)

Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis).

Microbiological research, 293:128084.

Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.

RevDate: 2025-02-15
CmpDate: 2025-02-15

Huang L, Dai W, Sun X, et al (2025)

Diet-driven diversity of antibiotic resistance genes in wild bats: implications for public health.

Microbiological research, 293:128086.

Wild bats may serve as reservoirs for antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria, potentially contributing to antibiotic resistance and pathogen transmission. However, current assessments of bats' antibiotic resistance potential are limited to culture-dependent bacterial snapshots. In this study, we present metagenomic evidence supporting a strong association between diet, gut microbiota, and the resistome, highlighting bats as significant vectors for ARG propagation. We characterized gut microbiota, ARGs, and mobile genetic elements (MGEs) in bats with five distinct diets: frugivory, insectivory, piscivory, carnivory, and sanguivory. Our analysis revealed high levels of ARGs in bat guts, with limited potential for horizontal transfer, encompassing 1106 ARGs conferring resistance to 26 antibiotics. Multidrug-resistant and polymyxin-resistant genes were particularly prevalent among identified ARG types. The abundance and diversity of ARGs/MGEs varied significantly among bats with different dietary habits, possibly due to diet-related differences in microbial composition. Additionally, genetic linkage between high-risk ARGs and multiple MGEs was observed on the genomes of various zoonotic pathogens, indicating a potential threat to human health from wild bats. Overall, our study provides a comprehensive analysis of the resistome in wild bats and underscores the role of dietary habits in wildlife-associated public health risks.

RevDate: 2025-02-15
CmpDate: 2025-02-15

Maphosa S, Steyn M, Lebre PH, et al (2025)

Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations.

Microbiological research, 293:128076.

Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.

RevDate: 2025-02-15
CmpDate: 2025-02-15

Labarga D, Mairata A, Puelles M, et al (2025)

Rootstocks and drought stress impact the composition and functionality of grapevine rhizosphere bacterial microbiota.

Microbiological research, 293:128073.

The microbiota, a component of the plant holobiont, plays an active role in the response to biotic and abiotic stresses. Nowadays, with recurrent drought and global warming, a growing challenge in viticulture is being addressed by different practices, including the use of adapted rootstocks. However, the relationships between these practices, abiotic stress and the composition and functions of the rhizosphere microbiota remain to be deciphered. This study aimed to unravel the impact of five rootstocks, water management and the combination of both on the rhizosphere bacterial microbiota in grapevines using shotgun metagenomics approach. The results showed that drought impacted the diversity, composition and functionality of the rhizosphere bacterial community. The genera Mycolicibacterium, Mycobacterium and Rhodococcus, and the bacterial functions, including DNA damage repair, fatty acid synthesis, sugar and amino acid transport, oxidative stress reduction, toxin synthesis and detoxification of exogenous compounds were significantly enriched under drought conditions. Rootstocks also significantly affected the rhizosphere bacterial richness but its influence on diversity and functionality compared to water management was weaker. Some taxa and function could be linked to water managements applied. The interaction between rootstocks and water management further influenced the rhizosphere composition, especially under drought conditions, where distinct clustering was observed for specific rootstocks. The results highlight the importance of conducting multifactorial studies to better understand their impact on shaping functional rhizosphere bacterial communities. This study paves the way for future research on beneficial bacterial inoculation and genetic engineering of rootstock to cope with drought stress.

RevDate: 2025-02-15
CmpDate: 2025-02-15

Lin W, Zhao K, Wu Q, et al (2025)

Biofilms on pipelines shape the microbiome and antibiotic resistome in drinking water.

Water research, 274:123136.

Biofilms in the drinking water distribution system (DWDS) provide shelter for pathogens and antibiotic resistance genes (ARGs). However, how biofilms alter the microbiome and antibiotic resistome in tap water, as well as the precise quantitative evaluation of their health risks, remains unclear. Herein, biofilm reactors supplied with municipal drinking water were operated for 120 days. Metagenomic sequencing identified significant differences in microbial compositions among the biofilms, influent, and effluents. A total of 69-305 ARGs were detected in this DWDS, and ARG abundances increased in the biofilms (0.246-1.576 cpc) and effluents (0.309-0.503 cpc) compared to the influent (0.131 cpc). Metagenomic assembly pinpointed potential pathogenic ARG hosts such as Acinetobacter, Pseudomonas, and Escherichia. The co-occurrence of ARGs and mobile genetic elements indicated potential mobility, which was further supported by transformation assays demonstrating gene transfers at a frequency of 10[-6]. Furthermore, source tracking revealed that biofilms contributed high proportions (19 %-34 %) to the ARG profiles of effluents. The ARG risk scores increased from the influent (20.39) to the effluents (39.85-55.50), with highest level (55.50) in the cast iron effluent. Overall, this study provides novel insights into the impacts of biofilm growth on the microbiome and antibiotic resistome in tap water, along with their potential health risks in the DWDS.

RevDate: 2025-02-15
CmpDate: 2025-02-15

Mao X, Yin X, Yang Y, et al (2025)

Longitudinal metagenomic analysis on antibiotic resistome, mobilome, and microbiome of river ecosystems in a sub-tropical metropolitan city.

Water research, 274:123102.

Rivers play an important role as reservoirs and sinks for antibiotic resistance genes (ARGs). However, it remains underexplored for the resistome and associated mobilome in river ecosystems, and hosts of riverine ARGs particularly the pathogenic ones are rarely studied. This study for the first time conducted a longitudinal metagenomic analysis to unveil the resistome, mobilome, and microbiome in river water, by collecting samples from 16 rivers in Hong Kong over a three-year period and using both short-read and long-read sequencing. Results revealed that aminoglycoside, bacitracin, β-lactam, macrolide lincosamide-streptogramin, and sulfonamide were the predominant ARG types in the river water samples. Riverine ARGs exhibited high spatial variations in abundance and diversity. Environmental factors such as fecal coliform count, Escherichia coli count, 5-day biochemical oxygen demand (BOD5), dissolved oxygen (DO), and total organic carbon (TOC) had a significant correlation to the absolute concentrations of ARGs. Nanopore sequencing was used to reveal the physical genetic linkage of mobile genetic elements (MGEs) with ARGs in river water samples. The results showed that qacEdelta, transposase, integrase, and Tn916 had a high prevalence in ARG-carrying long reads. Host tracking using ARG-carrying reads identified 23 pathogenic bacteria species that harbored ARGs. Some ARGs were shared by different bacterial groups. This study presented a nuanced insight of resistome in river water by a longitudinal metagenomic analysis and deepened our understanding of common and divergent riverine antimicrobial resistant risk across the regional patterns.

RevDate: 2025-02-14
CmpDate: 2025-02-14

Yan M, Andersen TO, Pope PB, et al (2025)

Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.

Genome research, 35(2):368-378 pii:gr.279825.124.

Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies owing to the lack of comprehensive reference genome databases and robust bioinformatic tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass but a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than 1000 rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for the in-depth study of GI tract eukaryotes.

RevDate: 2025-02-15
CmpDate: 2025-02-15

Gao B, Chen L, Wu L, et al (2025)

Association between microplastics and the functionalities of human gut microbiome.

Ecotoxicology and environmental safety, 290:117497.

As an integral part of humans, the gut microbiome plays a significant role in the physiological and pathological processes of the host, and dysbiosis of the gut microbiome is linked to various diseases. The impact of microplastics on the diversity and composition of human gut microbiome has been reported previously. However, effects of microplastics on the functionality of the gut microbiome in humans have not been well studied. In the present study, concentrations of microplastics in human blood were detected through pyrolysis-gas chromatography/mass spectrometry in 39 adults. Five types of microplastics were found in human blood, including polyvinyl chloride, polyethylene, polypropylene, polystyrene, and polyamide 66. Shotgun metagenomic sequencing was further employed to analyze the metagenomes of the human stool samples and fecal samples from mice exposed to microplastics. Associations were found between microplastics and microbial species, as well as microbial genes encoding invasion-related virulence factors, quorum sensing, autoinducer and transporter system, and microplastic biodegradation enzymes. The findings are of significance to improve the understanding of functional changes in the gut microbiome associated with microplastic exposure, as well as raising awareness regarding the health risks of microplastics in the human population.

RevDate: 2025-02-15
CmpDate: 2025-02-15

Talwar C, Davuluri GVN, Kamal AHM, et al (2025)

Identification of distinct stool metabolites in women with endometriosis for non-invasive diagnosis and potential for microbiota-based therapies.

Med (New York, N.Y.), 6(2):100517.

BACKGROUND: Endometriosis, a poorly studied gynecological condition, is characterized by the presence of ectopic endometrial lesions resulting in pelvic pain, inflammation, and infertility. These associated symptoms contribute to a significant burden, often exacerbated by delayed diagnosis. Current diagnostic methods involve invasive procedures, and existing treatments provide no cure.

METHODS: Microbiome-metabolome signatures in stool samples from individuals with and without endometriosis were determined using unbiased metabolomics and 16S bacteria sequencing. Functional studies for selected microbiota-derived metabolites were conducted in vitro using patient-derived cells and in vivo by employing murine and human xenograft pre-clinical disease models.

FINDINGS: We discovered a unique bacteria-derived metabolite signature intricately linked to endometriosis. The altered fecal metabolite profile exhibits a strong correlation with that observed in inflammatory bowel disease (IBD), revealing intriguing connections between these two conditions. Notably, we validated 4-hydroxyindole, a gut-bacteria-derived metabolite that is lower in stool samples of endometriosis. Extensive in vivo studies found that 4-hydroxyindole suppressed the initiation and progression of endometriosis-associated inflammation and hyperalgesia in heterologous mouse and in pre-clinical models of the disease.

CONCLUSIONS: Our findings are the first to provide a distinct stool metabolite signature in women with endometriosis, which could serve as stool-based non-invasive diagnostics. Further, the gut-microbiota-derived 4-hydroxyindole poses as a therapeutic candidate for ameliorating endometriosis.

FUNDING: This work was funded by the NIH/NICHD grants (R01HD102680, R01HD104813) and a Research Scholar Grant from the American Cancer Society to R.K.

RevDate: 2025-02-14
CmpDate: 2025-02-14

Li Q, Tan D, Xiong S, et al (2025)

Time-restricted feeding promotes glucagon-like peptide-1 secretion and regulates appetite via tryptophan metabolism of gut Lactobacillus in pigs.

Gut microbes, 17(1):2467185.

Previous clinical trials have shown that time-restricted feeding can be involved in regulating the metabolic health of humans and animals. However, the underlying mechanism has not been fully explored. In this study, the pig model was employed to simulate four prevalent human eating habits, with the aim of investigating the impact of gut microbiota and microbial metabolites on gut hormone secretion and appetite regulation. Compared to the ad libitum feeding (ALF) pattern, three time-restricted feeding patterns reduced total food intake and eating time. Meanwhile, three time-restricted feeding patterns induced elevated levels of serum and hypothalamic glucagon-like peptide-1 (GLP-1), while suppressing reward-related circuits in the hypothalamus. It is noteworthy that the early time-restricted feeding (eTRF) pattern increased the number of intestinal enteroendocrine cells (EECs) compared to ALF. Metagenomic and metabonomic analyses revealed that three time-restricted feeding patterns induced colonization of Lactobacillus and significantly increased the levels of its metabolite, indole-3-lactic acid (ILA). Dietary supplementation with ILA exhibited an increasing trend in fasting serum GLP-1 level of piglets. In vitro studies with pig intestinal organoids showed the Lactobacillus metabolite ILA enhanced GLP-1 secretion through the promotion of intestinal stem cell differentiation into EECs, rather than activating the ability of EECs to secrete GLP-1. Overall, time-restricted feeding promoted GLP-1 secretion and affected long-term appetite regulation by promoting the colonization of Lactobacillus and modulating microbial tryptophan metabolism.

RevDate: 2025-02-14
CmpDate: 2025-02-14

Ng HY, Zhang L, Tan JT, et al (2025)

Gut Microbiota Predicts Treatment Response to Empagliflozin Among MASLD Patients Without Diabetes Mellitus.

Liver international : official journal of the International Association for the Study of the Liver, 45(3):e70023.

BACKGROUND AND AIM: We aimed to investigate whether gut microbiota could predict the treatment response to pharmacological agents among metabolic dysfunction-associated steatotic liver disease (MASLD) patients without diabetes mellitus (DM), as data are lacking.

METHODS: We prospectively followed up non-diabetic MASLD patients who used empagliflozin. Clinical, anthropometric, laboratory assessments and magnetic resonance imaging-proton density fat fraction (MRI-PDFF) were performed from baseline to week 52 (EOT). Baseline stool samples were collected, and shotgun DNA metagenomic sequencing was performed to profile microbiome. The primary outcome was treatment response to empagliflozin at EOT, defined as MRI-PDFF decline ≥ 30% at EOT from baseline. Linear discriminant analysis [LDA] effect size was used to identify putative bacterial species. Multivariable logistic regression was used to derive adjusted odds ratio (aOR) of outcome with bacterial species by adjusting for clinical factors.

RESULTS: Twenty-two (48.9%) of 45 patients (median age: 56.9 years [IQR: 51.0-63.2]; male: 23 [51.1%]) achieved treatment response at EOT. There was difference in alpha diversity (Shannon index: p < 0.001; Simpson index: p = 0.001) and beta diversity (p = 0.048) in baseline microbiome between treatment response and non-response groups. Faecalibacterium prausnitzii (log10LDAscore = 4.27), Lachnospira pectinoschiza (log10LDAscore = 3.99), Anaerostipes hadrus (log10LDAscore = 3.98), Roseburia faecis (log10LDAscore = 3.97), Roseburia inulinivorans (log10LDAscore = 3.58) and Agathobaculum butyriciproducens (log10LDAscore = 2.77) were enriched in the treatment response group. L. pectinoschiza (aOR: 34.1; p = 0.015), A. hadrus (aOR:35.0; p = 0.032) and A. butyriciproducens (aOR:22.3; p = 0.023) independently predicted treatment response but not clinical factors. These three species collectively predicted treatment response with AUROC of 0.89 (95% CI: 0.80-0.99).

CONCLUSIONS: Certain gut bacterial species, particularly the combination of A. hadrus, L. pectinoschiza and A. butyriciproducens, may predict treatment response to empagliflozin in MAFLD patients without DM.

RevDate: 2025-02-13
CmpDate: 2025-02-13

Zang T, Zhang Z, Liu W, et al (2025)

Structural and functional changes in the oral microbiome of patients with craniofacial microsomia.

Scientific reports, 15(1):5400.

