Viewport Size Code:
Login | Create New Account
picture

  MENU

About | Classical Genetics | Timelines | What's New | What's Hot

About | Classical Genetics | Timelines | What's New | What's Hot

icon

Bibliography Options Menu

icon
QUERY RUN:
HITS:
PAGE OPTIONS:
Hide Abstracts   |   Hide Additional Links
NOTE:
Long bibliographies are displayed in blocks of 100 citations at a time. At the end of each block there is an option to load the next block.

Bibliography on: Microbiome

The Electronic Scholarly Publishing Project: Providing world-wide, free access to classic scientific papers and other scholarly materials, since 1993.

More About:  ESP | OUR CONTENT | THIS WEBSITE | WHAT'S NEW | WHAT'S HOT

ESP: PubMed Auto Bibliography 28 Mar 2024 at 01:53 Created: 

Microbiome

It has long been known that every multicellular organism coexists with large prokaryotic ecosystems — microbiomes — that completely cover its surfaces, external and internal. Recent studies have shown that these associated microbiomes are not mere contamination, but instead have profound effects upon the function and fitness of the multicellular organism. We now know that all MCEs are actually functional composites, holobionts, composed of more prokaryotic cells than eukaryotic cells and expressing more prokaryotic genes than eukaryotic genes. A full understanding of the biology of "individual" eukaryotes will now depend on an understanding of their associated microbiomes.

Created with PubMed® Query: microbiome[tiab] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

-->

RevDate: 2024-03-26

Vijay A, Dirain CO, Chen S, et al (2024)

Microbiome and Otic Quinolone Levels Following Tympanoplasty Assessed by Gelatin Sponge Analysis.

Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery [Epub ahead of print].

OBJECTIVE: To determine if absorbable gelatin sponge (AGS) can be used to assess the posttympanoplasty microbiome and otic antibiotic exposure.

STUDY DESIGN: Prospective.

SETTING: Tertiary hospital.

METHODS: Patients undergoing tympanoplasty were prospectively enrolled. Intraoperatively, AGS was applied to the medial ear canal/tympanic membrane (TM) for 1 minute after canal incision, then saved for analysis. Ear canals were packed with AGS at the end of surgery. Otic ofloxacin was administered until the first postoperative visit, when AGS was collected. Microbial presence was assessed by culture. Ofloxacin levels were assessed by liquid-chromatography mass-spectrometry.

RESULTS: Fifty-three patients were included. AGS was collected in 92.9% of patients seen within 21 days compared to 70.8% of those seen at 22 to 35 days. At surgery, AGS yielded bacteria and fungi in 81% and 11%, respectively, including Staphylococcus species (55%) and Pseudomonas species (25%). Postoperatively, AGS yielded bacteria in 71% and fungi in 21% at the meatus, (staphylococci 57% and pseudomonas 25%). TM samples yielded bacteria in 69%, fungi in 6%, staphylococci in 53%, and pseudomonas in 19%. Ofloxacin concentration at the meatus was 248 μg/mL (95% confidence interval [CI]: 119-377) and at the TM was 126 μg/mL (95% CI: 58-194). Ofloxacin-resistant colonies were found in 75% of patients.

CONCLUSION: Analysis of AGS is a viable technique for noninvasively studying healing metrics posttympanoplasty, including the microbiome and otic antibiotic exposure. Despite exposure to a high concentration of quinolones, the tympanoplasty wound is far from sterile, which may impact healing outcomes.

RevDate: 2024-03-27
CmpDate: 2024-03-27

Zhang X, Hu J, Li Y, et al (2024)

Gallbladder microbial species and host bile acids biosynthesis linked to cholesterol gallstone comparing to pigment individuals.

Frontiers in cellular and infection microbiology, 14:1283737.

Gallstones are crystalline deposits in the gallbladder that are traditionally classified as cholesterol, pigment, or mixed stones based on their composition. Microbiota and host metabolism variances among the different types of gallstones remain largely unclear. Here, the bile and gallstone microbial species spectra of 29 subjects with gallstone disease (GSD, 24 cholesterol and 5 pigment) were revealed by type IIB restriction site-associated DNA microbiome sequencing (2bRAD-M). Among them (21 subjects: 18 cholesterol and 3 pigment), plasma samples were subjected to liquid chromatography-mass spectrometry (LC-MS) untargeted metabolomics. The microbiome yielded 896 species comprising 882 bacteria, 13 fungi, and 1 archaeon. Microbial profiling revealed significant enrichment of Cutibacterium acnes and Microbacterium sp005774735 in gallstone and Agrobacterium pusense and Enterovirga sp013044135 in the bile of cholesterol GSD subjects. The metabolome revealed 2296 metabolites, in which malvidin 3-(6''-malonylglucoside), 2-Methylpropyl glucosinolate, and ergothioneine were markedly enriched in cholesterol GSD subjects. Metabolite set enrichment analysis (MSEA) demonstrated enriched bile acids biosynthesis in individuals with cholesterol GSD. Overall, the multi-omics analysis revealed that microbiota and host metabolism interaction perturbations differ depending on the disease type. Perturbed gallstone type-related microbiota may contribute to unbalanced bile acids metabolism in the gallbladder and host, representing a potential early diagnostic marker and therapeutic target for GSD.

RevDate: 2024-03-27

Ajeeb TT, Gonzalez E, Solomons NW, et al (2024)

Human milk microbiome: associations with maternal diet and infant growth.

Frontiers in nutrition, 11:1341777.

INTRODUCTION: Ingestion of human milk (HM) is identified as a significant factor associated with early infant gut microbial colonization, which has been associated with infant health and development. Maternal diet has been associated with the HM microbiome (HMM). However, a few studies have explored the associations among maternal diet, HMM, and infant growth during the first 6 months of lactation.

METHODS: For this cross-sectional study, Mam-Mayan mother-infant dyads (n = 64) were recruited from 8 rural communities in the Western Highlands of Guatemala at two stages of lactation: early (6-46 days postpartum, n = 29) or late (109-184 days postpartum, n = 35). Recruited mothers had vaginally delivered singleton births, had no subclinical mastitis or antibiotic treatments, and breastfed their infants. Data collected at both stages of lactation included two 24-h recalls, milk samples, and infant growth status indicators: head-circumference-for-age-z-score (HCAZ), length-for-age-z-score (LAZ), and weight-for-age-z-score (WAZ). Infants were divided into subgroups: normal weight (WAZ ≥ -1SD) and mildly underweight (WAZ < -1SD), non-stunted (LAZ ≥ -1.5SD) and mildly stunted (LAZ < -1.5SD), and normal head-circumference (HCAZ ≥ -1SD) and smaller head-circumference (HCAZ < -1SD). HMM was identified using 16S rRNA gene sequencing; amplicon analysis was performed with the high-resolution ANCHOR pipeline, and DESeq2 identified the differentially abundant (DA) HMM at the species-level between infant growth groups (FDR < 0.05) in both early and late lactation.

RESULTS: Using both cluster and univariate analyses, we identified (a) positive correlations between infant growth clusters and maternal dietary clusters, (b) both positive and negative associations among maternal macronutrient and micronutrient intakes with the HMM at the species level and (c) distinct correlations between HMM DA taxa with maternal nutrient intakes and infant z-scores that differed between breast-fed infants experiencing growth faltering and normal growth in early and late lactation.

CONCLUSION: Collectively, these findings provide important evidence of the potential influence of maternal diet on the early-life growth of breastfed infants via modulation of the HMM.

RevDate: 2024-03-27

Yang Z, Chen X, Yu M, et al (2024)

Metagenomic sequencing identified microbial species in the rumen and cecum microbiome responsible for niacin treatment and related to intramuscular fat content in finishing cattle.

Frontiers in microbiology, 15:1334068.

INTRODUCTION: Niacin is one of the essential vitamins for mammals. It plays important roles in maintaining rumen microecological homeostasis. Our previous study indicated that dietary niacin significantly elevated intramuscular fat content (IMF) in castrated finishing steers. Whether niacin affects fat deposition by regulating the microbial composition and functional capacities of gastrointestinal microbiome has been unknown yet.

METHODS: In this study, 16 castrated Xiangzhong Black cattle were randomly assigned into either control group fed with a basal concentrate diet (n = 8) or niacin group fed with a basal concentrate diet added 1000 mg/kg niacin (n = 8). Seven rumen samples and five cecum content samples were randomly collected from each of control and niacin groups for metagenomic sequencing analysis.

RESULTS: A total of 2,981,786 non-redundant microbial genes were obtained from all tested samples. Based on this, the phylogenetic compositions of the rumen and cecum microbiome were characterized. We found that bacteria dominated the rumen and cecum microbiome. Prevotella ruminicola and Ruminococcus flavefaciens were the most abundant bacterial species in the rumen microbiome, while Clostridiales bacterium and Eubacterium rectale were predominant bacterial species in the cecum microbiome. Rumen microbiome had significantly higher abundances of GHs, GTs, and PLs, while cecum microbiome was enriched by CBMs and AAs. We found a significant effect of dietary niacin on rumen microbiome, but not on cecum microbiome. Dietary niacin up-regulated the abundances of bacterial species producing lactic acid and butyrate, fermenting lactic acid, and participating in lipid hydrolysis, and degradation and assimilation of nitrogen-containing compounds, but down-regulated the abundances of several pathogens and bacterial species involved in the metabolism of proteins and peptides, and methane emissions. From the correlation analysis, we suggested that niacin improved nutrient digestion and absorption, but reduced energy loss, and Valine, leucine and isoleucine degradation of rumen microbiome, which resulted in the increased host IMF.

CONCLUSION: The results suggested that dietary manipulation, such as the supplementation of niacin, should be regarded as the effective and convenient way to improve IMF of castrated finishing steers by regulating rumen microbiome.

RevDate: 2024-03-27

Knapple WL, Yoho DS, Sheh A, et al (2024)

Retrospective subgroup analysis of fecal microbiota, live-jslm (REBYOTA[®]) administered by colonoscopy under enforcement discretion for the prevention of recurrent Clostridioides difficile infection.

Therapeutic advances in gastroenterology, 17:17562848241239547.

BACKGROUND: Fecal microbiota, live-jslm (RBL; REBYOTA[®]), is the first Food and Drug Administration (FDA)-approved, single-dose, rectally administered, microbiota-based live biotherapeutic product for preventing Clostridioides difficile infection (CDI) recurrence. Alternative routes of administration are of clinical interest.

OBJECTIVES: Evaluate the safety and efficacy of RBL administration via colonoscopy.

DESIGN: Retrospective analysis of electronic medical records of participants administered RBL via colonoscopy under FDA enforcement discretion.

METHODS: The number of participants with treatment and/or procedure-emergent adverse events (TEAEs) was evaluated. Treatment success and sustained clinical response, defined as the absence of CDI recurrence within 8 weeks and 6 months, respectively, were evaluated.

RESULTS: TEAEs were experienced by 75% (6/8) of participants; most were mild to moderate in severity, and none due to RBL or its administration. Most participants had treatment success (80%; 8/10); 75% (6/8) had sustained clinical response.

CONCLUSION: Real-world safety and efficacy of RBL administered via colonoscopy were consistent with clinical trials of rectally administered RBL.

RevDate: 2024-03-27

Igwe AN, Pearse IS, Aguilar JM, et al (2024)

Plant species within Streptanthoid Complex associate with distinct microbial communities that shift to be more similar under drought.

Ecology and evolution, 14(3):e11174.

Prolonged water stress can shift rhizoplane microbial communities, yet whether plant phylogenetic relatedness or drought tolerance predicts microbial responses is poorly understood. To explore this question, eight members of the Streptanthus clade with varying affinity to serpentine soil were subjected to three watering regimes. Rhizoplane bacterial communities were characterized using 16S rRNA gene amplicon sequencing and we compared the impact of watering treatment, soil affinity, and plant species identity on bacterial alpha and diversity. We determined which taxa were enriched among drought treatments using DESeq2 and identified features of soil affinity using random forest analysis. We show that water stress has a greater impact on microbial community structure than soil affinity or plant identity, even within a genus. Drought reduced alpha diversity overall, but plant species did not strongly differentiate alpha diversity. Watering altered the relative abundance of bacterial genera within Proteobacteria, Firmicutes, Bacteroidetes, Planctomycetes, and Acidobacteria, which responded similarly in the rhizoplane of most plant species. In addition, bacterial communities were more similar when plants received less water. Pseudarthrobacter was identified as a feature of affinity to serpentine soil while Bradyrhizobium, Chitinophaga, Rhodanobacter, and Paenibacillus were features associated with affinity to nonserpentine soils among Streptanthus. The homogenizing effect of drought on microbial communities and the increasing prevalence of Gram-negative bacteria across all plant species suggest that effects of water stress on root-associated microbiome structure may be predictable among closely related plant species that inhabit very different soil environments. The functional implications of observed changes in microbiome composition remain to be studied.

RevDate: 2024-03-27

Manzoor M, Leskelä J, Pietiäinen M, et al (2024)

Shotgun metagenomic analysis of the oral microbiome in gingivitis: a nested case-control study.

Journal of oral microbiology, 16(1):2330867.

BACKGROUND: Gingivitis, i.e. inflammation of the gums, is often induced by dentalplaque. However, its exact link to the oral microbiota remains unclear.

METHODS: In a case-control study involving 120 participants, comprising 60 cases and 60 controls (mean age (SD) 36.6 (7.6) years; 50% males), nested within a prospective multicentre cohort study, we examined theoral microbiome composition of gingivitis patients and their controlsusing shotgun metagenomic sequencing of saliva samples. Participants underwent clinical and radiographic oral health examinations, including bleeding on probing (BOP), at six tooth sites. BOP ≥33%was considered 'generalized gingivitis/initial periodontitis'(GG/IP), and BOP <33% as 'healthy and localized gingivitis'(H/LG). Functional potential was inferred using HUMANn3.

RESULTS: GG/IP exhibited an increase in the abundance of Actinomyces, Porphyromonas, Aggregatibacter, Corynebacterium, Olsenella, and Treponema, whereas H/LG exhibited an increased abundance of Candidatus Nanosynbacter. Nineteen bacterial species and fourmicrobial functional profiles, including L-methionine, glycogen, andinosine-5'-phosphate biosynthesis, were associated with GG/IP. Constructing models with multiple markers resulted in a strong predictive value for GG/IP, with an area under the curve (ROC) of 0.907 (95% CI: 0.848-0.966).

CONCLUSION: We observed distinct differences in the oral microbiome between the GG/IP and H/LG groups, indicating similar yet unique microbial profiles and emphasizing their potential role in progression of periodontal diseases.

RevDate: 2024-03-27

Yay E, Yilmaz M, Toygar H, et al (2024)

Oral and gut microbial profiling in periodontitis and Parkinson's disease.

Journal of oral microbiology, 16(1):2331264.

OBJECTIVES: We tested the hypothesis that Parkinson's disease (PA) alters the periodontitis-associated oral microbiome.

METHOD: Patients with periodontitis with Parkinson's disease (PA+P) and without PA (P) and systemically and periodontally healthy individuals (HC) were enrolled. Clinical, periodontal and neurological parameters were recorded. The severity of PA motor functions was measured. Unstimulated saliva samples and stool samples were collected. Next-generation sequencing of 16S ribosomal RNA (V1-V3 regions) was performed.

RESULTS: PA patients had mild-to-moderate motor dysfunction and comparable plaque scores as those without, indicating that oral hygiene was efficient in the PA+P group. In saliva, there were statistically significant differences in beta diversity between HC and PA+P (p = 0.001), HC and P (p = 0.001), and P and PA+P (p = 0.028). The microbial profiles of saliva and fecal samples were distinct. Mycoplasma faucium, Tannerella forsythia, Parvimonas micra, and Saccharibacteria (TM7) were increased in P; Prevotella pallens, Prevotella melaninogenica, Neisseria multispecies were more abundant in PA+P group, Ruthenibacterium lactatiformans, Dialister succinatiphilus, Butyrivibrio crossotus and Alloprevotella tannerae were detected in fecal samples in P groups compared to healthy controls.

CONCLUSIONS: No significant differences were detected between Parkinson's and non-Parkinson's gut microbiomes, suggesting that Parkinson's disease modifies the oral microbiome in periodontitis subjects independent of the gut microbiome.

RevDate: 2024-03-27
CmpDate: 2024-03-27

Ly YT, Leuko S, R Moeller (2024)

An overview of the bacterial microbiome of public transportation systems-risks, detection, and countermeasures.

Frontiers in public health, 12:1367324.

When we humans travel, our microorganisms come along. These can be harmless but also pathogenic, and are spread by touching surfaces or breathing aerosols in the passenger cabins. As the pandemic with SARS-CoV-2 has shown, those environments display a risk for infection transmission. For a risk reduction, countermeasures such as wearing face masks and distancing were applied in many places, yet had a significant social impact. Nevertheless, the next pandemic will come and additional countermeasures that contribute to the risk reduction are needed to keep commuters safe and reduce the spread of microorganisms and pathogens, but also have as little impact as possible on the daily lives of commuters. This review describes the bacterial microbiome of subways around the world, which is mainly characterized by human-associated genera. We emphasize on healthcare-associated ESKAPE pathogens within public transport, introduce state-of-the art methods to detect common microbes and potential pathogens such as LAMP and next-generation sequencing. Further, we describe and discuss possible countermeasures that could be deployed in public transportation systems, as antimicrobial surfaces or air sterilization using plasma. Commuting in public transport can harbor risks of infection. Improving the safety of travelers can be achieved by effective detection methods, microbial reduction systems, but importantly by hand hygiene and common-sense hygiene guidelines.