Craniofacial microsomia (CFM) is the second most common congenital craniofacial deformity, presenting diverse clinical manifestations and treatments that may influence oral bacteria dysbiosis (OBD). However, research linking CFM to OBD is limited. Saliva samples were collected from 20 patients with CFM and 24 controls. We compared oral microflora and gene function using 16 S ribosomal RNA sequencing and metagenomics. We also evaluated the correlation between CFM clinical phenotypes and microbiota community structure. Patients with CFM demonstrated greater richness and evenness in their oral microflora. The dominant genera included several pathogenic species, such as Actinomyces, Fusobacterium, and Prevotella. Notably, the severity of CFM correlated positively with the abundance of Neisseria and Porphyromonas. Upregulated pathways were primarily linked to biotin and amino acid metabolism, such as Tryptophan metabolism and Lysine degradation, and further underscored the need for focused oral health interventions in this population. This study is the first to indicate that CFM patients exhibit unique oral bacterial dysbiosis, marked by a higher presence of opportunistic pathogens and increased pathways related to oral and systemic health. These findings highlight the importance of monitoring oral health in patients with CFM.

RevDate: 2025-02-13
CmpDate: 2025-02-13

Chen A, Yu Q, Zheng L, et al (2025)

Dose-dependent M2 macrophage polarization induced by Talaromyces marneffei promotes lung cancer cell growth via arginine-ornithine-cycle activation.

Medical microbiology and immunology, 214(1):11.

It is now widely accepted that lungs are colonized by diverse microbes. Dysbiosis of the lung microbiota has been found to affect the progression of lung cancer. Fungi are a major component of the lung microbiota. However, the causal links between the mycobiome or specific species and lung cancer remain unclear. To address this, we conducted a study examining the composition of lung mycobiota in Non-Small-Cell Lung Cancer (NSCLC) patients using shotgun metagenomics. The differential taxa between NSCLC patients and non-cancer controls were defined by the Wilcoxon rank-sum test. Nested PCR was used to measure the abundance of specific fungal species. Metabolomics analysis was performed to investigate the metabolic reprogramming of macrophages triggered by intracellular infection of specific fungal species. In vitro and in vivo assays were conducted to examine the effect of the specific fungus on cancer cell growth. Our findings showed that Ascomycota, Microsporidia and Mucoromycota were the dominant fungal taxa in the lungs. Talaromyces marneffei (T.marneffei) was the most significantly differential fungus between lung cancer patients and non-cancer controls, with its abundance positively correlated with lung cancer. The lung cancer animal model demonstrated that T.marneffei promotes lung cancer growth. Our study also demonstrated that T.marneffei promotes lung cancer cell growth by inducing dose-dependent M2 macrophage polarization through arginine-ornithine-cycle activation. Furthermore, inhibition of arginase can reduce M2 polarization of macrophages and the survival of T. marneffei inside macrophages. In summary, our study reveals that the increased abundance of T. marneffei in the lungs affects lung cancer cell growth by triggering arginine-induced M2 polarization of macrophages. These findings provide potential drug targets for the development of therapies aimed at targeting the survival of fungi inside macrophages in the fight against cancer.

RevDate: 2025-02-13
CmpDate: 2025-02-13

Elmassry MM, Sugihara K, Chankhamjon P, et al (2025)

A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.

Cell host & microbe, 33(2):218-234.e12.

Gut microbiome changes have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a meta-analysis of small molecule biosynthetic gene clusters (BGCs) in metagenomic samples of the gut microbiome from inflammatory bowel disease (IBD) patients and matched healthy subjects and identified two Clostridia-derived BGCs that are significantly associated with Crohn's disease (CD), a main IBD type. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the CD-enriched BGCs, which we subsequently detected in fecal samples from IBD patients. Finally, we show that the discovered molecules disrupt gut permeability and exacerbate disease in chemically or genetically susceptible mouse models of colitis. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of disease-relevant microbiome-host interactions.

RevDate: 2025-02-13
CmpDate: 2025-02-13

Long C, Wang P, Wu J, et al (2025)

Structure and diversity of intestinal methanogens in black carp (Mylopharyngodon piceus), grass carp (Ctenopharyngodon idella) and water samples.

PloS one, 20(2):e0316456 pii:PONE-D-24-40975.

The present research investigation aims to examine the community features of methanogens in the intestinal tract of black and grass carp, as well as their association with methanogens in water samples. Samples of black carp, grass carp and water in a pond were gathered in Spring 2021. Using the Illumina HiSeq 2500 high-throughput sequencing platform, the metagenomic mcrA gene sequences of black carp, grass carp and cultured water specimens were determined and analyzed. The outcomes indicate that the richness and diversity of methanogens in the intestinal tract of black and carp grass carp were highly correlated with the cultured water. Five bacterial genera were found in the three sets of samples, Methanosarcina, Methanocorpusculum, Methanospirillum, Methanobacterium and Methanofollis, in which Methanosarcina and Methanocorpusculum were the dominant genera. In addition, Methanosarcina had the greatest amount in grass carp and Methanocorpusculum had the greatest quantity in black carp. In conclusion, Methanosarcina and Methanocorpusculum were the main methanogens in the digestive tract of black and grass carp and culture water, and hydrolytic fermentative bacteria were its main metabolic substrate, hydrotrophic was its main metabolic pathway. The results will provide a reference for the relationship between intestinal methanogens and aquaculture and the greenhouse effect.

RevDate: 2025-02-13
CmpDate: 2025-02-13

Saravanan C, Gopinath NK, Ganesan R, et al (2025)

Challenges and limitations in using bacterial metabolites as immunomodulators.

Frontiers in cellular and infection microbiology, 15:1535394.

Harnessing the immunomodulatory potential of bacterial metabolites opens up exciting possibilities for treating various immune-related disorders. However, turning this potential into a reality presents significant challenges. This review investigates these challenges, focusing on discovery, production, characterization, stability, formulation, safety, and individual variability limitations. The limited bioavailability of many metabolites, as well as potential improvements along with the potential for off-target effects and the importance of precise targeting, are emphasized. Furthermore, the complex interactions between gut bacterial metabolites and the microbiome are investigated, highlighting the importance of personalized approaches. We conclude by discussing promising advances in metagenomics, metabolomics, synthetic biology, and targeted delivery systems, which hold out hope for overcoming these limitations and paving the way for the clinical translation of bacterial metabolites as effective immunomodulators.

RevDate: 2025-02-13
CmpDate: 2025-02-13

Chen E, Ajami NJ, White DL, et al (2025)

Dairy Consumption and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Preliminary Investigation.

Nutrients, 17(3): pii:nu17030567.

BACKGROUND: Dairy consumption has been associated with various health outcomes that may be mediated by changes in gut microbiota.

METHODS: This cross-sectional study investigated the association between the colonic mucosa-associated gut microbiota and the self-reported intake of total dairy, milk, cheese, and yogurt. A total of 97 colonic mucosal biopsies collected from 34 polyp-free individuals were analyzed. Dairy consumption in the past year was assessed using a food frequency questionnaire. The 16S rRNA gene V4 region was amplified and sequenced. Operational taxonomic unit (OTU) classification was performed using the UPARSE and SILVA databases. OTU diversity and relative abundance were compared between lower vs. higher dairy consumption groups. Multivariable negative binomial regression models for panel data were used to estimate the incidence rate ratio and 95% confidence interval for bacterial counts and dairy consumption. False discovery rate-adjusted p values (q value) < 0.05 indicated statistical significance.

RESULTS: Higher total dairy and milk consumption and lower cheese consumption were associated with higher alpha microbial diversity (adjusted p values < 0.05). Higher total dairy and milk consumption was also associated with higher relative abundance of Faecalibacterium. Higher milk consumption was associated with higher relative abundance of Akkermansia. Higher total dairy and cheese consumption was associated with lower relative abundance of Bacteroides.

CONCLUSIONS: Dairy consumption may influence host health by modulating the structure and composition of the colonic adherent gut microbiota.

RevDate: 2025-02-13
CmpDate: 2025-02-13

Barata P, Oliveira A, Soares R, et al (2025)

Gut Microbiota Is Not Significantly Altered by Radioiodine Therapy.

Nutrients, 17(3): pii:nu17030395.

Purpose: Radiotherapy treatments are known to alter the gut microbiota. However, little is known regarding the effect of nuclear medicine treatments on gut microbiota, and it is established that nuclear medicine is inherently different from radiotherapy. To address this knowledge gap, we conducted a prospective study to identify changes in the gut microbiota of patients treated with [[131]I]NaI by comparing fecal samples before and after RAIT. Methods: Fecal samples of 64 patients (37 with thyroid cancer and 27 with hyperthyroidism) with indication for RAIT were collected 2 to 3 days before treatment and 8 to 10 days post-treatment. After DNA extraction, the gut microbiota's richness, diversity, and composition were analyzed by shotgun metagenomics. In addition, LEfSe was performed to compare compositional changes in specific bacteria. Results: Gut microbiome richness and diversity remained unchanged after RAIT, with few changes in its composition identified, especially in patients with hyperthyroidism. Conclusions: This study provides a conceptual and analytical basis for increasing our understanding of the effects of radiopharmaceuticals on gut microbiota. Our preliminary results indicate that RAIT, contrary to radiotherapy, does not cause major disruptions to the human gut microbiota.

RevDate: 2025-02-12
CmpDate: 2025-02-13

Schropp N, Bauer A, Stanislas V, et al (2025)

The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial.

Microbiome, 13(1):52.

BACKGROUND: Sauerkraut is a fermented food that has been suspected to have a beneficial impact on the gut microbiome, but scientific evidence is sparse. In this crossover intervention trial with 87 participants (DRKS00027007), we investigated the impact of daily consumption of fresh or pasteurized sauerkraut for 4 weeks on gut microbial composition and the metabolome in a healthy study population.

RESULTS: Using shotgun metagenomic sequencing, we observed changes in single bacterial species following fresh and pasteurized sauerkraut consumption. More pronounced changes were observed in the pasteurized sauerkraut intervention arm. Only pasteurized sauerkraut consumption increased serum short-chain fatty acids (SCFAs).

CONCLUSIONS: The gut microbiome of healthy individuals is rather resilient to short-term dietary interventions even though single species might be affected by sauerkraut consumption. Video Abstract.

RevDate: 2025-02-12
CmpDate: 2025-02-12

Soares KO, Da Rocha TF, Hale VL, et al (2025)

Comparing the impact of landscape on the gut microbiome of Apis mellifera in Atlantic Forest and Caatinga Biomes.

Scientific reports, 15(1):5293.

The composition of the gut microbiota in animals can be influenced by a variety of intrinsic and extrinsic factors in the host, such as diet, physiological state, and genetics. This study aimed to compare the structural composition of the gut microbiota of Apis mellifera bees from two distinct Brazilian biomes, the Atlantic Forest and the Caatinga, using high throughput 16 S rRNA sequencing. We identified a core microbiota composed of seven genera present in all samples: Lactobacillus, Commensalibacter, Rhizobiaceae, Snodgrassella, Gilliamella, Orbaceae and Bifidobacterium. These taxa accounted for 63% of all bacterial genera in the dataset. Interestingly, we observed a significantly differential abundance of the genus Apibacter between bees from the two biomes, with a marked increase in bees from Atlantic Forest. However, the overall variance in the gut structural composition attributable to landscape type, while significant, was relatively low. Notably, none of the members of the core microbiota were differently abundant between the biomes. Understanding the magnitude of landscape-associated effects on the microbiota of bees in different biomes is crucial for the accurate assessment of the impact of anthropogenic factors. These findings provide important insights into the resilience and adaptability of the honey bee gut microbiome across contrasting environments, contributing to the development of conservation and sustainable management strategies for these essential pollinators.

RevDate: 2025-02-12

Fernandes M, Palmieri O, Castellana S, et al (2025)

Gut microbiome composition changes in obstructive sleep apnoea syndrome also in relation to excessive daytime sleepiness.

Brain research bulletin pii:S0361-9230(25)00063-2 [Epub ahead of print].

INTRODUCTION: Obstructive sleep apnoea syndrome (OSAS) is considered a risk factor for several comorbidities. Alteration in gut microbiome was documented in OSAS animal models and in paediatric patients. This study analysed gut microbiome composition in adult patients with OSAS and compared to controls. Further, the effect of excessive daytime sleepiness (EDS) on gut microbiome was evaluated.

METHODS: Adult patients with OSAS underwent polysomnographic recording and completed the Epworth Sleepiness Scale (ESS) to assess EDS. Faecal samples were collected and compared between patients and healthy controls. Composition, community diversity, differences in taxa abundance profiles and sample dysbiosis were evaluated through 16S metagenomics and multiple bioinformatics algorithms. OSAS patients were distributed in two groups according to EDS (ESS score≥10) to assess differences in clinical, polysomnographic and faecal data.

RESULTS: Twenty-three OSAS patients were compared to 44 controls. Patients presented significant differences of gut microbiome biodiversity, specifically in qualitative alpha diversity metrics (Faith's PD Kruskal-Wallis test, p-value=0.003; Number_of_Observed_Features, p value =0.001). OSAS patients tend to cluster together, at least for Jaccard and Unweighted UniFrac distance-based PERMANOVA tests (q-values=0.02 and =0.003, respectively). Several taxa were detected as different in abundance between OSAS patients and controls, although, globally, OSAS patients cannot be considered as "dysbiotic". Differences in bacteria composition were evident between OSAS patients with and those without EDS.

CONCLUSIONS: OSAS is associated with gut microbiome alteration in adult patients. EDS in OSAS seems to characterize a different gut microbiome composition, although it can be only hypothesized a gut-mediated effect on EDS in OSAS.

RevDate: 2025-02-13
CmpDate: 2025-02-13

Lim B, Xu J, Wierzbicki IH, et al (2025)

A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability.

Cell host & microbe, 33(2):200-217.e24.

Antagonistic interactions play a key role in determining microbial community dynamics. Here, we report that one of the most widespread contact-dependent effectors in human gut microbiomes, Bte1, directly targets the PpiD-YfgM periplasmic chaperone complex in related microbes. Structural, biochemical, and genetic characterization of this interaction reveals that Bte1 reverses the activity of the chaperone complex, promoting substrate aggregation and toxicity. Using Bacteroides, we show that Bte1 is active in the mammalian gut, conferring a fitness advantage to expressing strains. Recipient cells targeted by Bte1 exhibit sensitivity to membrane-compromising conditions, and human gut microbes can use this effector to exploit pathogen-induced inflammation in the gut. Further, Bte1 allelic variation in gut metagenomes provides evidence for an arms race between Bte1-encoding and immunity-encoding strains in humans. Together, these studies demonstrate that human gut microbes alter the protein-folding capacity of neighboring cells and suggest strategies for manipulating community dynamics.

RevDate: 2025-02-13
CmpDate: 2025-02-13

Memon FU, Zhu Y, Cui Y, et al (2025)

Gut microbial communities and transcriptional profiles of black soldier fly (Hermitia illucens) larvae fed on fermented sericulture waste.

Waste management (New York, N.Y.), 194:158-168.