RevDate: 2024-03-26

Sealschott S, Pickler R, Fortney C, et al (2024)

Gut Microbiota and Symptom Expression and Severity in Neonatal Abstinence Syndrome.

Biological research for nursing [Epub ahead of print].

Problem: Neonatal abstinence syndrome (NAS) affecting neonates with fetal exposure to opioids, is defined by expression and severity of symptoms. The pathophysiology behind symptoms variability is lacking. The study aims were to examine (a) differences in gut microbiota of neonates with and without NAS, (b) the relationships between gut microbiota and symptom expression and NAS severity, and (c) the changes in the neonate gut microbiota diversity during the course of NAS treatment. Methods: A cross-sectional observational design was used to examine differences in microbiota and a longitudinal, repeated measures approach was used to determine relationships between gut microbiota and NAS symptoms. Symptom data were collected using the Finnegan Neonatal Abstinence Scoring Tool and the Neonatal Pain Agitation and Sedation Scale. Stool samples were collected for microbiome analyses with 16S rRNA microbiome sequencing. Results: Differences in alpha and beta diversity between neonates with and without NAS were seen. Relative abundance results revealed 18 taxa were different in neonates with NAS compared to neonates without NAS. No differences were found in alpha or beta diversity in neonates with NAS between enrollment and hospital discharge. There was increased abundance of Escherichia-Shigella and Bacteriodes genera related to higher symptom scores. Discussion: Differences in alpha and beta diversity between neonates with and without NAS may be due to differences in birth mode and type of feeding. The findings of specific increased bacteria related to increased symptoms in the neonates with NAS may also be influenced by birth mode and type of feeding.

RevDate: 2024-03-26

Yang C, Yang W, Wang Y, et al (2024)

Nonextractable Polyphenols from Fu Brick Tea Alleviates Ulcerative Colitis by Controlling Colon Microbiota-Targeted Release to Inhibit Intestinal Inflammation in Mice.

Journal of agricultural and food chemistry [Epub ahead of print].

This study was designed to elucidate the colon microbiota-targeted release of nonextractable bound polyphenols (NEPs) derived from Fu brick tea and to further identify the possible anti-inflammatory mechanism in dextran sulfate sodium (DSS)-induced ulcerative colitis (UC) mice. 1.5% DSS drinking water-induced C57BL/6J mice were fed rodent chow supplemented with or without 8% NEPs or dietary fibers (DFs) for 37 days. The bound p-hydroxybenzoic acid and quercetin in NEPs were liberated up to 590.5 ± 70.6 and 470.5 ± 51.6 mg/g by in vitro human gut microbiota-simulated fermentation, and released into the colon of the mice supplemented with NEPs by 4.4- and 1.5-fold higher than that of the mice supplemented without NEPs, respectively (p < 0.05). Supplementation with NEPs also enhanced the colonic microbiota-dependent production of SCFAs in vitro and in vivo (p < 0.05). Interestingly, Ingestion of NEPs in DSS-induced mice altered the gut microbiota composition, reflected by a dramatic increase in the relative abundance of Dubosiella and Enterorhabdus and a decrease in the relative abundance of Alistipes and Romboutsia (p < 0.05). Consumption of NEPs was demonstrated to be more effective in alleviating colonic inflammation and UC symptoms than DFs alone in DSS-treated mice (p < 0.05), in which the protective effects of NEPs against UC were highly correlated with the reconstruction of the gut microbiome, formation of SCFAs, and release of bound polyphenols. These findings suggest that NEPs as macromolecular carriers exhibit targeted delivery of bound polyphenols into the mouse colon to regulate gut microbiota and alleviate inflammation.

RevDate: 2024-03-27
CmpDate: 2024-03-27

Li M, Han X, Sun L, et al (2024)

Indole-3-acetic acid alleviates DSS-induced colitis by promoting the production of R-equol from Bifidobacterium pseudolongum.

Gut microbes, 16(1):2329147.

BACKGROUND: Inflammatory bowel disease (IBD) is characterized by immune-mediated, chronic inflammation of the intestinal tract. The occurrence of IBD is driven by the complex interactions of multiple factors. The objective of this study was to evaluate the therapeutic effects of IAA in colitis.

METHOD: C57/BL6 mice were administered 2.5% DSS in drinking water to induce colitis. IAA, Bifidobacterium pseudolongum, and R-equol were administered by oral gavage and fed a regular diet. The Disease Activity Index was used to evaluate disease activity. The degree of colitis was evaluated using histological morphology, RNA, and inflammation marker proteins. CD45+ CD4+ FOXP3+ Treg and CD45+ CD4+ IL17A+ Th17 cells were detected by flow cytometry. Analysis of the gut microbiome in fecal content was performed using 16S rRNA gene sequencing. Gut microbiome metabolites were analyzed using Untargeted Metabolomics.

RESULT: In our study, we found IAA alleviates DSS-induced colitis in mice by altering the gut microbiome. The abundance of Bifidobacterium pseudolongum significantly increased in the IAA treatment group. Bifidobacterium pseudolongum ATCC25526 alleviates DSS-induced colitis by increasing the ratio of Foxp3+T cells in colon tissue. R-equol alleviates DSS-induced colitis by increasing Foxp3+T cells, which may be the mechanism by which ATCC25526 alleviates DSS-induced colitis in mice.

CONCLUSION: Our study demonstrates that IAA, an indole derivative, alleviates DSS-induced colitis by promoting the production of Equol from Bifidobacterium pseudolongum, which provides new insights into gut homeostasis regulated by indole metabolites other than the classic AHR pathway.

RevDate: 2024-03-27

Bouilloud M, Galan M, Pradel J, et al (2024)

Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota.

Animal microbiome, 6(1):16.

Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.

RevDate: 2024-03-27
CmpDate: 2024-03-27

Buetas E, Jordán-López M, López-Roldán A, et al (2024)

Full-length 16S rRNA gene sequencing by PacBio improves taxonomic resolution in human microbiome samples.

BMC genomics, 25(1):310.

BACKGROUND: Sequencing variable regions of the 16S rRNA gene (≃300 bp) with Illumina technology is commonly used to study the composition of human microbiota. Unfortunately, short reads are unable to differentiate between highly similar species. Considering that species from the same genus can be associated with health or disease it is important to identify them at the lowest possible taxonomic rank. Third-generation sequencing platforms such as PacBio SMRT, increase read lengths allowing to sequence the whole gene with the maximum taxonomic resolution. Despite its potential, full length 16S rRNA gene sequencing is not widely used yet. The aim of the current study was to compare the sequencing output and taxonomic annotation performance of the two approaches (Illumina short read sequencing and PacBio long read sequencing of 16S rRNA gene) in different human microbiome samples. DNA from saliva, oral biofilms (subgingival plaque) and faeces of 9 volunteers was isolated. Regions V3-V4 and V1-V9 were amplified and sequenced by Illumina Miseq and by PacBio Sequel II sequencers, respectively.

RESULTS: With both platforms, a similar percentage of reads was assigned to the genus level (94.79% and 95.06% respectively) but with PacBio a higher proportion of reads were further assigned to the species level (55.23% vs 74.14%). Regarding overall bacterial composition, samples clustered by niche and not by sequencing platform. In addition, all genera with > 0.1% abundance were detected in both platforms for all types of samples. Although some genera such as Streptococcus tended to be observed at higher frequency in PacBio than in Illumina (20.14% vs 14.12% in saliva, 10.63% vs 6.59% in subgingival plaque biofilm samples) none of the differences were statistically significant when correcting for multiple testing.

CONCLUSIONS: The results presented in the current manuscript suggest that samples sequenced using Illumina and PacBio are mostly comparable. Considering that PacBio reads were assigned at the species level with higher accuracy than Illumina, our data support the use of PacBio technology for future microbiome studies, although a higher cost is currently required to obtain an equivalent number of reads per sample.

RevDate: 2024-03-26

Cho H, Kim J, Kim S, et al (2024)

Postpartum Maternal Anxiety Affects the Development of Food Allergy Through Dietary and Gut Microbial Diversity During Early Infancy.

Allergy, asthma & immunology research, 16(2):154-167.

PURPOSE: We aimed to investigate the mediating factors between maternal anxiety and the development of food allergy (FA) in children until 2 years from birth.

METHODS: In this longitudinal cohort of 122 mother-child dyads from pregnancy to 24 months of age, we regularly surveyed maternal psychological states, infant feeding data, and allergic symptoms and collected stool samples at 6 months of age for microbiome analysis. Considering the temporal order of data collection, we investigated serial mediating effects and indirect effects among maternal anxiety, dietary diversity (DD), gut microbial diversity, and FA using structural equation modeling.

RESULTS: Among the 122 infants, 15 (12.3%) were diagnosed with FA. Increased maternal anxiety between 3 and 6 months after delivery was associated with a lower DD score. Infants with low DD at 4 months showed low gut microbial richness, which was associated with FA development. When the infants were grouped into 4 subtypes, using consensus clustering of 13 gut bacteria significantly associated with maternal anxiety and DD, Prevotella, Eubacterium, Clostridiales and Lachnospiraceae were more abundant in the group with lower FA occurrence.

CONCLUSIONS: Postpartum maternal anxiety, mediated by reduced DD and gut microbial diversity, may be a risk factor for the development of FA in infants during the first 2 years of life.

RevDate: 2024-03-26

Liu Y, Ritchie SC, Teo SM, et al (2024)

Integration of polygenic and gut metagenomic risk prediction for common diseases.

Nature aging [Epub ahead of print].

Multiomics has shown promise in noninvasive risk profiling and early detection of various common diseases. In the present study, in a prospective population-based cohort with ~18 years of e-health record follow-up, we investigated the incremental and combined value of genomic and gut metagenomic risk assessment compared with conventional risk factors for predicting incident coronary artery disease (CAD), type 2 diabetes (T2D), Alzheimer disease and prostate cancer. We found that polygenic risk scores (PRSs) improved prediction over conventional risk factors for all diseases. Gut microbiome scores improved predictive capacity over baseline age for CAD, T2D and prostate cancer. Integrated risk models of PRSs, gut microbiome scores and conventional risk factors achieved the highest predictive performance for all diseases studied compared with models based on conventional risk factors alone. The present study demonstrates that integrated PRSs and gut metagenomic risk models improve the predictive value over conventional risk factors for common chronic diseases.

RevDate: 2024-03-26

Ryan D, Bornet E, Prezza G, et al (2024)

An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity.

Nature microbiology [Epub ahead of print].

Plasticity in gene expression allows bacteria to adapt to diverse environments. This is particularly relevant in the dynamic niche of the human intestinal tract; however, transcriptional networks remain largely unknown for gut-resident bacteria. Here we apply differential RNA sequencing (RNA-seq) and conventional RNA-seq to the model gut bacterium Bacteroides thetaiotaomicron to map transcriptional units and profile their expression levels across 15 in vivo-relevant growth conditions. We infer stress- and carbon source-specific transcriptional regulons and expand the annotation of small RNAs (sRNAs). Integrating this expression atlas with published transposon mutant fitness data, we predict conditionally important sRNAs. These include MasB, which downregulates tetracycline tolerance. Using MS2 affinity purification and RNA-seq, we identify a putative MasB target and assess its role in the context of the MasB-associated phenotype. These data-publicly available through the Theta-Base web browser (http://micromix.helmholtz-hiri.de/bacteroides/)-constitute a valuable resource for the microbiome community.

RevDate: 2024-03-27
CmpDate: 2024-03-27

Wang B, Sun F, Y Luan (2024)

Comparison of the effectiveness of different normalization methods for metagenomic cross-study phenotype prediction under heterogeneity.

Scientific reports, 14(1):7024.

The human microbiome, comprising microorganisms residing within and on the human body, plays a crucial role in various physiological processes and has been linked to numerous diseases. To analyze microbiome data, it is essential to account for inherent heterogeneity and variability across samples. Normalization methods have been proposed to mitigate these variations and enhance comparability. However, the performance of these methods in predicting binary phenotypes remains understudied. This study systematically evaluates different normalization methods in microbiome data analysis and their impact on disease prediction. Our findings highlight the strengths and limitations of scaling, compositional data analysis, transformation, and batch correction methods. Scaling methods like TMM show consistent performance, while compositional data analysis methods exhibit mixed results. Transformation methods, such as Blom and NPN, demonstrate promise in capturing complex associations. Batch correction methods, including BMC and Limma, consistently outperform other approaches. However, the influence of normalization methods is constrained by population effects, disease effects, and batch effects. These results provide insights for selecting appropriate normalization approaches in microbiome research, improving predictive models, and advancing personalized medicine. Future research should explore larger and more diverse datasets and develop tailored normalization strategies for microbiome data analysis.

RevDate: 2024-03-25

Boyd A, El Dani M, Ajrouche R, et al (2024)

Gut microbiome diversity and composition in individuals with and without extended-spectrum β-lactamase-Producing enterobacterales carriage: a matched case-control study in infectious diseases department.

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases pii:S1198-743X(24)00146-0 [Epub ahead of print].

OBJECTIVE: Little is known on the effect of gut microbial and Extended-Spectrum β-Lactamase-Producing Enterobacterales (ESBL-E) carriage, particularly in the general population. The aim of this study was to identify microbiota signatures uniquely correlated with ESBL-E carriage.

METHODS: We conducted a case-control study among individuals seeking care at the Sexual Health Clinic or Department of Infectious and Tropical Diseases at Saint-Antoine Hospital, Paris, France. Using coarsened exact matching, 176 participants with ESBL-carriage (i.e., cases) were matched 1:1 to those without ESBL-carriage (i.e., controls) based on sexual group, ESBL-E prevalence of countries traveled in <12 months, number of sexual partners in <6 months, geographic origin, and any antibiotic use in <6 months. 16S rRNA gene amplicon sequencing was used to generate differential abundances at the genus level and measures of α- and β-diversity.

RESULTS: Participants were mostly men (83.2%, n=293/352) and had a median age of 33 years (IQR=27-44). Nine genera were found associated with ESBL-E carriage (Figure 2C): Proteus (p<0.0001), Carnobacterium (p<0.0001), Enterorhabdus (p=0.0079), Catonella (p=0.017), Dermacoccus (p=0.017), Escherichia/Shigella (p=0.021), Kocuria (p=0.023), Bacillus (p=0.040), and Filifactor (p=0.043); however, differences were no longer significant after Benjamini-Hochberg correction (q>0.05). There were no differences between those with versus without ESBL-E carriage in measures of α-diversity (Shannon Diversity Index, p=0.49; Simpson Diversity Index, p=0.54; and Chao1 Richness Estimator, p=0.16) or β-diversity (Bray-Curtis dissimilarity index, p=0.42).

CONCLUSION: In this large carefully controlled study, there is lacking evidence that gut microbial composition and diversity is any different between individuals with and without ESBL-E carriage.

RevDate: 2024-03-25

Sookhak Lari K, Davis GB, Rayner JL, et al (2024)

Advective and diffusive gas phase transport in vadose zones: Importance for defining vapour risks and natural source zone depletion of petroleum hydrocarbons.

Water research, 255:121455 pii:S0043-1354(24)00357-9 [Epub ahead of print].

Quantifying the interlinked behaviour of the soil microbiome, fluid flow, multi-component transport and partitioning, and biodegradation is key to characterising vapour risks and natural source zone depletion (NSZD) of light non-aqueous phase liquid (LNAPL) petroleum hydrocarbons. Critical to vapour transport and NSZD is transport of gases through the vadose zone (oxygen from the atmosphere, volatile organic compounds (VOCs), methane and carbon dioxide from the zone of LNAPL biodegradation). Volatilisation of VOCs from LNAPL, aerobic biodegradation, methanogenesis and heat production all generate gas pressure changes that may lead to enhanced gas fluxes apart from diffusion. Despite the importance of the gaseous phase dynamics in the vadose zone processes, the relative pressure changes and consequent scales of advective (buoyancy and pressure driven) / diffusive transport is less studied. We use a validated multi-phase multi-component non-isothermal modelling framework to differentiate gas transport mechanisms. We simulate a multicomponent unweathered gasoline LNAPL with high VOC content to maximise the potential for pressure changes due to volatilisation and to enable the joint effects of methanogenesis and shallower aerobic biodegradation of vapours to be assessed, along with heat production. Considering a uniform fine sand profile with LNAPL resident in the water table capillary zone, results suggest that biodegradation plays the key role in gas phase formation and consequent pressure build-up. Results suggest that advection is the main transport mechanism over a thin zone inside the LNAPL/capillary region, where the effective gaseous diffusion is very low. In the bulk of the vadose zone above the LNAPL region, the pressure change is minimal, and gaseous diffusion is dominant. Even for high biodegradation rate cases, pressure build-up due to heat generation (inducing buoyancy effects) is smaller than the contribution of gas formation due to biodegradation. The findings are critical to support broader assumptions of diffusive transport being dominant in vapour transport and NSZD assessments.

RevDate: 2024-03-27
CmpDate: 2024-03-27

Kim H, Jo JH, Lee HG, et al (2024)

Inflammatory response in dairy cows caused by heat stress and biological mechanisms for maintaining homeostasis.