Sericulture waste poses significant challenges to industrial and environmental safety. Black soldier fly larvae (BSFL) offer a promising solution for organic waste management by converting it into insect protein. This study aimed to develop a microbial fermented method for utilizing sericulture waste to feed BSFL and explore the underlying mechanisms. Our results showed that all fermented sericulture waste groups had positive effects on body weight, survival rate, substrate consumption rate, and substrate conversion rate. Metagenomic analysis revealed a notable increase in the abundances of commensal genera, including Sedimentibacter, Clostridium, Enterococcus, Bacteroides, and Bacillus, in the gut of BSFL fed on sericulture waste fermented with the most effective combination of microbial strains (B. subtilis, B. licheniformis, and E. faecalis). In contrast, BSFL reared on unfermented sericulture waste exhibited higher abundances of potentially pathogenic and harmful genera, including Providencia, Klebsiella, Escherichia, Brucella, and Enterobacter. Clusters of orthologous genes (COG) analysis indicated that altered microbial communities in the fermented group mainly participated in metabolic pathways, defense mechanism, and signal transduction mechanism. Transcriptome analysis further revealed that the upregulated genes were functionally associated with key metabolic pathways and immune mechanisms in the fermented group. These findings underscore the pivotal role of selected microbial fermentation in utilizing sericulture waste as BSFL feed, providing a sustainable solution for organic waste management.

RevDate: 2025-02-13
CmpDate: 2025-02-13

Yadav V, Kilambi R, Sharma R, et al (2025)

Radiocarbon dating of gallstones for timeline of formation, dormancy analysis, and correlation with chemical/microbial composition: a pilot study on gallstone geobiology.

Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract, 29(3):101937.

BACKGROUND: India has a high incidence of gallstones, which can cause chronic inflammation and increase the risk of gallbladder cancer. Understanding the age and composition of gallstones can provide insights into their formation and growth. This study used radiocarbon dating ([14]C dating), Fourier transform infrared (FTIR) spectroscopy, and metagenome analysis to explore the natural history, deposition rate, and microbial/chemical composition of gallstones.

METHODS: In this pilot study, 3 cholesterol gallstones were chosen with different tissue histopathologies (normal, metaplasia, and dysplasia), and respective layers were analyzed for [14]C bomb-pulse dating and FTIR for age and chemical composition, respectively. The core of each gallstone was subjected to scanning electron microscopy and further to 16S rRNA sequencing for microbial analysis.

RESULTS: The [14]C data indicated that the largest stone with dysplastic epithelium formed over 6 years, whereas stones with metaplasia and normal pathology took 13 and 12 years to develop, respectively. Furthermore, the largest stone was dormant for 6 years before the individual experienced acute pain, whereas the other 2 stones laid dormant for 7 and 18 years. FTIR analysis revealed that all 3 gallstones were primarily composed of cholesterol. In addition, calcium oxalate, calcium carbonate, and calcium bilirubinate were present in stones with underlying dysplasia. The 16S rRNA analysis revealed an increased abundance of Corynebacterium sp. in stones associated with metaplasia and dysplasia. Moreover, pathogenic Klebsiella and Escherichia coli species were abundant in calcium oxalate-rich gallstones with underlying dysplasia.

CONCLUSION: Overall, the pilot study established the feasibility of [14]C bomb pulse for evaluating the timeline of gallstone formation. In addition, [14]C dating combined with FTIR/metagenome analysis helped in understanding the natural history of gallstone-associated disease.

RevDate: 2025-02-13
CmpDate: 2025-02-13

Yang C, Hu J, Su Q, et al (2025)

A review on recent taxonomic updates of gut bacteria associated with social bees, with a curated genomic reference database.

Insect science, 32(1):2-23.

Honeybees and bumblebees play a crucial role as essential pollinators. The special gut microbiome of social bees is a key factor in determining the overall fitness and health of the host. Although bees harbor relatively simple microbial communities at the genus level, recent studies have unveiled significant genetic divergence and variations in gene content within each bacterial genus. However, a comprehensive and refined genomics-based taxonomic database specific to social bee gut microbiomes remains lacking. Here, we first provided an overview of the current knowledge on the distribution and function of social bee gut bacteria, as well as the factors that influence the gut population dynamics. We then consolidated all available genomes of the gut bacteria of social bees and refined the species-level taxonomy, by constructing a maximum-likelihood core genome phylogeny and calculating genome-wide pairwise average nucleotide identity. On the basis of the refined species taxonomy, we constructed a curated genomic reference database, named the bee gut microbe genome sequence database (BGM-GDb). To evaluate the species-profiling performance of the curated BGM-GDb, we retrieved a series of bee gut metagenomic data and inferred the species-level composition using metagenomic intra-species diversity analysis system (MIDAS), and then compared the results with those obtained from a prebuilt MIDAS database. We found that compared with the default database, the BGM-GDb excelled in aligned read counts and bacterial richness. Overall, this high-resolution and precise genomic reference database will facilitate research in understanding the gut community structure of social bees.

RevDate: 2025-02-11

Xu CCY, Fugère V, Barbosa da Costa N, et al (2025)

Pre-exposure to stress reduces loss of community and genetic diversity following severe environmental disturbance.

Current biology : CB pii:S0960-9822(25)00067-3 [Epub ahead of print].

Environmental stress caused by anthropogenic impacts is increasing worldwide. Understanding the ecological and evolutionary consequences for biodiversity will be crucial for our ability to respond effectively. Historical exposure to environmental stress is expected to select for resistant species, shifting community composition toward more stress-tolerant taxa. Concurrent with this species sorting process, genotypes within resistant taxa that have the highest relative fitness under severe stress are expected to increase in frequency, leading to evolutionary adaptation. However, empirical demonstrations of these dual ecological and evolutionary processes in natural communities are rare. Here, we provide evidence for simultaneous species sorting and evolutionary adaptation across multiple species within a natural freshwater bacterial community. Using a two-phase stressor experimental design (acidification pre-exposure followed by severe acidification) in aquatic mesocosms, we show that pre-exposed communities were more resistant than naive communities to taxonomic loss when faced with severe acid stress. However, after sustained severe acidification, taxonomic richness of both pre-exposed and naive communities eventually converged. All communities experiencing severe acidification became dominated by an acidophilic bacterium, Acidiphilium rubrum, but this species retained greater genetic diversity and followed distinct evolutionary trajectories in pre-exposed relative to naive communities. These patterns were shared across other acidophilic species, providing repeated evidence for the impact of pre-exposure on evolutionary outcomes despite the convergence of community profiles. Our results underscore the need to consider both ecological and evolutionary processes to accurately predict the responses of natural communities to environmental change.

RevDate: 2025-02-11
CmpDate: 2025-02-11

Tepekule B, Barcik W, Staiger WI, et al (2025)

Computational and in vitro evaluation of probiotic treatments for nasal Staphylococcus aureus decolonization.

Proceedings of the National Academy of Sciences of the United States of America, 122(7):e2412742122.

Despite the rising challenge of antibiotic resistance, current approaches to eradicate nasal pathobionts Staphylococcus aureus and Streptococcus pneumoniae rely on antibacterials. An alternative is the artificial inoculation of commensal bacteria, i.e., probiotic treatment, supported by the increasing evidence for commensal-mediated inhibition of pathogens. To systematically investigate the potential of this approach, we developed a quantitative framework simulating the nasal microbiome dynamics by combining mathematical modeling with longitudinal microbiota data. By inferring community parameters using 16S ribosomal RNA (rRNA) amplicon sequencing data and simulating the nasal microbial dynamics of patients colonized with S. aureus, we compared the decolonization performance of probiotic and antibiotic treatments under different assumptions on patients' community composition and susceptibility profile. To further compare the robustness of these treatments, we simulated an S. aureus challenge and quantified the recolonization probability. Through in vitro experiments using nasal swabs of adults colonized with S. aureus, we confirmed that after antibiotic treatment, recolonization of S. aureus was inhibited in samples treated with a probiotic mixture compared to the nontreated control. Our results suggest that probiotic treatment outperforms antibiotics in terms of decolonization performance, recolonization robustness, and leads to less collateral reduction in the microbiome diversity. Thus, probiotic treatment may provide a promising alternative to combat antibiotic resistance, with the additional advantage of personalized treatment options via using the patient's own metagenomic data. The combination of an in silico framework with in vitro experiments using clinical samples reported in this work is an important step forward to further investigate this alternative in clinical trials.

RevDate: 2025-02-12
CmpDate: 2025-02-12

Wang XP, Han NN, Yang JH, et al (2025)

Metagenomic insight into the diffusion signal factor mediated social traits of anammox consortia after starvation.

Journal of environmental management, 375:124270.

Biomass starvation is common in biological wastewater treatment. As a social trait of microbial community, how quorum sensing (QS) regulated bacterial trade-off through interactions after starvation remains unclear. This study deciphered the mechanism of anaerobic ammonium oxidation (anammox) consortia in response to starvation, including reducing extracellular electron transfer (EET), adenosine 5'-triphosphate (ATP) content and amino acid metabolism. Metagenomic analysis has shown that the addition of the diffusion signal factor (DSF) resulted in a high abundance of antioxidant genes, which contributed to achieving redox balance in anammox bacteria. There was an enrichment of Geobacter and Methanosarcina, which were QS-responsive direct interspecific electron transfer participants. Furthermore, DSF stimulated the nitrogen and carbon metabolism of Ca. Kuenenia_stuttgartiensis, promoting syntrophy of metabolic intermediates within microbial community. This study highlighted the effect of DSF on the microbial interaction patterns and deciphered the QS-based social traits of anammox consortia after starvation, facilitating the stable operation of the anammox process.

RevDate: 2025-02-12
CmpDate: 2025-02-12

Li S, Zhen Y, Chen Y, et al (2025)

Geochemical and microbial controls on methane distribution in coastal sediments: A case study from the Bohai and South Yellow Seas, China.

Marine pollution bulletin, 211:117448.

CH4 is among the most potent greenhouse gases. In this study, we investigated one of the important CH4 production hotspots, the continental margins. We examined the spatiotemporal distributions of CH4 in sediment cores from the Bohai and South Yellow Seas, China. Using real-time PCR and metagenomic sequencing, we analyzed the microbial communities related to CH4 production. Our results indicated that concentrations of CH4 generally increased with depth gradually, minimal seasonal variation observed between spring and summer. Notably, spatial heterogeneity, rather than temporal variation, was the predominant factor affecting CH4 distribution and methanogen community differences in sediments. Furthermore, the structure of microbial communities, in conjunction with environmental factors, significantly impacts potential CH4 production. These findings provide valuable insights into the mechanisms underlying methane production and its environmental controls in marine sediments.

RevDate: 2025-02-12
CmpDate: 2025-02-12

Hu Y, Wang ML, Yang RL, et al (2025)

Symbiotic bacteria play crucial roles in a herbivorous mite host suitability.

Pest management science, 81(3):1657-1668.

BACKGROUND: The tomato russet mite (TRM), Aculops lycopersici, is a strictly herbivorous and economically significant pest that infests Solanaceae plants, but its host suitability varies, showing high performance on tomatoes. Although symbiotic bacteria have been suggested to play crucial roles in the host adaptation of herbivores, their effects on TRM remain unclear.

RESULTS: In this study, using next generation high-throughput sequencing of the bacterial 16S rRNA data, we identified the bacterial diversity and community composition of TRM feeding on tomato, eggplant, and chili. Our results show no significant difference in the bacterial community composition of TRM across three host plants. However, the relative density of Escherichia coli (TRM_Escherichia) showed 9.36-fold higher on tomato than on eggplant and chili. These results align with the observed TRM performance among three host plants. When TRM_Escherichia was reduced using antibiotics, the treated TRM decreased the population density on tomato. However, when we transferred TRM from eggplant to tomato, the population density of TRM increased, coinciding with an increase of the TRM_Escherichia density. These results indicate that TRM_Escherichia may affect the host suitability of TRM. Our fluorescence in situ hybridization (FISH) results further showed that TRM_Escherichia is primarily distributed in the salivary glands. Metagenomic data results suggest that TRM_Escherichia functions in food digestion and energy metabolism.

CONCLUSION: We provided the first comprehensive analysis of TRM bacterial communities. Our findings demonstrate that the symbiotic bacterium TRM_Escherichia may play crucial roles in the suitability of TRM feeding on different Solanaceae hosts. © 2024 Society of Chemical Industry.

RevDate: 2025-02-11

Cui H, Wang S, Fan S, et al (2025)

Branched-chain amino acid metabolism supports Roseobacteraceae positive interactions in marine biofilms.

Applied and environmental microbiology [Epub ahead of print].

UNLABELLED: Interspecies interactions are key factors affecting the stability of microbial communities. However, microbial interactions in marine biofilms, which constitute up to 80% of the microbial biomass in certain marine environments, are not well understood. We addressed this knowledge gap by coculturing four marine biofilm-derived Roseobacteraceae strains (Leisingera aquaemixtae M597, Roseibium aggregatum S1616, Alloyangia pacifica T6124, and Sulfitobacter indolifex W002) in 14 single carbon sources. Overall, 140 coculture experiments revealed 39.3% positive interactions compared to 8.3% negative interactions. When the carbon source was consumed by only one strain, the interaction between the strains was more likely to be positive. The interaction between S1616 and M597, when cultured in D-gluconic acid, was further studied as an example. S1616-M597 coculture displayed a higher D-gluconic acid consumption rate than S1616 monoculture, whereas M597 could not use D-gluconic acid as the sole carbon source. The supernatant of S1616 monoculture supported the growth of M597, and branched-chain amino acids in the supernatant were consumed. Transcriptomic analysis suggested that M597 induced the expression of genes for branched-chain amino acid biosynthesis in S1616. Additionally, metagenomic analysis revealed the wide distribution and a strongly correlated co-occurrence of the four strains in global oceanic biofilms. Together, our findings show that interspecies positive interactions are prevalent among marine-biofilm Roseobacteraceae, and the interactions are likely to be mediated by branched-chain amino acids metabolism.

IMPORTANCE: Interspecies interactions are crucial for microbial community structure and function. Despite well-studied social behaviors in model microorganisms, species interactions in natural marine biofilms especially Roseobacteraceae with complex metabolic pathways are not well understood. Our findings suggest that positive microbial interactions, which can be mediated by branched-chain amino acid biosynthesis, are common among marine-biofilm Roseobacteraceae. This study provides new insights into microbial interactions and the ecology of marine biofilms.

RevDate: 2025-02-10
CmpDate: 2025-02-11

Dong L, Ji Z, Hu J, et al (2025)

Oral microbiota shifts following tooth loss affect gut health.

BMC oral health, 25(1):213.

BACKGROUND: Tooth loss not only impairs oral function but also affects gut health by altering the host microbiota. Understanding the oral-gut axis can provide insights into systemic health implications following tooth loss.