PloS one, 19(3):e0300719.

Climate change increases global temperatures, which is lethal to both livestock and humans. Heat stress is known as one of the various livestock stresses, and dairy cows react sensitively to high-temperature stress. We aimed to better understand the effects of heat stress on the health of dairy cows and observing biological changes. Individual cows were divided into normal (21-22 °C, 50-60% humidity) and high temperature (31-32 °C, 80-95% humidity), respectively, for 7-days. We performed metabolomic and transcriptome analyses of the blood and gut microbiomes of feces. In the high-temperature group, nine metabolites including linoleic acid and fructose were downregulated, and 154 upregulated and 72 downregulated DEGs (Differentially Expressed Genes) were identified, and eighteen microbes including Intestinimonas and Pseudoflavonifractor in genus level were significantly different from normal group. Linoleic acid and fructose have confirmed that associated with various stresses, and functional analysis of DEG and microorganisms showing significant differences confirmed that high-temperature stress is related to the inflammatory response, immune system, cellular energy mechanism, and microbial butyrate production. These biological changes were likely to withstand high-temperature stress. Immune and inflammatory responses are known to be induced by heat stress, which has been identified to maintain homeostasis through modulation at metabolome, transcriptome and microbiome levels. In these findings, heat stress condition can trigger alteration of immune system and cellular energy metabolism, which is shown as reduced metabolites, pathway enrichment and differential microbes. As results of this study did not include direct phenotypic data, we believe that additional validation is required in the future. In conclusion, high-temperature stress contributed to the reduction of metabolites, changes in gene expression patterns and composition of gut microbiota, which are thought to support dairy cows in withstanding high-temperature stress via modulating immune-related genes, and cellular energy metabolism to maintain homeostasis.

RevDate: 2024-03-26
CmpDate: 2024-03-26

Kurotschka PK, Serafini A, Shaughnessy AF, et al (2024)

[Top 5 Research Studies of the month for Italian Primary Care Physicians: March 2024.].

Recenti progressi in medicina, 115(4):189-194.

This monthly article provides a collection of summaries of the most relevant studies identified as POEMs (patient-oriented evidence that matters) for Italian primary care physicians. 1) A simple, well-validated risk score can help clinicians counsel patients with atrial fibrillation regarding the use of DOACs to prevent stroke. The score shares its name with the drug class (the "DOAC" score). 2) Presumably by perturbing the intestinal microbiome, antibiotic treatment is associated with an increase in the likelihood of the development of irritable bowel disease; this is especially true with multiple courses of antibiotics. 3) Patients with uncomplicated gallstones can be managed over time with analgesia and monitoring, though approximately 25% will eventually undergo cholecystectomy over the next 18 months. Still, there appears to be no need to rush to surgery without evidence of common bile duct blockage or acute pancreatitis. 4) Delivering bad news (e.g. a cancer diagnosis) by telephone does not affect levels of anxiety, depression, or satisfaction with care as compared with delivering the news in person. 5) An updated high quality systematic review found that, in conjunction with psychosocial interventions, oral naltrexone (50 mg/day) and oral acamprosate have the strongest evidence for being effective in the treatment of alcohol use disorder.

RevDate: 2024-03-25

Trefny MP, S Kobold (2024)

CAR T cells for solid tumors - developments to watch in 2023.

RevDate: 2024-03-26

Mitra D, Panneerselvam P, Chidambaranathan P, et al (2024)

Strigolactone GR24-mediated mitigation of phosphorus deficiency through mycorrhization in aerobic rice.

Current research in microbial sciences, 6:100229.

Strigolactones (SLs) are a new class of plant hormones that play a significant role in regulating various aspects of plant growth promotion, stress tolerance and influence the rhizospheric microbiome. GR24 is a synthetic SL analog used in scientific research to understand the effects of SL on plants and to act as a plant growth promoter. This study aimed to conduct hormonal seed priming at different concentrations of GR24 (0.1, 0.5, 1.0, 5.0 and 10.0 µM with and without arbuscular mycorrhizal fungi (AMF) inoculation in selected aerobic rice varieties (CR Dhan 201, CR Dhan 204, CR Dhan 205, and CR Dhan 207), Kasalath-IC459373 (P-tolerant check), and IR-36 (P-susceptible check) under phosphorus (P)-deficient conditions to understand the enhancement of growth and priming effects in mycorrhization. Our findings showed that seed priming with 5.0 µM SL GR24 enhanced the performance of mycorrhization in CR Dhan 205 (88.91 %), followed by CR Dhan 204 and 207, and AMF sporulation in CR Dhan 201 (31.98 spores / 10 gm soil) and CR Dhan 207 (30.29 spores / 10 g soil), as well as rice growth. The study showed that the highly responsive variety CR Dhan 207 followed by CR Dhan 204, 205, 201, and Kasalath IC459373 showed higher P uptake than the control, and AMF treated with 5.0 µM SL GR24 varieties CR Dhan 205 followed by CR Dhan 207 and 204 showed the best performance in plant growth, chlorophyll content, and soil functional properties, such as acid and alkaline phosphatase activity, soil microbial biomass carbon (MBC), dehydrogenase activity (DHA), and fluorescein diacetate activity (FDA). Overall, AMF intervention with SL GR24 significantly increased plant growth, soil enzyme activity, and uptake of P compared to the control. Under P-deficient conditions, seed priming with 5.0 µM strigolactone GR24 and AMF inoculum significantly increased selected aerobic rice growth, P uptake, and soil enzyme activities. Application of SLs formulations with AMF inoculum in selected aerobic rice varieties, CR Dhan 207, CR Dhan 204, and CR Dhan 205, will play an important role in mycorrhization, growth, and enhancement of P utilization under P- nutrient deficient conditions.

RevDate: 2024-03-26
CmpDate: 2024-03-26

Bekar C, Ozmen O, Ozkul C, et al (2024)

Inulin protects against the harmful effects of dietary emulsifiers on mice gut microbiome.

PeerJ, 12:e17110.

BACKGROUND: The prevalence of inflammatory bowel diseases is increasing, especially in developing countries, with adoption of Western-style diet. This study aimed to investigate the effects of two emulsifiers including lecithin and carboxymethyl cellulose (CMC) on the gut microbiota, intestinal inflammation and the potential of inulin as a means to protect against the harmful effects of emulsifiers.

METHODS: In this study, male C57Bl/6 mice were divided into five groups (n:6/group) (control, CMC, lecithin, CMC+inulin, and lecithin+inulin). Lecithin and CMC were diluted in drinking water (1% w/v) and inulin was administered daily at 5 g/kg for 12 weeks. Histological examination of the ileum and colon, serum IL-10, IL-6, and fecal lipocalin-2 levels were analyzed. 16S rRNA gene V3-V4 region amplicon sequencing was performed on stool samples.

RESULTS: In the CMC and lecithin groups, shortening of the villus and a decrease in goblet cells were observed in the ileum and colon, whereas inulin reversed this effect. The lipocalin level, which was 9.7 ± 3.29 ng in the CMC group, decreased to 4.1 ± 2.98 ng with the administration of inulin. Bifidobacteria and Akkermansia were lower in the CMC group than the control, while they were higher in the CMC+inulin group. In conclusion, emulsifiers affect intestinal health negatively by disrupting the epithelial integrity and altering the composition of the microbiota. Inulin is protective on their harmful effects. In addition, it was found that CMC was more detrimental to microbiota composition than lecithin.

RevDate: 2024-03-26
CmpDate: 2024-03-26

Guse K, JE Pietri (2024)

Endosymbiont and gut bacterial communities of the brown-banded cockroach, Supella longipalpa.

PeerJ, 12:e17095.

The brown-banded cockroach (Supella longipalpa) is a widespread nuisance and public health pest. Like the German cockroach (Blattella germanica), this species is adapted to the indoor biome and completes the entirety of its life cycle in human-built structures. Recently, understanding the contributions of commensal and symbiotic microbes to the biology of cockroach pests, as well as the applications of targeting these microbes for pest control, have garnered significant scientific interest. However, relative to B. germanica, the biology of S. longipalpa, including its microbial associations, is understudied. Therefore, the goal of the present study was to quantitatively examine and characterize both the endosymbiont and gut bacterial communities of S. longipalpa for the first time. To do so, bacterial 16S rRNA gene amplicon sequencing was conducted on DNA extracts from whole adult females and males, early instar nymphs, and late instar nymphs. The results demonstrate that the gut microbiome is dominated by two genera of bacteria known to have beneficial probiotic effects in other organisms, namely Lactobacillus and Akkermansia. Furthermore, our data show a significant effect of nymphal development on diversity and variation in the gut microbiome. Lastly, we reveal significant negative correlations between the two intracellular endosymbionts, Blattabacterium and Wolbachia, as well as between Blattabacterium and the gut microbiome, suggesting that Blattabacterium endosymbionts could directly or indirectly influence the composition of other bacterial populations. These findings have implications for understanding the adaptation of S. longipalpa to the indoor biome, its divergence from other indoor cockroach pest species such as B. germanica, the development of novel control approaches that target the microbiome, and fundamental insect-microbe interactions more broadly.