METHODS: Using an animal model, we extracted the molars of C57 mice. Saliva and fecal samples were collected for 16S rRNA and metagenomic sequencing to analyze changes in the oral and gut microbiota. Pearson correlation analysis assessed the relationship between altered microbial communities.

RESULTS: The study found a significant reduction in oral microbiota diversity following tooth loss, with increased Proteobacteria and decreased Muribacter. Gut microbiota showed increased Firmicutes and decreased Bacteroidota. Correlations between oral and gut microbiota changes were observed, indicating a potential link between tooth loss and alterations in intestinal microbial balance.

CONCLUSION: In the mouse model, tooth loss disrupted the balance of the oral-gut microbiota, with potential implications for intestinal health. Although these findings are from a murine model, considering the existence of the oral-gut axis balance in the human body, it is reasonable to postulate that following tooth loss in humans, the health of the intestinal microecology may also warrant attention.

RevDate: 2025-02-11
CmpDate: 2025-02-10

Safika S, Indrawati A, Hidayat R, et al (2024)

Characterizing the gut microbiome of birds-of-paradise in the northwest lowland of Papua Island.

Open veterinary journal, 14(12):3345-3354.

BACKGROUND: Birds-of-paradise, renowned for their stunning plumage and intricate mating rituals, have been extensively studied for their external characteristics. However, the microbial communities inhabiting their digestive tracts remain largely unexplored. The gut microbiome plays a vital role in host health and physiology, influencing digestion, nutrient absorption, and immune function. Understanding the microbiome of birds-of-paradise, particularly in their unique tropical rainforest habitats, may offer valuable insights into their adaptation and overall health.

AIM: This study aims to characterize the gut microbiome of birds-of-paradise and to explore the relationship between microbiome and host.

METHODS: Fecal samples were collected from Jayapura Regency, Indonesia, with non-invasive sampling methods. DNA was extracted using the DNeasy PowerSoil Pro Kit. Shotgun metagenomic sequencing was performed on the MGI DNBSEQ-G400 platform to obtain DNA sequences. DNA sequences were analyzed using DIAMOND followed by MEGAN6 to provide insights into the relative abundance of bacterial taxa within the microbiome.

RESULTS: Using Operational Taxonomy Unit analysis we identified 1,398,117 sequences from 5,048,280 initial sequences. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria were the dominant phyla, with other phyla present in smaller amounts. Burkholderiales, Hyphomicrobiales, Sphingobacteriales, and Enterobacterales were dominant orders, each with specific functional roles. Family and Genus-Level Abundance: Flavobacteriaceae, Comamonadaceae, and Sphingobacteriaceae were dominant families, while Flavobacterium, Delftia, and Pedobacter were dominant genera. Delftia sp., Pedobacter sp., Klebsiella pneumoniae, Achromobacter sp., Bacillus pumilus, Rhizobium sp., and Brevundimonas sp. were among the most abundant species.

CONCLUSION: The microbiome in the gut of birds-of-paradise is characterized by a diverse community of bacteria, fungi, and other microorganisms. The abundance of specific orders, families, and genera varies between samples, suggesting that differences in diet, habitat, or host genetics may influence microbiome composition. The findings reveal a diverse and complex microbial community that likely plays a crucial role in host health and physiology.

RevDate: 2025-02-11
CmpDate: 2025-02-10

Gao Y, Qin G, Liang S, et al (2025)

Metagenomic Sequencing Combined with Metabolomics to Explore Gut Microbiota and Metabolic Changes in Mice with Acute Myocardial Infarction and the Potential Mechanism of Allicin.

Drug design, development and therapy, 19:771-791.

BACKGROUND: Acute myocardial infarction (AMI) is a significant contributor to global morbidity and mortality. Allicin exhibits promising therapeutic potential in AMI as a primary bioactive component derived from garlic; however, its underlying mechanisms remain incompletely elucidated.

METHODS: Our study induced AMI in mice by ligating the left coronary artery, and administered allicin orally for 28 days. The cardioprotective effects of allicin treatment were comprehensively assessed using echocardiography, histopathological examinations, intestinal barrier function, and serum inflammatory factors. The potential mechanisms of allicin were elucidated through analysis of metagenomics and serum metabolomics. Network pharmacology (NP) was used to further investigate and validate the possible molecular mechanisms of allicin.

RESULTS: Our findings revealed allicin's capacity to ameliorate cardiac impairments, improve intestinal barrier integrity, and reduce serum IL-18 and IL-1β levels after AMI. Further analysis demonstrated that the administration of allicin has the potential to ameliorate intestinal flora disorder following AMI by modulating the abundance of beneficial bacteria, such as g_Lactobacillus, g_Prevotella, g_Alistipes, and g_Limosilactobacillus, while reducing the abundance of harmful bacteria g_Parasutterella. Additionally, it exhibits the ability to enhance myocardial energy metabolism flexibility through modulating metabolites and key enzymes associated with the fatty acid metabolic pathway. Mechanistically, NP and in vivo experiments indicated that allicin might suppress pyroptosis and reduce inflammatory response via blocked activation of the NF-κB-mediated NLRP3/Caspase-1/GSDMD pathway. Moreover, Spearman correlation analysis suggested a significant association between the allicin-induced alterations in microbiota and metabolites with cardiac function and inflammatory cytokines.

CONCLUSION: Our study demonstrated that allicin alleviated myocardial injury and reduced inflammatory response by inhibiting the NF-κB-mediated NLRP3/Caspase-1/GSDMD pathway while remodeling microbiota disturbance, improving serum metabolic disorder, and enhancing the intestinal barrier. These research findings offer a novel perspective on the potential therapeutic value of allicin as an adjunctive dietary supplement to conventional treatments for AMI.

RevDate: 2025-02-11
CmpDate: 2025-02-11

Ye G, Chen G, Avellán-Llaguno RD, et al (2025)

Distinctive gut antibiotic resistome, potential health risks and underlying pathways upon cerebral ischemia-reperfusion injury.

Environmental pollution (Barking, Essex : 1987), 367:125614.

Antibiotic resistance genes (ARGs) as emerging pollutants pose health risks to humans and the environment. Gut microbiota is an important reservoir for ARGs and hotspot for ARG acquisition and dissemination. Non-antibiotic factors (such as disease pathophysiology) affect ARG emergence and dissemination. Cerebral ischemia-reperfusion injury (I/R) commonly occurs in stroke patients. However, effects of I/R on ARG emergence and dissemination are unknown. Therefore, metagenomics was used to unveil selective collection of gut antibiotic resistome and its health risks, key ARG hosts and underlying pathways upon I/R. Changes in gut antibiotic resistome upon I/R were characterized by tetracycline ARG accumulation and decreases in aminoglycoside and glycopeptide ARGs. Besides, changes in gut antibiotic resistome were corrected with those in gut microbiota from phylum to species, serum lipid accumulation and glucose depletion upon I/R. Additionally, health risks of gut microbial multidrug ARGs (such as abem, adek and TolC), macA, aph(3')-I and carO, co-localized with mobile gene elements, were increased upon I/R. Moreover, phyla Firmicutes (especially order Eubacteriales, class Clostridia) and Bacteroidota were key ARG hosts in gut microbiota of I/R gerbils. Furthermore, suppression of vancomycin resistance, and lantibiotic biosynthesis and immunity, disturbances in peptidoglycan biosynthesis and hydrolysis, activation of antimicrobial peptide resistance, lipopolysaccharide biosynthesis, teichoic acid biosynthesis, arabinogalactan biosynthesis, aromatic compound degradation, oxidative phosphorylation, the tricarboxylic acid cycle and its anaplerotic pathways were observed in upon I/R. This study provides novel insights and intervention targets related to selective collection of gut antibiotic resistome and its potential health risks upon I/R.

RevDate: 2025-02-11
CmpDate: 2025-02-11

Lee D, Ahn K, Yun K, et al (2024)

Aerobic bacterial group as an early-stage biomarker from faecal samples of patients with colorectal cancer without distant metastasis.

Beneficial microbes, 16(2):201-219.

The current approaches for detecting most colorectal polyps and early neoplasms lack sufficient sensitivity and specificity, potentially hindering treatment and ultimately reducing survival rates. Here, we performed a metagenomic analysis to identify microbiome markers in stool samples from patients with early-stage colorectal cancer (CRC). We compared the composition of gut microbiota between patients with CRC and healthy individuals, specifically focusing on patients with early-stage CRC, defined as those without core mutations (KRAS, BRAF) for CRC diagnosis, stable microsatellite instability, and distant metastasis. The aim of our study is to identify potential biomarkers from gut microbiota at different cancer stages in colorectal cancer (CRC) patients through 16S rRNA amplicon sequencing, thereby proposing a novel non-invasive method for the early diagnosis of CRC. Specific microbes were detected from groups divided based on the TNM criteria, with one group classified by tumour size only (named the T group) and another group with lymph node metastasis (named the TN group). Aerobic bacteria, such as Delftia, Stenotrophomonas, Sphingobacterium, Rhodococcus, Devosia, Ensifer, and Psychrobacter were predominantly detected in patients with CRC without lymph node metastasis. The diagnostic prediction was evaluated using the CatBoost algorithm; these microbes presented high diagnostic accuracy with a receiver operating characteristics-area under curve of 0.8, which was validated using qPCR. In conclusion, this study identified specific aerobic microbial groups as non-invasive biomarkers for early diagnosis in patients with CRC without genetic or environmental factors.

RevDate: 2025-02-10
CmpDate: 2025-02-10

Chen Y, Fang H, Chen H, et al (2025)

Bifidobacterium inhibits the progression of colorectal tumorigenesis in mice through fatty acid isomerization and gut microbiota modulation.

Gut microbes, 17(1):2464945.

Colorectal cancer (CRC) represents the third most common cancer worldwide. Consequently, there is an urgent need to identify novel preventive and therapeutic strategies for CRC. This study aimed to screen for beneficial bacteria that have a preventive effect on CRC and to elucidate the potential mechanisms. Initially, we compared gut bacteria and bacterial metabolites of healthy volunteers and CRC patients, which demonstrated that intestinal conjugated linoleic acid (CLA), butyric acid, and Bifidobacterium in CRC patients were significantly lower than those in healthy volunteers, and these indicators were significantly negatively correlated with CRC. Next, spontaneous CRC mouse model were conducted to explore the effect of supplemental CLA-producing Bifidobacterium on CRC. Supplementation of mice with CLA-producing Bifidobacterium breve CCFM683 and B. pseudocatenulatum MY40C significantly prevented CRC. Moreover, molecular approaches demonstrated that CLA and the CLA-producing gene, bbi, were the key metabolites and genes for CCFM683 to prevent CRC. Inhibitor intervention results showed that PPAR-γ was the key receptor for preventing CRC. CCFM683 inhibited the NF-κB signaling pathway, up-regulated MUC2, Claudin-1, and ZO-1, and promoted tumor cell apoptosis via the CLA-PPAR-γ axis. Additionally, fecal microbiota transplantation (FMT) and metagenomic analysis showed that CCFM683 up-regulated Odoribacter splanchnicus through CLA production, which then prevented CRC by producing butyric acid, up-regulating TJ proteins, regulating cytokines, and regulating gut microbiota. These results will contribute to the clinical trials of Bifidobacterium and the theoretical research and development of CRC dietary products.

RevDate: 2025-02-08
CmpDate: 2025-02-08

Das BK, Gadnayak A, Chakraborty HJ, et al (2025)

Exploring microbial players for metagenomic profiling of carbon cycling bacteria in sundarban mangrove soils.

Scientific reports, 15(1):4784.

The Sundarbans, the world's largest tidal mangrove forest, acts as a crucial ecosystem for production, conservation, and the cycling of carbon and nitrogen. The study explored the hypothesis that microbial communities in mangrove ecosystems exhibit unique taxonomic and functional traits that play a vital part in carbon cycling and ecosystem resilience. Using metagenomic analysis to evaluate microbial communities in mangrove and non-mangrove environment, evaluating their composition, functional functions, and ecological relevance. The analysis revealed distinct microbial profiles, in mangrove and non-mangrove environments, with bacteria, proteobacteria, and viruses being the most prevalent groups, with varying abundances in each environment. Functional and taxonomical analysis identified genes involved in carbon regulation, including Triacylglycerol lipase, NarG, DsrB, DNA-binding transcriptional dual regulator CRP, Vanillate O-demethylase oxygenase, succinate-CoA ligase, Tetrahydrofolate ligase, Carboxylase, Ribulose-1,5-bisphosphate carboxylase/oxygenase, Glycine hydroxymethyltransferase, MAG: urease, Endosymbiont of Oligobrachia haakonmosbiensis, Ribulose bisphosphate carboxylase, Aconitate hydratase AcnA, and nitrous oxide reductase, suggesting the metabolic versatility of these microbial communities for carbon cycling. The findings emphasize the key role of microbial activity in preserving mangrove ecosystem health and resilience, highlighting the intricate interplay between microbial diversity, functional capabilities, and environmental factors.

RevDate: 2025-02-08
CmpDate: 2025-02-08

Vieira S, Adão H, CSL Vicente (2025)

Assessing spatial and temporal patterns of benthic bacterial communities in response to different sediment conditions.

Marine environmental research, 204:106963.

Benthic bacterial communities are sensitive to habitat condition and present a fast response to environmental stressors, which makes them powerful ecological indicators of estuarine environments. The aim of this work is to study the spatial-temporal patterns of benthic bacterial communities in response to contrasting environmental conditions and assess their potential as ecological indicators of estuarine sediments. We characterized the diversity of bacterial communities in three contrasting sites on Sado Estuary (SW Coast, Portugal) and 4 sampling occasions, using 16S metagenomic approach. Based on previous studies, we hypothesized that diversity patterns of bacterial communities will be distinct between sites and across sampling occasions. Bacterial communities were more influenced by each site conditions than by temporal variations in the sediments. The main drivers of bacterial distribution were sediments' composition, organic contents, and hydrodynamic activity. This work provided an important baseline dataset from Sado estuary to explore bacterial networks concerning benthic ecosystem functioning.

RevDate: 2025-02-10
CmpDate: 2025-02-10

Zhong S, Yang YN, Huo JX, et al (2025)

Cyanidin-3-rutinoside from Mori Fructus ameliorates dyslipidemia via modulating gut microbiota and lipid metabolism pathway.

The Journal of nutritional biochemistry, 137:109834.