RevDate: 2024-03-26

Lachmansingh DA, Valderrama B, Bastiaanssen T, et al (2023)

Impact of dietary fiber on gut microbiota composition, function and gut-brain-modules in healthy adults - a systematic review protocol.

HRB open research, 6:62.

BACKGROUND: The gut microbiota has been extensively implicated in health and disease. The functional outputs of the gut microbiota, such as microbial metabolites, are considered particularly important in this regard. Significant associations exist between alterations in the relative abundance of specific microbial taxa and mental health disorders. Dietary fiber has the potential to alter gut microbiota composition and function, modifying bacterial enzymatic function and the production of metabolites. As many taxa of microorganisms have enzymes capable of producing or degrading neurochemicals i.e. neuroactive gut brain modules, new predictive tools can be applied to existing datasets such as those harvested from dietary fiber interventions. We endeavor to perform a systematic review in order to identify studies reporting compositional gut microbiota alterations after interventions with dietary fiber in healthy individuals. We aim to also extract from the selected studies publicly available microbial genomic sequence datasets for reanalysis with a consistent bioinformatics pipeline, with the ultimate intention of identifying altered gut brain modules following dietary fiber interventions.

METHODS: Interventional trials and randomized controlled studies that are originally published, including cross-over and non-crossover design and involving healthy adult humans will be included. A systematic search of PubMed/MEDLINE and EMBASE, two electronic databases, will be completed.

DISCUSSION: Various types of dietary fiber have an impact on the gut microbiota composition, with some promoting the growth of particular taxa while others are reduced in relative abundance. Our search focuses on the impact of this food component on the microbiota of healthy individuals. Compositional gut microbial changes have been reported and our review will compile and update these observations after reanalysis of their datasets with a consistent bioinformatic pipeline. From this it may be possible to predict more detailed functional consequences in terms of neuroactive gut brain modules, of the compositional alterations in gut microbial taxa.

RevDate: 2024-03-26

Tomczyk G, Niczyporuk JS, Kozdruń W, et al (2024)

Probiotic supplementation as an alternative to antibiotics in broiler chickens.

Journal of veterinary research, 68(1):147-154.

INTRODUCTION: The broiler chicken digestive tract microbiome maintains the bird's immunity. Its composition has been shown to be important not only for the immune system but also for the gastrointestinal function and productivity of broiler chickens. If the microbiome is populated by supplementation with Lactobacillus, Pediococcus and Saccharomyces spp. - microorganisms with probiotic properties and alternatives to antibiotics - the immune system is stimulated. The use of probiotic supplements in the broiler production cycle can boost bird immunity and prevent adenovirus infection. The resilience of broiler chickens in different feeding schemes including supplementation with these microorganisms was assessed.

MATERIAL AND METHODS: Four groups of Ross 308 chickens vaccinated on the standard scheme were investigated over 42 days. Group P received probiotics, prebiotics and vitamins; group AO received antibiotics; group P&AO received probiotics, prebiotics, vitamins and antibiotics; and the control group C received none of these. The birds' immunocompetence against common viral poultry pathogens and their immune response to an experimental challenge with a field strain of infectious bronchitis was evaluated by ELISA and production parameters were recorded.

RESULTS: Mortality was only observed in the control group and was 10%. All birds from the P, P&AO and AO groups responded to the challenge as would be expected of appropriately immunised chickens.

CONCLUSION: The obtained results indicated that supplementation with synbiotic products and vitamins can enhance broiler chicken immunity and result in better production parameters.

RevDate: 2024-03-26

Mirsalami SM, M Mirsalami (2024)

Effects of duo-strain probiotics on growth, digestion, and gut health in broiler chickens.

Veterinary and animal science, 24:100343.

The goal of this inquiry was to analyze the impact of incorporating Enterococcus faecium and Streptococcus thermophilus using a novel premix-spray method on the following aspects: growth rate, digestive enzyme activity, antioxidant levels, gut microbiome composition, and the morphological characteristics of the duodenum, jejunum, and ileum in broiler chickens. Furthermore, this study explored the potential benefits of duo strains of probiotics (DSP) in reducing flatulence, regulating stool microbial population, and improving diarrhea symptoms. A total of 360 one-day-old mixed-sex Plymouth Rock chicks (IW: 51 ± 33 g) were randomly divided into two treatment groups. Each treatment group was further divided into 9 replicated cages, with 20 chicks housed in each cage. The control group (CG) received a basal diet composed of a soy-corn mixture, whereas the experimental group was provided with DSP (CON + 0.5 % probiotic). The results showed that the increase in the body weight of broilers at the end of the fourth week in the control group and the treatment group was 1.576 versus 1.847 kg, respectively. Throughout the 30-day trial period, the DSP diet significantly improved the specific growth rate (SGR), survival rate (SR), and body weight gain (BWG) while decreasing the feed conversion ratio (FCR) (P < 0.05). The DSP diet also enhanced the Enzymatic digestion (protease, amylase, lipase, and trypsin) and antioxidant potential (SOD, MDA, and catalase) of the broilers compared to those in the CG. The results revealed significant enhancements in the tissue morphology of the duodenum and jejunum following the combined treatment for a duration of 4 weeks. The DSP treatments significantly increased microvillus height in the duodenum and jejunum but had no notable effects in the ileum. Incorporating 0.5 % DSP in poultry feed improved the relative abundance of Ruminococcaceae and Faecalibacteriumin, leading to better management of diarrhea and reduced presence of E. coli compared to the control diet. Additionally, including probiotics in the basal diet reduced H2S, CO2, NH3, and CH4 levels. Overall, the study suggests that the new spray-drying approach with these strains has potential for supplementing probiotics in poultry feed processing, and including DSP in broiler chicken diets has beneficial effects.

RevDate: 2024-03-26

Jiang B, Qin C, Xu Y, et al (2024)

Multi-omics reveals the mechanism of rumen microbiome and its metabolome together with host metabolome participating in the regulation of milk production traits in dairy buffaloes.

Frontiers in microbiology, 15:1301292.

Recently, it has been discovered that certain dairy buffaloes can produce higher milk yield and milk fat yield under the same feeding management conditions, which is a potential new trait. It is unknown to what extent, the rumen microbiome and its metabolites, as well as the host metabolism, contribute to milk yield and milk fat yield. Therefore, we will analyze the rumen microbiome and host-level potential regulatory mechanisms on milk yield and milk fat yield through rumen metagenomics, rumen metabolomics, and serum metabolomics experiments. Microbial metagenomics analysis revealed a significantly higher abundance of several species in the rumen of high-yield dairy buffaloes, which mainly belonged to genera, such as Prevotella, Butyrivibrio, Barnesiella, Lachnospiraceae, Ruminococcus, and Bacteroides. These species contribute to the degradation of diets and improve functions related to fatty acid biosynthesis and lipid metabolism. Furthermore, the rumen of high-yield dairy buffaloes exhibited a lower abundance of methanogenic bacteria and functions, which may produce less methane. Rumen metabolome analysis showed that high-yield dairy buffaloes had significantly higher concentrations of metabolites, including lipids, carbohydrates, and organic acids, as well as volatile fatty acids (VFAs), such as acetic acid and butyric acid. Meanwhile, several Prevotella, Butyrivibrio, Barnesiella, and Bacteroides species were significantly positively correlated with these metabolites. Serum metabolome analysis showed that high-yield dairy buffaloes had significantly higher concentrations of metabolites, mainly lipids and organic acids. Meanwhile, several Prevotella, Bacteroides, Barnesiella, Ruminococcus, and Butyrivibrio species were significantly positively correlated with these metabolites. The combined analysis showed that several species were present, including Prevotella.sp.CAG1031, Prevotella.sp.HUN102, Prevotella.sp.KHD1, Prevotella.phocaeensis, Butyrivibrio.sp.AE3009, Barnesiella.sp.An22, Bacteroides.sp.CAG927, and Bacteroidales.bacterium.52-46, which may play a crucial role in rumen and host lipid metabolism, contributing to milk yield and milk fat yield. The "omics-explainability" analysis revealed that the rumen microbial composition, functions, metabolites, and serum metabolites contributed 34.04, 47.13, 39.09, and 50.14%, respectively, to milk yield and milk fat yield. These findings demonstrate how the rumen microbiota and host jointly affect milk production traits in dairy buffaloes. This information is essential for developing targeted feeding management strategies to improve the quality and yield of buffalo milk.