Dyslipidemia is responsible for pathologies of cardiovascular diseases and gut microbiota plays an essential role in lipid metabolism. Dietary supplementation is an important supplement to medicine in management of dyslipidemia. Mori Fructus is a popular Asia medical food with various pharmacological benefits including anti-hyperlipidemia. Cyanidin-3-rutinoside (C3R) is the main anthocyanin component in Mori Fructus, but the lipid-lowering effect and underlying mechanism of Mori Fructus-derived C3R remains unknown. In this study, we assessed the beneficial effect of Mori Fructus-derived C3R in HFD-induced hyperlipidemic mice and investigated its potential mechanism through 16S rRNA-based metagenomics and transcriptomics analysis. Our results showed that C3R from Mori Fructus significantly decreased serum lipid levels and attenuated hepatic damage induced by HFD. Analysis of the gut microbiota revealed that C3R altered the specific gut micorbiota but not changed its diversity. Among changed genera, Family_XIII_UCG-001 was significantly enriched by C3R, and it was positively associated with HDL-c, but negatively related with TC, TG, LDL-c, insulin and body weight. Transcriptomic analysis showed that C3R activates the lipid metabolism related pathways including MAPK signaling pathway, Rap1 signaling pathway, Ras signaling pathway and PI3K-Akt signaling pathway. Additionally, correlation analysis unraveled that C3R-enriched Family_XIII_UCG-001 was negatively associated with C3R-inhibited genes of Camk2a, Eef1a2, Gad1, Kif5a and Sv2b, which further positively related with TC, TG, LDL-c, insulin and body weight, but negatively associated with HDL-c. In sum, C3R may inhibit expression of immune-related genes by enriching the Family_XIII_UCG-001 genus, further ameliorating lipid metabolism disorders in HFD-challenged mice. This study provides an optional strategy for the daily management of dyslipidemia.

RevDate: 2025-02-10
CmpDate: 2025-02-10

Zou X, Yan M, Wang Y, et al (2025)

Accurate Diagnosis of Lower Respiratory Infections Using Host Response and Respiratory Microbiome from a Single Metatranscriptome Test of Bronchoalveolar Lavage Fluid.

Advanced science (Weinheim, Baden-Wurttemberg, Germany), 12(6):e2405087.

Lower respiratory tract infections (LRTIs) diagnosis is challenging because noninfectious diseases mimic its clinical features. The altered host response and respiratory microbiome following LRTIs have the potential to differentiate LRTIs from noninfectious respiratory diseases (non-LRTIs). Patients suspected of having LRTIs are retrospectively enrolled and a clinical metatranscriptome test is performed on bronchoalveolar lavage fluid (BALF). Transcriptomic and metagenomic analysis profiled the host response and respiratory microbiome in patients with confirmed LRTI (n = 126) or non-LRTIs (n = 75). Patients with evidenced LRTIs exhibited enhanced pathways on chemokine and cytokine response, neutrophile recruitment and activation, along with specific gene modules linked to LRTIs status and key blood markers. Moreover, LRTIs patients exhibited reduced diversity and evenness in the lower respiratory microbiome, likely driven by an increased abundance of bacterial pathogens. Host marker genes are selected, and classifiers are developed to distinguish patients with LRTIs, non-LRTIs, and indeterminate status, achieving an area under the receiver operating characteristic curve of 0.80 to 0.86 and validated in a subsequently enrolled cohort. Incorporating respiratory microbiome features further enhanced the classifier's performance. In summary, a single metatranscriptome test of BALF proved detailed profiles of host response and respiratory microbiome, enabling accurate LRTIs diagnosis.

RevDate: 2025-02-10
CmpDate: 2025-02-10

Malham M, Vestergaard MV, Bataillon T, et al (2025)

The Composition of the Fecal and Mucosa-adherent Microbiota Varies Based on Age and Disease Activity in Ulcerative Colitis.

Inflammatory bowel diseases, 31(2):501-513.

BACKGROUND: Pediatric-onset ulcerative colitis (pUC) represents a more aggressive disease phenotype compared with adult-onset UC. We hypothesized that this difference can, in part, be explained by the composition of the microbiota.

METHODS: In a prospective, longitudinal study, we included pediatric (N = 30) and adult (N = 30) patients with newly or previously (>1 year) diagnosed UC. We analyzed the microbiota composition in the mucosa-adherent microbiota at baseline, using 16S rRNA gene sequencing, and the fecal microbiota at baseline and at 3-month intervals, using shotgun metagenomics.

RESULTS: For fecal samples, the bacterial composition differed between pUC and aUC in newly diagnosed patients (β-diversity, Bray Curtis: R2 = 0.08, P = .02). In colon biopsies, microbial diversity was higher in aUC compared with pUC (α-diversity, Shannon: estimated difference 0.54, P = .006). In the mucosa-adherent microbiota, Alistipes finegoldii was negatively associated with disease activity in pUC while being positively associated in aUC (estimate: -0.255 and 0.098, P = .003 and P = .02 in pUC and aUC, respectively). Finally, we showed reduced stability of the fecal microbiota in pediatric patients, evidenced by a different composition of the fecal microbiota in newly and previously diagnosed pUC, a pattern not found in adults.

CONCLUSIONS: Our results indicate that pediatric UC patients have a more unstable fecal microbiota and a lower α diversity than adult patients and that the microbiota composition differs between aUC and pUC patients. These findings offer some explanation for the observed differences between pUC and aUC and indicate that individualized approaches are needed if microbiota modifications are to be used in the future treatment of UC.

RevDate: 2025-02-07
CmpDate: 2025-02-08

Kennedy EA, Weagley JS, Kim AH, et al (2025)

Bacterial community assembly of specific pathogen-free neonatal mice.

Microbiome, 13(1):46.

BACKGROUND: Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We address this gap by characterizing the assembly of the bacterial microbiota of C57BL/6 and BALB/c litters from birth to adulthood across multiple independent litters.

RESULTS: The fecal microbiome of young pups is dominated by only a few pioneering bacterial taxa. These taxa are present at low levels in the microbiota of multiple maternal body sites, precluding a clear identification of maternal source. The pup microbiota begins diversifying after 14 days, coinciding with the beginning of coprophagy and the consumption of solid foods. Pup stool bacterial community composition and diversity are not significantly different from dams from day 21 onwards. Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species.

CONCLUSIONS: Assembly of the murine microbiome occurs over the first weeks of postnatal life and is largely complete by day 21. This detailed view of bacterial community development across multiple commonly employed mouse strains informs experimental design, allowing researchers to better target interventions before, during, or after the maturation of the bacterial microbiota. The source of pioneer bacterial strains appears heterogeneous, as the most abundant taxa identified in young pup stool were found at low levels across multiple maternal body sites, suggesting diverse routes for seeding of the murine microbiome. Video Abstract.

RevDate: 2025-02-09
CmpDate: 2025-02-09

Li L, Nielsen J, Y Chen (2025)

Personalized gut microbial community modeling by leveraging genome-scale metabolic models and metagenomics.

Current opinion in biotechnology, 91:103248.

The impact of the gut microbiome on human health is increasingly recognized as dysbiosis has been found to be associated with a spectrum of diseases. Here, we review the databases of genome-scale metabolic models (GEMs), which have paved the way for investigations into the metabolic capabilities of gut microbes and their interspecies dynamics. We further discuss the strategies for developing community-level GEMs, which are crucial for understanding the complex interactions within microbial communities and between the microbiome and its host. Such GEMs can guide the design of synthetic microbial communities for disease treatment. Finally, we explore advances in personalized gut microbiome modeling. These advancements broaden our mechanistic understanding and hold promise for applications in precision medicine and therapeutic interventions.

RevDate: 2025-02-08
CmpDate: 2025-02-08

Khedpande N, K Barve (2025)

Role of gut dysbiosis in drug-resistant epilepsy: Pathogenesis and available therapeutic strategies.

Brain research, 1850:149385.

Over 70 million people worldwide suffer from epilepsy, a persistent brain disorder. Although there are more than 20 antiseizure drugs available for the symptomatic treatment of epilepsy, about one-third of patients with epilepsy experience seizures that show resistance to pharmacotherapy. Since patients with drug-resistant epilepsy are more prone to physical injuries, psychosocial dysfunction, early death, and deteriorated life quality, the development of safer and more effective treatments is a crucial clinical need. The gut-brain axis and microbiome research advances have provided new insights into the pathophysiology of epilepsy, the resistance to anti-seizure medicine, and potential treatment targets. Inflammation, disturbance of the blood-brain barrier, and altered neurotransmitters are key pathways linked to gut dysbiosis. The characterization of microbial species and functional pathways has advanced thanks to metagenomic sequencing and high-throughput analysis. In this review, we elaborate on the gut-mediated molecular pathways involved in drug-resistant epilepsy, the gut- modulatory therapeutic options, and their combination with antiseizure medications for drug-resistant epilepsy.

RevDate: 2025-02-08
CmpDate: 2025-02-07

Liu Y, Yang B, Qi Q, et al (2024)

Metagenomic next-generation sequencing for lung cancer low respiratory tract infections diagnosis and characterizing microbiome features.

Frontiers in cellular and infection microbiology, 14:1518199.

BACKGROUND: The capability of mNGS in diagnosing suspected LRTIs and characterizing the respiratory microbiome in lung cancer patients requires further evaluation.

METHODS: This study evaluated mNGS diagnostic performance and utilized background microbial sequences to characterize LRT microbiome in these patients. GSVA was used to analyze the potential functions of identified genera.

RESULTS: Bacteria were the most common pathogens (n=74) in LRTIs of lung cancer patients, and polymicrobial infections predominated compared to monomicrobial infections (p<0.001). In diagnosing LRTIs in lung cancer patients, the pathogen detection rate of mNGS (83.3%, 70/84) was significantly higher than that of sputum culture (34.5%, 29/84) (p<0.001). This result was consistent with that of non-lung cancer patients (p<0.001). Furthermore, in the specific detection of bacteria (95.7% vs. 22.6%) and fungi (96.0% vs. 22.2%), the detection rate of mNGS was also significantly higher than that of CMTs mainly based on culture (p<0.001, p<0.001). However, in the detection of CMV/EBV viruses, there was no significant difference between the detection rate of mNGS and that of viral DNA quantification (p = 1.000 and 0.152). mNGS analysis revealed Prevotella, Streptococcus, Veillonella, Rothia, and Capnocytophaga as the most prevalent genera in the LRT of lung cancer patients. GSVA revealed significant correlations between these genera and tumor metabolic pathways as well as various signaling pathways including PI3K, Hippo, and p53.

CONCLUSION: mNGS showed a higher pathogen detection rate than culture-based CMTs in lung cancer patients with LRTIs, and also characterizing LRT microbiome composition and revealing potential microbial functions linked to lung carcinogenesis.

RevDate: 2025-02-08
CmpDate: 2025-02-07

Zhang Y, Li HZ, Breed M, et al (2025)

Soil warming increases the active antibiotic resistome in the gut of invasive giant African snails.

Microbiome, 13(1):42.

BACKGROUND: Global warming is redrawing the map for invasive species, spotlighting the globally harmful giant African snail as a major ecological disruptor and public health threat. Known for harboring extensive antibiotic resistance genes (ARGs) and human pathogens, it remains uncertain whether global warming exacerbates these associated health risks.

METHODS: We use phenotype-based single-cell Raman with D2O labeling (Raman-D2O) and genotype-based metagenomic sequencing to investigate whether soil warming increases active antibiotic-resistant bacteria (ARBs) in the gut microbiome of giant African snails.

RESULTS: We show a significant increase in beta-lactam phenotypic resistance of active ARBs with rising soil temperatures, mirrored by a surge in beta-lactamase genes such as SHV, TEM, OCH, OKP, and LEN subtypes. Through a correlation analysis between the abundance of phenotypically active ARBs and genotypically ARG-carrying gut microbes, we identify species that contribute to the increased activity of antibiotic resistome under soil warming. Among 299 high-quality ARG-carrying metagenome-assembled genomes (MAGs), we further revealed that the soil warming enhances the abundance of "supercarriers" including human pathogens with multiple ARGs and virulence factors. Furthermore, we identified elevated biosynthetic gene clusters (BGCs) within these ARG-carrying MAGs, with a third encoding at least one BGC. This suggests a link between active ARBs and secondary metabolism, enhancing the environmental adaptability and competitive advantage of these organisms in warmer environments.

CONCLUSIONS: The study underscores the complex interactions between soil warming and antibiotic resistance in the gut microbiome of the giant African snail, highlighting a potential escalation in environmental health risks due to global warming. These findings emphasize the urgent need for integrated environmental and health strategies to manage the rising threat of antibiotic resistance in the context of global climate change. Video Abstract.

RevDate: 2025-02-08
CmpDate: 2025-02-08

Broderick CM, Benucci GMN, Bachega LR, et al (2025)

Long-term climate establishes functional legacies by altering microbial traits.

The ISME journal, 19(1):.

Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.

RevDate: 2025-02-08
CmpDate: 2025-02-08

Danckert NP, Freidin MB, Granville Smith I, et al (2024)

Treatment response in rheumatoid arthritis is predicted by the microbiome: a large observational study in UK DMARD-naive patients.

Rheumatology (Oxford, England), 63(12):3486-3495.

OBJECTIVES: Disease-modifying antirheumatic drugs (DMARDs) are a first-line treatment in rheumatoid arthritis (RA). Treatment response to DMARDs is patient-specific, dose efficacy is difficult to predict and long-term results are variable. The gut microbiota are known to play a pivotal role in prodromal and early-disease RA, manifested by Prevotella spp. enrichment. The clinical response to therapy may be mediated by microbiota, and large-scale studies assessing the microbiome are few. This study assessed whether microbiome signals were associated with, and predictive of, patient response to DMARD treatment. Accurate early identification of those who will respond poorly to DMARD therapy would allow selection of alternative treatment (e.g. biologic therapy) and potentially improve patient outcome.

METHODS: A multicentre, longitudinal, observational study of stool- and saliva microbiome was performed in DMARD-naive, newly diagnosed RA patients during introduction of DMARD treatment. Clinical data and samples were collected at baseline (n = 144) in DMARD-naive patients and at six weeks (n = 117) and 12 weeks (n = 95) into DMARD therapy. Samples collected (n = 365 stool, n = 365 saliva) underwent shotgun sequencing. Disease activity measures were collected at each timepoint and minimal clinically important improvement determined.

RESULTS: In total, 26 stool microbes were found to decrease in those manifesting a minimal clinically important improvement. Prevotella spp. and Streptococcus spp. were the predominant taxa to decline following six weeks and 12 weeks of DMARDs, respectively. Furthermore, baseline microbiota of DMARD-naive patients were indicative of future response.

CONCLUSION: DMARDs appear to restore a perturbed microbiome to a eubiotic state. Moreover, microbiome status can be used to predict likelihood of patient response to DMARD.

RevDate: 2025-02-06
CmpDate: 2025-02-06

Zhao S, Lin H, Li W, et al (2025)

Post sleeve gastrectomy-enriched gut commensal Clostridia promotes secondary bile acid increase and weight loss.

Gut microbes, 17(1):2462261.

The gut microbiome is altered after bariatric surgery and is associated with weight loss. However, the commensal bacteria involved and the underlying mechanism remain to be determined. We performed shotgun metagenomic sequencing in obese subjects before and longitudinally after sleeve gastrectomy (SG), and found a significant enrichment in microbial species in Clostridia and bile acid metabolizing genes after SG treatment. Bile acid profiling further revealed decreased primary bile acids (PBAs) and increased conjugated secondary bile acids (C-SBAs) after SG. Specifically, glycodeoxycholic acid (GDCA) and taurodeoxycholic acid (TDCA) were increased at different follow-ups after SG, and were associated with the increased abundance of Clostridia and body weight reduction. Fecal microbiome transplantation with post-SG feces increased SBA levels, and alleviated body weight gain in the recipient mice. Furthermore, both Clostridia-enriched spore-forming bacteria and GDCA supplementation increased the expression of genes responsible for lipolysis and fatty acid oxidation in adipose tissue and reduced adiposity via Takeda G-protein-coupled receptor 5 (TGR5) signaling. Our findings reveal post-SG gut microbiome and C-SBAs as contributory to SG-induced weight loss, in part via TGR5 signaling, and suggest SBA-producing gut microbes as a potential therapeutic target for obesity intervention.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Fumagalli A, Castells-Nobau A, Trivedi D, et al (2025)

Archaea methanogens are associated with cognitive performance through the shaping of gut microbiota, butyrate and histidine metabolism.

Gut microbes, 17(1):2455506.

The relationship between bacteria, cognitive function and obesity is well established, yet the role of archaeal species remains underexplored. We used shotgun metagenomics and neuropsychological tests to identify microbial species associated with cognition in a discovery cohort (IRONMET, n = 125). Interestingly, methanogen archaeas exhibited the strongest positive associations with cognition, particularly Methanobrevibacter smithii (M. smithii). Stratifying individuals by median-centered log ratios (CLR) of M. smithii (low and high M. smithii groups: LMs and HMs) revealed that HMs exhibited better cognition and distinct gut bacterial profiles (PERMANOVA p = 0.001), characterized by increased levels of Verrucomicrobia, Synergistetes and Lentisphaerae species and reduced levels of Bacteroidetes and Proteobacteria. Several of these species were linked to the cognitive test scores. These findings were replicated in a large-scale validation cohort (Aging Imageomics, n = 942). Functional analyses revealed an enrichment of energy, butyrate, and bile acid metabolism in HMs in both cohorts. Global plasma metabolomics by CIL LC-MS in IRONMET identified an enrichment of methylhistidine, phenylacetate, alpha-linolenic and linoleic acid, and secondary bile acid metabolism associated with increased levels of 3-methylhistidine, phenylacetylgluamine, adrenic acid, and isolithocholic acid in the HMs group. Phenylacetate and linoleic acid metabolism also emerged in the Aging Imageomics cohort performing untargeted HPLC-ESI-MS/MS metabolic profiling, while a targeted bile acid profiling identified again isolithocholic acid as one of the most significant bile acid increased in the HMs. 3-Methylhistidine levels were also associated with intense physical activity in a second validation cohort (IRONMET-CGM, n = 116). Finally, FMT from HMs donors improved cognitive flexibility, reduced weight, and altered SCFAs, histidine-, linoleic acid- and phenylalanine-related metabolites in the dorsal striatum of recipient mice. M. smithii seems to interact with the bacterial ecosystem affecting butyrate, histidine, phenylalanine, and linoleic acid metabolism with a positive impact on cognition, constituting a promising therapeutic target to enhance cognitive performance, especially in subjects with obesity.

RevDate: 2025-02-07
CmpDate: 2024-12-23

Borton MA, McGivern BB, Willi KR, et al (2025)

A functional microbiome catalogue crowdsourced from North American rivers.

Nature, 637(8044):103-112.

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept[1], we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures[2,3], so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.

RevDate: 2025-02-07
CmpDate: 2025-02-07

Zelasko S, Swaney MH, Sandstrom S, et al (2025)

Early-life upper airway microbiota are associated with decreased lower respiratory tract infections.

The Journal of allergy and clinical immunology, 155(2):436-450.

BACKGROUND: Microbial interactions mediating colonization resistance play key roles within the human microbiome, shaping susceptibility to infection from birth. The role of the nasal and oral microbiome in the context of early life respiratory infections and subsequent allergic disease risk remains understudied.

OBJECTIVES: Our aim was to gain insight into microbiome-mediated defenses and respiratory pathogen colonization dynamics within the upper respiratory tract during infancy.

METHODS: We performed shotgun metagenomic sequencing of nasal (n = 229) and oral (n = 210) microbiomes from our Wisconsin Infant Study Cohort at age 24 months and examined the influence of participant demographics and exposure history on microbiome composition. Detection of viral and bacterial respiratory pathogens by RT-PCR and culture-based studies with antibiotic susceptibility testing, respectively, to assess pathogen carriage was performed. Functional bioassays were used to evaluate pathogen inhibition by respiratory tract commensals.

RESULTS: Participants with early-life lower respiratory tract infection were more likely to be formula fed, attend day care, and experience wheezing. Composition of the nasal, but not oral, microbiome associated with prior lower respiratory tract infection, namely lower alpha diversity, depletion of Prevotella, and enrichment of Moraxella catarrhalis including drug-resistant strains. Prevotella originating from healthy microbiomes had higher biosynthetic gene cluster abundance and exhibited contact-independent inhibition of M catarrhalis.

CONCLUSIONS: These results suggest interbacterial competition affects nasal pathogen colonization. This work advances understanding of protective host-microbe interactions occurring in airway microbiomes that alter infection susceptibility in early life.

RevDate: 2025-02-07
CmpDate: 2025-02-07

Davidson IM, Nikbakht E, Haupt LM, et al (2025)

Methodological approaches in 16S sequencing of female reproductive tract in fertility patients: a review.

Journal of assisted reproduction and genetics, 42(1):15-37.

BACKGROUND: The female genital tract microbiome has become a particular area of interest in improving assisted reproductive technology (ART) outcomes with the emergence of next-generation sequencing (NGS) technology. However, NGS assessment of microbiomes currently lacks uniformity and poses significant challenges for accurate and precise bacterial population representation.

OBJECTIVE: As multiple NGS platforms and assays have been developed in recent years for microbiome investigation-including the advent of long-read sequencing technologies-this work aimed to identify current trends and practices undertaken in female genital tract microbiome investigations.

RESULTS: Areas like sample collection and transport, DNA extraction, 16S amplification vs. metagenomics, NGS library preparation, and bioinformatic analysis demonstrated a detrimental lack of uniformity. The lack of uniformity present is a significant limitation characterised by gap discrepancies in generation and interpretation of results. Minimal consistency was observed in primer design, DNA extraction techniques, sample transport, and bioinformatic analyses.

CONCLUSION: With third-generation sequencing technology highlighted as a promising tool in microbiota-based research via full-length 16S rRNA sequencing, there is a desperate need for future studies to investigate and optimise methodological approaches of the genital tract microbiome to ensure better uniformity of methods and results interpretation to improve clinical impact.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Griffiths ME, Broos A, Morales J, et al (2025)

Dynamics of influenza transmission in vampire bats revealed by longitudinal monitoring and a large-scale anthropogenic perturbation.

Science advances, 11(6):eads1267.

Interrupting pathogen transmission between species is a priority strategy to mitigate zoonotic threats. However, avoiding counterproductive interventions requires knowing animal reservoirs of infection and the dynamics of transmission within them, neither of which are easily ascertained from the cross-sectional surveys that now dominate investigations into newly discovered viruses. We used biobanked sera and metagenomic data to reconstruct the transmission of recently discovered bat-associated influenza virus (BIV; H18N11) over 12 years in three zones of Peru. Mechanistic models fit under a Bayesian framework, which enabled joint inference from serological and molecular data, showed that common vampire bats maintain BIV independently of the now assumed fruit bat reservoir through immune waning and seasonal transmission pulses. A large-scale vampire bat cull targeting rabies incidentally halved BIV transmission, confirming vampire bats as maintenance hosts. Our results show how combining field studies, perturbation responses, and multi-data-type models can elucidate pathogen dynamics in nature and reveal pathogen-dependent effects of interventions.

RevDate: 2025-02-06
CmpDate: 2025-02-06

Yen TY, Hsu C, Lee NC, et al (2025)

Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing.

Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi, 58(1):86-93.

BACKGROUND: Severe community-acquired pneumonia was associated with high morbidity and mortality in children. However, species-level microbiome of lower airway was sparse, and we used shotgun metagenomic next-generation sequencing to explore microbial signatures.

METHODS: We conducted a prospective cohort study to recruit children under 18 who required admission to an intensive care unit for community-acquired pneumonia between December 2019 and February 2022. Lower respiratory specimens were collected on admission for shotgun metagenomic sequencing. The children were divided into two groups. Critical cases were patients with respiratory failure requiring endotracheal ventilator support, and severe cases did not require intubation. Signatures of lower respiratory tract microbiome were compared between groups using an exact k-mer matching metagenomic analysis pipeline (Kraken 2) and a metagenome-assembled genomes pipeline (MetaWRAP).

RESULTS: Totally 66 children were enrolled, and 27 children were critical cases, and the rest were severe cases. There were significant differences in microbial community structure between different severity groups, and microbial abundance was negatively correlated with disease severity. The results showed that Haemophilus influenzae was more prominent in children who were critical, accompanied with increased expression of intracellular transport, secretion, and vesicle transport genes. Rothia mucilaginosa, Dolosigranulum pigrum, and Prevotella melaninogenica tended to be present in less severe community-acquired pneumonia group.

CONCLUSION: This study demonstrated that significantly different microbial community was associated with severity of community-acquired pneumonia requiring intensive care admission. Species-level shotgun metagenomic sequencing facilitates the exploration of potentially pathogenic or protective microbes and shed the light of probiotic development in lower respiratory tract.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Cuong NC, Hung NV, Linh TK, et al (2025)

Structure of fungal community and culturable fungi on the discolored surfaces of pine storage boxes in the tropical region in Dong Nai, Vietnam.

Brazilian journal of biology = Revista brasleira de biologia, 84:e289015 pii:S1519-69842024000101378.

Wood and wood-based materials are commonly used for storage, but their surfaces are prone to biodegradation by microorganisms, especially fungi. This study focuses on the microbial communities on pine wood storage boxes treated with an anti-termite and mold solution in a tropical region in Dong Nai, Vietnam. We isolated 13 fungal strains from these surfaces and classified them into six genera: Rhizopus, Aspergillus, Fusarium, Curvularia, Penicillium, and Trichoderma. Enzyme activity tests revealed that strains Curvularia eragrostidis TD4.2 and Aspergillus sydowii TD5 were the most effective producers of cellulase, amylase, and laccase. Shotgun metagenomics analysis of the biological sample of the discolored surface of pine storage boxes indicated that Ascomycota was the dominant phylum, with Dothideomycetes and Sordariomycetes as the prevalent class. Aureobasidium (0.33%) and Chaetomium (1.1%) were the most abundant genera in the Dothideomycetes and Sordariomycetes, respectively. This research illustrates the complexity of microbial communities on wood surfaces, providing insights into the fungal dynamics affecting wooden storage materials in tropical climates.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Alifia L, Zulaika E, Soeprijanto S, et al (2025)

Microbial diversity and biotechnological potential of mangrove leaf litter in Kebun Raya Mangrove, Surabaya, Indonesia.

Brazilian journal of biology = Revista brasleira de biologia, 84:e288968 pii:S1519-69842024000101377.

Mangrove ecosystems play a crucial role in maintaining ecological balance with leaf litter serving as an important substrate for diverse microbial communities. This study investigates the microbial communities inhabiting leaf litter from four different mangrove species: Rhizophora apiculata, Rhizophora stylosa, Sonneratia caseolaris, and Avicennia marina collected from Kebun Raya Mangrove, Surabaya, Indonesia. Using metagenomic sequencing, we revealed that Proteobacteria were predominant, followed by Chlorobi and Actinobacteria in the samples. Interestingly, we detected notable populations of anaerobic bacteria, including genus of Chlorobaculum and Allochromatium. Metagenomic analyses exhibited high levels of adaptation to stressors, evidenced by the prevalence of genes conferring resistance to antibiotics (e.g., beta-lactams, tetracyclines), heavy metals (e.g., chromium, arsenic), and hydrocarbons. Furthermore, the metagenomic analysis revealed the presence of genes involved in the biosynthesis of polyunsaturated fatty acids (PUFAs), antimicrobial compounds, and plant growth-promoting activities. These findings highlight the potential of mangrove leaf litter as a reservoir of beneficial microbes with diverse biotechnological applications, including bioremediation, nutraceuticals, pharmaceuticals, and agriculture.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Xi Z, Chen J, Wang L, et al (2024)

Characteristics of lower respiratory microbiota in children's refractory Mycoplasma pneumoniae pneumonia pre- and post-COVID-19 era.

Frontiers in cellular and infection microbiology, 14:1438777.

INTRODUCTION: Little was known about the characteristics of low respiratory tract (LRT) microbiota of refractory M. pneumoniae pneumonia (RMPP) in children before and after the COVID-19 pandemic.

METHODS: Forty-two children diagnosed with RMPP in 2019 (Y2019 group) and 33 children diagnosed with RMPP in 2023 (Y2023 group), entered into the study. The characteristics of the clinical findings were examined, and the LRT microbiota was analyzed by metagenomic next generation sequencing.

RESULTS: The ratio of consolidate, atelectasis, lung necrosis, and erythema multiforme in Y2023 group was significantly higher than that in Y2019 (P<0.05). Mycoplasmoides pneumoniae was the top species of the LRT microbiota in both groups. The rate of macrolide resistance MP in Y2023 was significantly higher than that in Y2019 (P<0.05), and the mutant site was all 23S rRNA A2063G. There were no significant differences in α-diversity and β-diversity of LRT microbiota between Y2019 and Y2023 group. Trichoderma citrinoviride, Canine mastadenovirus A, Ralstonia pickettii, Lactococcus lactis, Pseudomonas aeruginosa were the biomarkers of LRT microbiota in children with RMPP of Y2023. The abundance of Mycoplasmoides pneumoniae positively correlated with the levels of D-dimer and LDH, negatively correlated with the counts of CD3[+] T cells, CD8[+] T cells, CD19[+] B cells and CD16[+]CD56[+] NK cells.

DISCUSSION: Our study showed that high abundance of MP was correlated with the severity of RMPP and decrease of immune cells. Trichoderma citrinoviride, Canine mastadenovirus A, Ralstonia pickettii, Lactococcus lactis, Pseudomonas aeruginosa were the biomarkers in microbiota of LRT in children with RMPP post COVID-19 era.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Armstrong E, Liu R, Pollock J, et al (2025)

Quantitative profiling of the vaginal microbiota improves resolution of the microbiota-immune axis.

Microbiome, 13(1):39.