RevDate: 2024-03-26

Abo-Hammam RH, Salah M, Shabayek S, et al (2024)

Metagenomic analysis of fecal samples in colorectal cancer Egyptians patients post colectomy: A pilot study.

AIMS microbiology, 10(1):148-160.

One of the most prevalent malignancies that significantly affects world health is colorectal cancer (CRC). While genetics are involved in a portion of CRC patients, most cases are sporadic. The microbiome composition could be a new source of tumor initiation and progression. This research was conducted to investigate the microbiota composition of CRC patients post colectomy at taxonomic and functional levels. Using a next-generation sequencing approach, using an Illumina Novaseq 6000, the fecal samples of 13 patients were analyzed and the obtained data was subjected to a bioinformatics analysis. The bacterial abundance and uniqueness varied in CRC patients alongside differences in bacterial counts between patients. Bacteroides fragilis, Bacteroides vulgatus, Escherichia coli, and Fusobacterium nucleatum were among the pro-cancerous microorganisms found. Concurrently, bacteria linked to CRC progression were detected that have been previously linked to metastasis and recurrence. At the same time, probiotic bacteria such as Bifidobacterium dentium, Bifidobacterium bifidum, and Akkermansia muciniphila increased in abundance after colectomies. Additionally, numerous pathways were deferentially enriched in CRC, which emerged from functional pathways based on bacterial shotgun data. CRC-specific microbiome signatures include an altered bacterial composition. Our research showed that microbial biomarkers could be more usefully employed to explore the link between gut microbiota and CRC using metagenomic techniques in the diagnosis, prognosis, and remission of CRC, thereby opening new avenues for CRC treatment.

RevDate: 2024-03-26

Bring Horvath ER, Brazelton WJ, Kim MC, et al (2024)

Bacterial diversity and chemical ecology of natural product-producing bacteria from Great Salt Lake sediment.

ISME communications, 4(1):ycae029.

Great Salt Lake (GSL), located northwest of Salt Lake City, UT, is the largest terminal lake in the USA. While the average salinity of seawater is ~3.3%, the salinity in GSL ranges between 5% and 28%. In addition to being a hypersaline environment, GSL also contains toxic concentrations of heavy metals, such as arsenic, mercury, and lead. The extreme environment of GSL makes it an intriguing subject of study, both for its unique microbiome and its potential to harbor novel natural product-producing bacteria, which could be used as resources for the discovery of biologically active compounds. Though work has been done to survey and catalog bacteria found in GSL, the Lake's microbiome is largely unexplored, and little to no work has been done to characterize the natural product potential of GSL microbes. Here, we investigate the bacterial diversity of two important regions within GSL, describe the first genomic characterization of Actinomycetota isolated from GSL sediment, including the identification of two new Actinomycetota species, and provide the first survey of the natural product potential of GSL bacteria.

RevDate: 2024-03-26

D'Amico F, Rinaldi M, Pascale R, et al (2024)

Gut microbiome dynamics and Enterobacterales infection in liver transplant recipients: A prospective observational study.

JHEP reports : innovation in hepatology, 6(4):101039.

BACKGROUND & AIMS: The aim of this study was to investigate gut microbiome (GM) dynamics in relation to carbapenem-resistant Enterobacterales (CRE) colonization, CRE infection, and non-CRE infection development within 2 months after liver transplant (LT).

METHODS: A single-center, prospective study was performed in patients undergoing LT from November 2018 to January 2020. The GM was profiled through 16S rRNA amplicon sequencing of a rectal swab taken on the day of transplantation, and fecal samples were collected weekly until 1 month after LT. A subset of samples was subjected to shotgun metagenomics, including resistome dynamics. The primary endpoint was to explore changes in the GM in the following groups: (1) CRE carriers developing CRE infection (CRE_I); (2) CRE carriers not developing infection (CRE_UI); (3) non-CRE carriers developing microbial infection (INF); and (4) non-CRE carriers not developing infection (NEG).

RESULTS: Overall, 97 patients were enrolled, and 91 provided fecal samples. Of these, five, nine, 22, and 55 patients were classified as CRE_I, CRE_UI, INF, and NEG, respectively. CRE_I patients showed an immediate and sustained post-LT decrease in alpha diversity, with depletion of the GM structure and gradual over-representation of Klebsiella and Enterococcus. The proportions of Klebsiella were significantly higher in CRE_I patients than in NEG patients even before LT, serving as an early marker of subsequent CRE infection. CRE_UI patients had a more stable and diverse GM, whose compositional dynamics tended to overlap with those of NEG patients.

CONCLUSIONS: GM profiling before LT could improve patient stratification and risk prediction and guide early GM-based intervention strategies to reduce infectious complications and improve overall prognosis.

IMPACT AND IMPLICATIONS: Little is known about the temporal dynamics of gut microbiome (GM) in liver transplant recipients associated with carbapenem-resistant Enterobacterales (CRE) colonization and infection. The GM structure and functionality of patients colonized with CRE and developing infection appeared to be distinct compared with CRE carriers without infection or patients with other microbial infection or no infection and CRE colonization. Higher proportions of antimicrobial-resistant pathogens and poor representation of bacteria and metabolic pathways capable of promoting overall host health were observed in CRE carriers who developed infection, even before liver transplant. Therefore, pretransplant GM profiling could improve patient stratification and risk prediction and guide early GM-based intervention strategies to reduce infectious complications and improve overall prognosis.

RevDate: 2024-03-26

Wang H, Yan G, Wu Y, et al (2024)

Fecal microbiota related to postoperative endoscopic recurrence in patients with Crohn's disease.

Gastroenterology report, 12:goae017.

BACKGROUND: Postoperative recurrence (POR) remains a major challenge for patients with Crohn's disease (CD). Gut microbial dysbiosis has been reported to be involved in the pathogenesis of POR. This study aims to investigate the relationship between fecal microbiome and endoscopic recurrence in patients with CD after ileocolonic resection.

METHODS: This is a cross-sectional study. Fecal samples were collected from 52 patients with CD after surgical intervention from 6 to 12 months before endoscopic examination. Endoscopic recurrence was defined as Rutgeerts score ≥ i2. The microbiome was analyzed by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene.

RESULTS: A total of 52 patients were included and classified into POR (n = 27) and non-POR (n = 25) groups. Compared with the non-POR group, the POR group had a significantly lower community richness (Chao1 index: 106.5 vs 124, P = 0.013) and separated microbial community (P = 0.007 for Adonis, P = 0.032 for Anosim), combined with different distribution of 16 gut microbiotas and decrease of 11 predicted metabolic pathways (P < 0.05). Lactobacillus and Streptococcus were identified to closely correlate to non-POR (P < 0.05) after controlling for confounding factors. Kaplan-Meier analysis indicated that the patients with higher abundance of Streptococcus experienced longer remission periods (P < 0.01), but this was not for Lactobacillus. The predicted ethylmalonyl-coA pathway related to increased amount of succinate was positively correlated with Streptococcus (r > 0.5, P < 0.05).

CONCLUSIONS: The characteristic alterations of fecal microbiota are associated with postoperative endoscopic recurrence in patients with CD; particularly, high abundance of Streptococcus may be closely related to endoscopic remission.

RevDate: 2024-03-25

Hsiao PY, Huang RY, Huang LW, et al (2024)

MyD88 exacerbates inflammation-induced bone loss by modulating dynamic equilibrium between Th17/Treg cells and subgingival microbiota dysbiosis.

Journal of periodontology [Epub ahead of print].

BACKGROUND: This study aimed to investigate the contribution of myeloid differentiation primary-response gene 88 (MyD88) on the differentiation of T helper type 17 (Th17) and regulatory T (Treg) cells and the emerging subgingival microbiota dysbiosis in Porphyromonas gingivalis-induced experimental periodontitis.

METHODS: Alveolar bone loss, infiltrated inflammatory cells, immunostained cells for tartrate-resistant acid phosphatase (TRAP), the receptor activator of nuclear factor-kB ligand (RANKL), and osteoprotegerin (OPG) were quantified by microcomputerized tomography and histological staining between age- and sex-matched homozygous littermates (wild-type [WT, Myd88[+/+]] and Myd88[-/-] on C57BL/6 background). The frequencies of Th17 and Treg cells in cervical lymph nodes (CLNs) and spleen were determined by flow cytometry. Cytokine expression in gingival tissues, CLNs, and spleens were studied by quantitative polymerase chain reaction (qPCR). Analysis of the composition of the subgingival microbiome and functional annotation of prokaryotic taxa (FAPROTAX) analysis were performed.