BACKGROUND: The composition of the vaginal microbiota is closely linked to adverse sexual and reproductive health outcomes, due in part to effects on genital immunology. Compositional approaches such as metagenomic sequencing provide a snapshot of all bacteria in a sample and have become the standard for characterizing the vaginal microbiota, but only provide microbial relative abundances. We hypothesized that the addition of absolute abundance data would provide a more complete picture of host-microbe interactions in the female genital tract.

RESULTS: We analyzed cervicovaginal secretions from 196 female sex workers in Kenya and found that bacterial load was elevated among women with diverse, bacterial vaginosis (BV)-type microbiota and lower among women with Lactobacillus predominance. Bacterial load was also positively associated with proinflammatory cytokines, such as IL-1α, and negatively associated with chemokines, such as IP-10. The associations between bacterial load and immune factors differed across bacterial community states, but L. crispatus predominance was the only microbial community where higher bacterial load was not associated with higher proinflammatory cytokines. Total vaginal bacterial load was also a stronger predictor of the genital immune environment than BV by Nugent score, the current clinical standard, in the Kenya-based cohort and in a Uganda-based confirmatory cohort.

CONCLUSIONS: Our results suggest that total vaginal bacterial load is at least as strong a predictor of the genital immune milieu as current BV clinical diagnostic tools, supporting exploration of the vaginal bacterial load as a predictor of adverse reproductive and sexual health outcomes. Video Abstract.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Molina-Pardines C, Haro-Moreno JM, Rodriguez-Valera F, et al (2025)

Extensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations.

Microbiome, 13(1):41.

BACKGROUND: The oceanic microbiome is dominated by members of the SAR11 clade. Despite their abundance, challenges in recovering the full genetic diversity of natural populations have hindered our understanding of the eco-evolutionary mechanisms driving intra-species variation. In this study, we employed a combination of single-amplified genomes and long-read metagenomics to recover the genomic diversity of natural populations within the SAR11 genomospecies Ia.3/VII, the dominant group in the Mediterranean Sea.

RESULTS: The reconstruction of the first complete genome within this genomospecies revealed that the core genome represents a significant proportion of the genome (~ 81%), with highly divergent areas that allow for greater strain-dependent metabolic flexibility. The flexible genome was concentrated in small regions, typically containing a single gene, and was located in equivalent regions within the genomospecies. Each variable region was associated with a specific set of genes that, despite exhibiting some divergence, maintained equivalent biological functionality within the population. The environmental pangenome is large and enriched in genes involved in nutrient transport, as well as cell wall synthesis and modification, showing an extremely high degree of functional redundancy in the flexible genome (i.e. paralogisms).

CONCLUSIONS: This genomic architecture promotes polyclonality, preserving genetic variation within the population. This, in turn, mitigates intraspecific competition and enables the population to thrive under variable environmental conditions and selective pressures. Furthermore, this study demonstrates the power of long-read metagenomics in capturing the full genetic diversity of environmental SAR11 populations, overcoming the limitations of second-generation sequencing technologies in genome assembly. Video Abstract.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Qu Q, Dou Q, Xiang Z, et al (2025)

Population-level gut microbiome and its associations with environmental factors and metabolic disorders in Southwest China.

NPJ biofilms and microbiomes, 11(1):24.

Gut microbiota affects host health and disease. Large-scale cohorts have explored the interactions between the microbiota, host, and environment to reveal the disease-associated microbiota variation. A population-level gut metagenomic cohort is still rare in China. Here, we performed metagenomic sequencing on fecal samples from the CMEC Microbiome Project in Southwest China. In this study, we identified host socioeconomics, diet, lifestyle, and medical measurements that were significantly associated with microbiome function and composition. We revealed extensive novel associations between the host microbiome and common metabolic disorders. Our results provide new insight into associations of gut microbiota with metabolic disorders so as to support the translation of gut microbiome findings into potential clinical practice.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Boulton W, Salamov A, Grigoriev IV, et al (2025)

Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC.

Scientific data, 12(1):204.

The Multidisciplinary Observatory for Study of the Arctic Climate (MOSAiC) expedition consisted of a year-long drifting survey of the Central Arctic Ocean. The ecosystems component of MOSAiC included the sampling of molecular data, with metagenomes collected from a diverse range of environments. The generation of metagenome-assembled-genomes (MAGs) from metagenomes are a starting point for genome-resolved analyses. This dataset presents a catalogue of MAGs recovered from a set of 73 samples from MOSAiC, including 2407 prokaryotic and 56 eukaryotic MAGs, as well as annotations of a near complete eukaryotic MAG using the Joint Genome Institute (JGI) annotation pipeline. The metagenomic samples are from the surface ocean, chlorophyll maximum, mesopelagic and bathypelagic, within leads and under-ice ocean, as well as melt ponds, ice ridges, and first- and second-year sea ice. This set of MAGs can be used to benchmark microbial biodiversity in the Central Arctic Ocean, compare individual strains across space and time, and to study changes in Arctic microbial communities from the winter to summer, at a genomic level.

RevDate: 2025-02-04
CmpDate: 2025-02-04

Yan Z, Zheng Z, Cao L, et al (2025)

Altered gut microbiome and serum metabolome profiles associated with essential tremor.

Metabolic brain disease, 40(2):118.

The genetic predisposition and environmental factors both trigger the complex neurological dyskinesia of essential tremor (ET). Gut dysbiosis may facilitate the occurrence and development of neurological diseases. Therefore, it is worth exploring the inner connections between gut microbiota and ET. First, the gut microbiota of 19 ET patients and 21 healthy controls (HCs) were analysed with metagenomics approach. Second, the potential linkages between gut microbiome and serum metabolome profiles were explored by integrative analysis. The gut microbiota disorders were present in ET patients. The LEfSe method showed a significant decrease in Bacteroides. The functional analysis revealed that there were differences in gut microbial apoptosis, retinol metabolism, and steroid hormone biosynthesis pathways. The levels of various lipids and lipid-like molecules alter in serum of ET patients, which correlated with altered gut microbial abundance, indicating the alterations in lipid metabolism involved in apoptosis pathway in ET. All of these data point to the gut dysbiosis in ET, and some changed gut microbial species were linked to abnormalities in blood lipid metabolism, which open up new avenues for investigation into the pathophysiology of ET.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Fonseca de Souza L, Oliveira HG, Pellegrinetti TA, et al (2025)

Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity.

FEMS microbiology ecology, 101(2):.

Despite the beneficial effects of plant growth-promoting rhizobacteria on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 days after sowing. However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Miebach J, Green D, Strittmatter M, et al (2025)

Importance, structure, cultivability, and resilience of the bacterial microbiota during infection of laboratory-grown Haematococcus spp. by the blastocladialean pathogen Paraphysoderma sedebokerense: evidence for a domesticated microbiota and its potential for biocontrol.

FEMS microbiology ecology, 101(2):.

Industrial production of the unicellular green alga Haematococcus lacustris is compromised by outbreaks of the fungal pathogen Paraphysoderma sedebokerense (Blastocladiomycota). Here, using axenic algal and fungal cultures and antibiotic treatments, we show that the bacterial microbiota of H. lacustris is necessary for the infection by P. sedebokerense and that its modulation affects the outcome of the interaction. We combined metagenomics and laboratory cultivation to investigate the diversity of the bacterial microbiota associated to three Haematococcus species and monitor its change upon P. sedebokerense infection. We unveil three types of distinct, reduced bacterial communities, which likely correspond to keystone taxa in the natural Haematococcus spp. microbiota. Remarkably, the taxonomic composition and functionality of these communities remained stable during infection. The major bacterial taxa identified in this study have been cultivated by us or others, paving the way to developing synthetic communities to experimentally explore interactions within this tripartite system. We discuss our results in the light of emerging evidence concerning the structuring and domestication of plant and animal microbiota, thus providing novel experimental tools and a new conceptual framework necessary to enable the engineering of Haematococcus spp. microbiota toward the biocontrol of P. sedebokerense.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Zhou Z, Liu S, Saleem M, et al (2025)

Unraveling phase-dependent variations of viral community, virus-host linkage, and functional potential during manure composting process.

Bioresource technology, 419:132081.

The temporal dynamics of bacterial and fungal communities significantly impact the manure composting process, yet viral communities are often underexplored. Bulk metagenomes, viromes, metatranscriptomes, and metabolomes were integrated to investigate dynamics of double-stranded DNA (dsDNA) virus and virus-host interactions throughout a 63-day composting process. A total of 473 viral operational taxonomic units (vOTUs), predominantly Caudoviricetes, showed distinct phase-dependent differentiation. In phase I (initial-mesophilic), viruses targeted Gammaproteobacteria and Firmicutes, utilizing restriction-modification (RM) systems. In phase II (thermophilic-maturing), viruses infected Alphaproteobacteria, Chloroflexi, and Planctomycetes, employing CRISPR-Cas systems. Lysogenic and lytic viruses exerting differential effects on bacterial pathogens across phases. Additionally, six types of auxiliary metabolic genes (AMGs) related to galactose and cysteine metabolisms were identified. The homologous lineages of AMGs with bacterial genes, along with the significant temporal correlation observed between virus-host-metabolite interactions, underscore the critical yet often overlooked role of viral communities in modulating microbial metabolisms and pathogenesis within composting ecosystems.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Nakatsu G, Ko D, Michaud M, et al (2025)

Virulence factor discovery identifies associations between the Fic gene family and Fap2[+] fusobacteria in colorectal cancer microbiomes.

mBio, 16(2):e0373224.

Fusobacterium is a bacterium associated with colorectal cancer (CRC) tumorigenesis, progression, and metastasis. Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates Fusobacterium adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2. Here, we analyze genomes of Fusobacterium colon tumor isolates and find that a family of post-translational modification enzymes containing Fic domains is associated with Fap2 positivity in these strains. We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2[+] Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. Using a global data set of CRC shotgun metagenomes, we show that fusobacterial Fic and Fap2 genes frequently co-occur in the fecal microbiomes of individuals with late-stage CRC. We further characterize specific Fic gene families harbored by Fap2[+] Fusobacterium animalis genomes and detect recombination events and elements of horizontal gene transfer via synteny analysis of Fic gene loci. Exposure of a F. animalis strain to a colon adenocarcinoma cell line increases gene expression of fusobacterial Fic and virulence-associated adhesins. Finally, we demonstrate that Fic proteins are synthesized by F. animalis as Fic peptides are detectable in F. animalis monoculture supernatants. Taken together, our study uncovers Fic genes as potential virulence factors in Fap2[+] fusobacterial genomes.IMPORTANCEAccumulating data support that bacterial members of the intra-tumoral microbiota critically influence colorectal cancer progression. Yet, relatively little is known about non-adhesin fusobacterial virulence factors that may influence carcinogenesis. Our genomic analysis and expression assays in fusobacteria identify Fic domain-containing genes, well-studied virulence factors in pathogenic bacteria, as potential fusobacterial virulence features. The Fic family proteins that we find are encoded by fusobacteria and expressed by Fusobacterium animalis merit future investigation to assess their roles in colorectal cancer development and progression.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Larsson SC, Ericson U, Dekkers KF, et al (2025)

Meat intake in relation to composition and function of gut microbiota.

Clinical nutrition (Edinburgh, Scotland), 45:124-133.

OBJECTIVE: Meat intake is suggested to affect gut microbiome composition and the risk of chronic diseases. We aimed to identify meat-associated gut microbiome features and their association with host factors.

DESIGN: Gut microbiota species were profiled by deep shotgun metagenomics sequencing in 9669 individuals. Intake of white meat, unprocessed red meat, and processed red meat was assessed using a food frequency questionnaire. The associations of meat intake with alpha-diversity and relative abundance of gut microbiota species were tested using linear regression models with adjustment for dietary fiber intake, body mass index, and other potential confounders. Meat-associated species were further assessed for association with enrichment of microbial gene function, meat-associated plasma metabolites, and clinical biomarkers.

RESULTS: Higher intake of processed red meat was associated with reduced alpha microbial diversity. White meat, unprocessed, and processed red meat intakes were associated with 36, 14, and 322 microbiota species, respectively. Species associated with processed red meat were enriched for bacterial pathways like amino acid degradation, while those negatively linked were enriched for pathways like homoacetogenesis. Furthermore, species positively associated with processed red meat were to a large extent associated with reduced trimethylamine N-oxide and glutamine levels but increased creatine and carnitine metabolites, fasting insulin and glucose, C-reactive protein, apolipoprotein A1, and triglyceride levels and higher blood pressure.

CONCLUSION: This largest to date population-based study on meat and gut microbiota suggests that meat intake, particularly processed red meat, may modify the gut microbiota composition, functional capacity, and health-related biomarkers.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Qi Y, Fu R, Yan C, et al (2025)

Enrichment of a heterotrophic nitrifying and aerobic denitrifying bacterial consortium: Microbial community succession and nitrogen removal characteristics and mechanisms.

Bioresource technology, 419:132013.

This study cultivated a bacterial consortium (S60) from landfill leachate that exhibited effective heterotrophic nitrification and aerobic denitrification (HN-AD) properties. Under aerobic conditions, the removal of NH4[+]-N reached 100 % when the S60 consortium utilised NH4[+]-N either as the sole nitrogen source or in combination with NO2[-]-N and NO3[-]-N. Optimal HN-AD performance was achieved with sodium acetate as a carbon source and a pH of 7.0-8.0, dissolved oxygen concentration of 4.0-5.0 mg/L, and a C/N ratio of 10. Furthermore, the presence of functional genes (amoA, hao, napA, nirK, nirS, nosZ), hydroxylamine oxidase, nitrate reductase, and nitrite reductase was confirmed in the S60 consortium. Drawing from these findings, two HN-AD pathways were delineated: NH4[+]-N → NH2OH → NO2[-]-N → NO3[-]-N → NO2[-]-N → NO → N2O → N2 and NH4[+]-N → NH2OH → N2O → N2. Metagenomic binning analysis of the S60 consortium uncovered complete pathways for dissimilatory nitrate reduction and denitrification within Halomonas, Zobellella, Stutzerimonas, Marinobacter, and Pannonibacter. These findings offer new insights into the application of HN-AD bacteria and their collaborative nitrogen removal in environments with varying nitrogen sources.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Kaur S, Patel BCK, Collen A, et al (2025)

The microbiome and the eye: a new era in ophthalmology.

Eye (London, England), 39(3):436-448.

The human microbiome has progressively been recognised for its role in various disease processes. In ophthalmology, complex interactions between the gut and distinct ocular microbiota within each structure and microenvironment of the eye has advanced our knowledge on the multi-directional relationships of these ecosystems. Increasingly, studies have shown that modulation of the microbiome can be achieved through faecal microbiota transplantation and synbiotics producing favourable outcomes for ophthalmic diseases. As ophthalmologists, we are obliged to educate our patients on measures to cultivate a healthy gut microbiome through a range of holistic measures. Further integrative studies combining microbial metagenomics, metatranscriptomics and metabolomics are necessary to fully characterise the human microbiome and enable targeted therapeutic interventions.

RevDate: 2025-02-05
CmpDate: 2025-02-05

Williams AD, Leung VW, Tang JW, et al (2025)

Ancient environmental microbiomes and the cryosphere.

Trends in microbiology, 33(2):233-249.

In this review, we delineate the unique set of characteristics associated with cryosphere environments (namely, ice and permafrost) which present both challenges and opportunities for studying ancient environmental microbiomes (AEMs). In a field currently reliant on several assumptions, we discuss the theoretical and empirical feasibility of recovering microbial nucleic acids (NAs) from ice and permafrost with varying degrees of antiquity. We also summarize contamination control best practices and highlight considerations for the latest approaches, including shotgun metagenomics, and downstream bioinformatic authentication approaches. We review the adoption of existing software and provide an overview of more recently published programs, with reference to their suitability for AEM studies. Finally, we summarize outstanding challenges and likely future directions for AEM research.

RevDate: 2025-02-03
CmpDate: 2025-02-04

Richardson M, Zhao S, Lin L, et al (2025)

SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.

Nature microbiology, 10(2):527-540.

The local arrangement of microbes can profoundly impact community assembly, function and stability. However, our understanding of the spatial organization of the human gut microbiome at the micron scale is limited. Here we describe a high-throughput and streamlined method called Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) to capture spatial co-localization in a complex microbial consortium. The method obtains microbial composition of micron-scale subcommunities through split-and-pool barcoding. SAMPL-seq analysis of the healthy human gut microbiome identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These co-localized microbes organize into spatially distinct groups or 'spatial hubs' dominated by Bacteroidaceae, Ruminococcaceae and Lachnospiraceae families. Using inulin as a dietary perturbation, we observed reversible spatial rearrangement of the gut microbiome where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock insights into microbiomes at the micron scale.

RevDate: 2025-02-04
CmpDate: 2025-02-04

Forry SP, Servetas SL, Dootz JN, et al (2025)

A sensitivity analysis of methodological variables associated with microbiome measurements.

Microbiology spectrum, 13(2):e0069624.

The experimental methods employed during metagenomic sequencing analyses of microbiome samples significantly impact the resulting data and typically vary substantially between laboratories. In this study, a full factorial experimental design was used to compare the effects of a select set of methodological choices (sample, operator, lot, extraction kit, variable region, and reference database) on the analysis of biologically diverse stool samples. For each parameter investigated, a main effect was calculated that allowed direct comparison both between methodological choices (bias effects) and between samples (real biological differences). Overall, methodological bias was found to be similar in magnitude to real biological differences while also exhibiting significant variations between individual taxa, even between closely related genera. The quantified method biases were then used to computationally improve the comparability of data sets collected under substantially different protocols. This investigation demonstrates a framework for quantitatively assessing methodological choices that could be routinely performed by individual laboratories to better understand their metagenomic sequencing workflows and to improve the scope of the datasets they produce.IMPORTANCEMethod-specific bias is a well-recognized challenge in metagenomic sequencing characterization of microbiome samples, but rigorous bias quantification is challenging. This report details a full factorial exploration of 48 experimental protocols by systematically varying microbiome sample, iterations of material production, laboratory personnel, DNA extraction kit, marker gene selection, and reference databases. Quantification of the biases associated with each parameter revealed similar magnitudes of variation arising from real biological differences and from varied analysis procedures. Furthermore, these measurement biases varied substantially with taxa, even between closely related genera. However, computational correction of method bias using a reference material was demonstrated that significantly harmonized metagenomic sequencing results collected using different analysis protocols.

RevDate: 2025-02-04
CmpDate: 2025-02-04

Daruka L, Czikkely MS, Szili P, et al (2025)

ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro.

Nature microbiology, 10(2):313-331.

Despite ongoing antibiotic development, evolution of resistance may render candidate antibiotics ineffective. Here we studied in vitro emergence of resistance to 13 antibiotics introduced after 2017 or currently in development, compared with in-use antibiotics. Laboratory evolution showed that clinically relevant resistance arises within 60 days of antibiotic exposure in Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, priority Gram-negative ESKAPE pathogens. Resistance mutations are already present in natural populations of pathogens, indicating that resistance in nature can emerge through selection of pre-existing bacterial variants. Functional metagenomics showed that mobile resistance genes to antibiotic candidates are prevalent in clinical bacterial isolates, soil and human gut microbiomes. Overall, antibiotic candidates show similar susceptibility to resistance development as antibiotics currently in use, and the corresponding resistance mechanisms overlap. However, certain combinations of antibiotics and bacterial strains were less prone to developing resistance, revealing potential narrow-spectrum antibacterial therapies that could remain effective. Finally, we develop criteria to guide efforts in developing effective antibiotic candidates.

RevDate: 2025-02-04
CmpDate: 2025-02-04

Yin Q, da Silva AC, Zorrilla F, et al (2025)

Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations.

Nature microbiology, 10(2):541-553.

Gut bacteria from the Enterobacteriaceae family are a major cause of opportunistic infections worldwide. Given their prevalence among healthy human gut microbiomes, interspecies interactions may play a role in modulating infection resistance. Here we uncover global ecological patterns linked to Enterobacteriaceae colonization and abundance by leveraging a large-scale dataset of 12,238 public human gut metagenomes spanning 45 countries. Machine learning analyses identified a robust gut microbiome signature associated with Enterobacteriaceae colonization status, consistent across health states and geographic locations. We classified 172 gut microbial species as co-colonizers and 135 as co-excluders, revealing a genus-wide signal of colonization resistance within Faecalibacterium and strain-specific co-colonization patterns of the underexplored Faecalimonas phoceensis. Co-exclusion is linked to functions involved in short-chain fatty acid production, iron metabolism and quorum sensing, while co-colonization is linked to greater functional diversity and metabolic resemblance to Enterobacteriaceae. Our work underscores the critical role of the intestinal environment in the colonization success of gut-associated opportunistic pathogens with implications for developing non-antibiotic therapeutic strategies.

RevDate: 2025-02-04
CmpDate: 2025-02-04

Gulyaeva A, Liu L, Garmaeva S, et al (2025)

Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements.

Microbiology spectrum, 13(2):e0106624.

Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria. Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. We applied our approach to 22 strains of bacteria belonging to the genus Faecalibacterium, resulting in identification of 15 candidate prophages, and validated the approach by demonstrating the activity of five prophages from four of the strains. The genomes of three active phages were identical or similar to those of known phages, while the other two active phages were not represented in the Viral RefSeq database. Four of the active phages possessed a diversity-generating retroelement (DGR), and one retroelement had two variable regions. DGRs of two phages were active at the time of the induction experiments, as evidenced by nucleotide variation in sequencing reads. We also predicted that the host range of two active phages may include multiple bacterial species. Finally, we noted that four phages were less prevalent in the metagenomes of inflammatory bowel disease patients compared to a general population cohort, a difference mainly explained by differences in the abundance of the host bacteria. Our study highlights the utility of prophage identification and induction for unraveling phage molecular mechanisms and ecological interactions.IMPORTANCEWhile hundreds of thousands of phage genomes have been discovered in metagenomics studies, only a few of these phages have been characterized experimentally. Here, we explore phage characterization through bioinformatic identification of prophages in genomes of cultured bacteria, followed by prophage induction. Using this approach, we detect the activity of five prophages in four strains of commensal gut bacteria Faecalibacterium. We further note that four of the prophages possess diversity-generating retroelements implicated in rapid mutation of phage genome loci associated with phage-host and phage-environment interactions and analyze the intricate patterns of retroelement activity. Our study highlights the potential of prophage characterization for elucidating complex molecular mechanisms employed by the phages.

RevDate: 2025-02-04
CmpDate: 2025-02-04

Bai X, Wu J, Zhang B, et al (2025)

Metagenomics reveals functional profiles of soil nitrogen and phosphorus cycling under different amendments in saline-alkali soil.

Environmental research, 267:120686.

High salinity, low fertility and poor structure in saline-alkali soils led to nutrient cycling slow and microbial activity loss. The application of amendments has proven effective in enhancing soil nutrients, which significantly affects soil nitrogen and phosphorus cycling process. However, the specific impact of different amendments on the microbial functional potential related to nutrient cycling in saline-alkali soils remains unclear. Hence, metagenomics sequencing was used to investigate soil microbial communities and nitrogen and phosphorus cycling genes in response to different amendments, and to examine the influence of soil physicochemical properties on functional genes in the Hetao irrigation district of China. The results showed that amendments application enriched the Proteobacteria abundance, while inhibiting oligotrophic groups such as Chloroflexi. Compared to the control (CK), the combined application of desulfurization gypsum and cattle manure (DC) notably increased nasA (assimilatory nitrate reduction) and nirB (dissimilatory nitrate reduction), as well as phoD and phoA genes (organic P mineralization). Furthermore, soil AK and AP were primary factors affecting microbial communities and N and P cycling genes. Overall, this study offers valuable insights into soil nitrogen and phosphorus cycling genes and their interactions in response to different amendments, where the application of amendments affects nitrogen and phosphorus cycling by altering soil nutrient availability.

RevDate: 2025-02-04
CmpDate: 2025-02-04

Liu J, Zhou M, Zhou L, et al (2025)

Methane production related to microbiota in dairy cattle feces.

Environmental research, 267:120642.

Methane (CH4) emission from livestock feces, led by ruminants, shows a profound impact on global warming. Despite this, we have almost no information on the syntrophy of the intact microbiome metabolisms, from carbohydrates to the one-carbon units, covering multiple stages of ruminant development. In this study, syntrophic effects of polysaccharide degradation and acetate-producing bacteria, and methanogenic archaea were revealed through metagenome-assembled genomes from water saturated dairy cattle feces. Although CH4 is thought to be produced by archaea, more edges, nodes, and balanced interaction types revealed by network analysis provided a closed bacteria-archaea network. The CH4 production potential and pathways were further evaluated through dynamic, thermodynamic and [13]C stable isotope analysis. The powerful CH4 production potential benefited from the metabolic flux: classical polysaccharides, soluble sugar (glucose, galactose, lactose), acetate, and CH4 produced via typical acetoclastic methanogenesis. In comparison, a cooperative model dominated by hydrogenotrophic methanogenic archaea presented a weak ability to generate CH4. Our findings comprehensively link carbon and CH4 metabolism paradigm to specific microbial lineages which are shaped related to developmental stages of the dairy cattle, directing influencing global warming from livestock and waste treatment.

RevDate: 2025-02-04
CmpDate: 2025-02-04

Peterson D, Weidenmaier C, Timberlake S, et al (2025)

Depletion of key gut bacteria predicts disrupted bile acid metabolism in inflammatory bowel disease.

Microbiology spectrum, 13(2):e0199924.

The gut microbiome plays a key role in bile acid (BA) metabolism, where a diversity of metabolic products contribute to human health and disease. In particular, Inflammatory Bowel Disease (IBD) is characterized by a low concentration of secondary bile acids (SBAs), whose transformation from primary bile acids (PBAs) is an essential function performed solely by gut bacteria. BA-transformation activity mediated by the bile acid inducible (bai) operon has been functionally characterized in the genus Clostridium, and homologous bai gene sequences have been found in metagenome-assembled genomes (MAGs) belonging to other taxa in the human gut, but it is unclear which species of bai-carrying bacteria perform physiologically significant amounts of bile acid transformation in healthy and sick individuals. Here, we analyzed hundreds of stool samples with paired metagenomic and metabolomic data from IBD patients and controls and found that the abundance of the bai operon in metagenomic samples was highly predictive of that sample's high- or low-SBA metabolic state. We further found that bai genes from the Clostridium species best characterized as BA transformers were more prevalent in IBD patients than in non-IBD controls, while bai genes from uncharacterized taxa known only from MAGs were much more physiologically relevant in non-IBD samples. These un-isolated clades of BA-transforming bacteria merit further research; as beyond their prevalence in the human population, we found some cases in which they engrafted in IBD patients who had undergone fecal microbiota transplantation and experienced a clinical response.IMPORTANCEIn this paper, we identify specific bacteria that perform an important metabolic function in the human gut and demonstrate that in the guts of a large subset of patients with IBD, these bacteria are missing and the function is defective. This is a rare example where the correlation between the absence of specific bacteria and the dysfunction of metabolism is directly observed, not in mice nor in the lab, but in physiologic microbial communities in the human gut. Our results point to a path for studying how a small but important set of bacteria is affected by conditions in the IBD gut and perhaps to the development of interventions to mitigate the loss of these bacteria in IBD.

RevDate: 2025-02-04
CmpDate: 2025-02-04

Gao X, Liang H, Hu T, et al (2025)

Cultivated genome references for protein database construction and high-resolution taxonomic annotation in metaproteomics.

Microbiology spectrum, 13(2):e0175524.

Metaproteomics offers a profound understanding of the functional dynamics of the gut microbiome, which is crucial for personalized healthcare strategies. The selection of an appropriate database is a critical step for the identification of peptides and proteins, as well as for the provision of accurate taxonomic and functional annotations. The matched metagenomic-derived database is considered to be the best, but its limitations include the identification of low-abundance organisms and taxonomic resolution. Herein, we constructed a protein database (DBCGR2) based on Cultivated Genome Reference 2 (CGR2) and developed a complete peptide-centric analysis workflow for database searching and for the annotation of taxonomy and function. This workflow was subsequently appraised in comparison with metagenomics-derived databases for the analysis of metaproteomic data. Our findings suggested that the performance of DBCGR2 in identification was comparable with metagenomics-derived databases with improvement in identification rates of peptides from low-abundance species. The database searching results could be fully annotated using the pepTaxa taxonomic annotation approach developed in this study, and the taxonomic resolution was enhanced to strain level. Additionally, the results demonstrated that the sensitivity of functional annotation could be enhanced by employing DBCGR2. Overall, the DBCGR2 combined with pepTaxa can be considered an alternative for metaproteomic data analysis with superior analysis performances.IMPORTANCEMass spectrometry-based metaproteomics offers a profound understanding of the gut microbial taxonomy and functionality. The databases utilized in the analysis of metaproteomic data are crucial, as they determine the identification of proteins that can be recognized and linked to overall human health, in addition to the quality of taxonomic and functional annotation. Among the most effective approaches for constructing protein databases is the utilization of metagenomic sequencing to create matched databases. However, the database, derived from isolated genomes, has yet to undergo rigorous testing for their efficacy and accuracy in protein identification and taxonomic and functional annotation. Here, we constructed a protein database DBCGR2 derived from Cultivated Genome Reference 2 (CGR2) and a complete workflow for data analysis. We compared the performances of DBCGR2 and metagenomics-derived databases. Our results indicated that DBCGR2 can be regarded as an alternative to metagenomics-derived databases, which contribute to metaproteomic data analysis.