RESULTS: P. gingivalis-infected Myd88[-/-] mice showed alleviated bone loss, TRAP[+] osteoclasts, and RANKL/OPG ratio compared to WT mice. A significantly higher percentage of Foxp3[+]CD4[+] T cells in infected Myd88[-/-] CLNs and a higher frequency of RORγt[+]CD4[+] T cells in infected WT mice was noted. Increased IL-10 and IL-17a expressions in gingival tissue at D14-D28 then declined in WT mice, whereas an opposite pattern was observed in Myd88[-/-] mice. The Myd88[-/-] mice exhibited characteristic increases in gram-positive species and species having probiotic properties, while gram-negative, anaerobic species were noted in WT mice. FAPROTAX analysis revealed increased aerobic chemoheterotrophy in Myd88[-/-] mice, whereas anaerobic chemoheterotrophy was noted in WT mice after P. gingivalis infection.

CONCLUSIONS: MyD88 plays an important role in inflammation-induced bone loss by modulating the dynamic equilibrium between Th17/Treg cells and dysbiosis in P. gingivalis-induced experimental periodontitis.

RevDate: 2024-03-25

Jendraszak M, Skibińska I, Kotwicka M, et al (2024)

The elusive male microbiome: revealing the link between the genital microbiota and fertility. Critical review and future perspectives.

Critical reviews in clinical laboratory sciences [Epub ahead of print].

There is a growing focus on understanding the role of the male microbiome in fertility issues. Although research on the bacterial communities within the male reproductive system is in its initial phases, recent discoveries highlight notable variations in the microbiome's composition and abundance across distinct anatomical regions like the skin, foreskin, urethra, and coronary sulcus. To assess the relationship between male genitourinary microbiome and reproduction, we queried various databases, including MEDLINE (available via PubMed), SCOPUS, and Web of Science to obtain evidence-based data. The literature search was conducted using the following terms "gut/intestines microbiome," "genitourinary system microbiome," "microbiome and female/male infertility," "external genital tract microbiome," "internal genital tract microbiome," and "semen microbiome." Fifty-one relevant papers were analyzed, and eleven were strictly semen quality or male fertility related. The male microbiome, especially in the accessory glands like the prostate, seminal vesicles, and bulbourethral glands, has garnered significant interest because of its potential link to male fertility and reproduction. Studies have also found differences in bacterial diversity present in the testicular tissue of normozoospermic men compared to azoospermic suggesting a possible role of bacterial dysbiosis and reproduction. Correlation between the bacterial taxa in the genital microbiota of sexual partners has also been found, and sexual activity can influence the composition of the urogenital microbiota. Exploring the microbial world within the male reproductive system and its influence on fertility opens doors to developing ways to prevent, diagnose, and treat infertility. The present work emphasizes the importance of using consistent methods, conducting long-term studies, and deepening our understanding of how the reproductive tract microbiome works. This helps make research comparable, pinpoint potential interventions, and smoothly apply microbiome insights to real-world clinical practices.

RevDate: 2024-03-27
CmpDate: 2024-03-26

Gavillet H, Hatfield L, Jones A, et al (2024)

Ecological patterns and processes of temporal turnover within lung infection microbiota.

Microbiome, 12(1):63.

BACKGROUND: Chronic infection and consequent airway inflammation are the leading causes of morbidity and early mortality for people living with cystic fibrosis (CF). However, lower airway infections across a range of chronic respiratory diseases, including in CF, do not follow classical 'one microbe, one disease' concepts of infection pathogenesis. Instead, they are comprised of diverse and temporally dynamic lung infection microbiota. Consequently, temporal dynamics need to be considered when attempting to associate lung microbiota with changes in disease status. Set within an island biogeography framework, we aimed to determine the ecological patterns and processes of temporal turnover within the lung microbiota of 30 paediatric and adult CF patients prospectively sampled over a 3-year period. Moreover, we aimed to ascertain the contributions of constituent chronic and intermittent colonizers on turnover within the wider microbiota.

RESULTS: The lung microbiota within individual patients was partitioned into constituent chronic and intermittent colonizing groups using the Leeds criteria and visualised with persistence-abundance relationships. This revealed bacteria chronically infecting a patient were both persistent and common through time, whereas intermittently infecting taxa were infrequent and rare; respectively representing the resident and transient portions of the wider microbiota. It also indicated that the extent of chronic colonization was far greater than could be appreciated with microbiological culture alone. Using species-time relationships to measure temporal turnover and Vellend's rationalized ecological processes demonstrated turnover in the resident chronic infecting groups was conserved and underpinned principally by the deterministic process of homogenizing dispersal. Conversely, intermittent colonizing groups, representing newly arrived immigrants and transient species, drove turnover in the wider microbiota and were predominately underpinned by the stochastic process of drift. For adult patients, homogenizing dispersal and drift were found to be significantly associated with lung function. Where a greater frequency of homogenizing dispersal was observed with worsening lung function and conversely drift increased with better lung function.

CONCLUSIONS: Our work provides a novel ecological framework for understanding the temporal dynamics of polymicrobial infection in CF that has translational potential to guide and improve therapeutic targeting of lung microbiota in CF and across a range of chronic airway diseases. Video Abstract.

RevDate: 2024-03-24

Marcos CN, Bach A, Gutiérrez-Rivas M, et al (2024)

The oral microbiome as a proxy for feed intake in dairy cattle.

Journal of dairy science pii:S0022-0302(24)00616-7 [Epub ahead of print].

Genetic material from rumen microorganisms can be found within the oral cavity, and hence there is potential in using the oral microbiome as a proxy of the ruminal microbiome. Feed intake (FI) influences the composition of rumen microbiota and might directly influence the oral microbiome in dairy cattle. Ruminal content samples (RS) from 29 cows were collected at the beginning of the study and also 42 d later (RS0 and RS42, respectively). Additionally, 18 oral samples were collected through buccal swabbing at d 42 (OS42) from randomly selected cows. Samples were used to characterize and compare the taxonomy and functionality of the oral microbiome using Nanopore sequencing and to evaluate the feasibility of using the oral microbiome to estimate FI. Up to 186 taxonomical features were found differentially abundant (DA) between RS and OS42. Similar results were observed when comparing OS42 to RS collected at different days. Microorganisms associated with the liquid fraction of the rumen were less abundant in OS42 as these were probably swallowed after regurgitation. Up to 1,102 KEGGs were found to be DA between RS and OS42 and these results differed when comparing time of collection, but differentially abundant KEGGs were mainly associated to metabolism in both situations. Models based on the oral microbiome and rumen microbiome differed in their selection of microbial groups and biological pathways to predict FI. In the rumen, fiber-associated microorganisms are considered suitable indicators of feed intake. On the other hand, biofilm formers like Gammaproteobacteria or Bacteroidia classes are deemed appropriate proxies for predicting feed intake from oral samples. Models from RS exhibited some predictive ability to estimate FI, but OS significantly outperformed them. The best lineal model to estimate FI was obtained with the relative abundance of taxonomical feature at genera level, achieving an average R[2] equal to 0.88 within the training data, and a root mean square error equal to 3.46 ± 0.83 (standard deviation; SD) kg of DM/ as well as a Pearson correlation coefficient between observed and estimated FI of 0.48 ± 0.30 in the test data. The results from this study suggest that oral microbiome has potential to predict FI in dairy cattle, and it encourages validating this potential in other populations.

RevDate: 2024-03-24

Gao Y, Zhang W, Zhang T, et al (2024)

Fructo-oligosaccharides supplementation enhances the growth of nursing dairy calves while stimulating the persistence of Bifidobacterium and hindgut microbiome's maturation.

Journal of dairy science pii:S0022-0302(24)00623-4 [Epub ahead of print].

The colonization and development of the gut microbiome in dairy calves play a crucial role in their overall health and future productivity. Despite the widely proposed benefits of inulin-related products on the host, there is insufficient information about how supplementing fructo-oligosaccharides (FOS) impacts the colonization and development of the gut microbiome in calves. In a randomized intervention trial involving newborn male Holstein dairy calves, we investigated the impact of FOS on the calf hindgut microbiome, short-chain fatty acids, growth performance, and the incidence of diarrhea. The daily administration of FOS exhibited a time-dependent increase in the average daily gain and the concentration of short-chain fatty acids. Concurrently, FOS delayed the natural decline of Bifidobacterium, promoting the maturation and stabilization of the hindgut microbiome. These findings not only contribute to a theoretical understanding of the judicious application of prebiotics but also hold significant practical implications for the design of early life dietary interventions in the rearing of dairy calves.

RevDate: 2024-03-24

Chang L, Goff HD, Ding C, et al (2024)

Enhanced hypoglycemic effects of konjac glucomannan combined with Polygonatum cyrtonema Hua polysaccharide in complete nutritional liquid diet fed type 2 diabetes mice.

International journal of biological macromolecules pii:S0141-8130(24)01926-3 [Epub ahead of print].

In our aging society, dysphagia and malnutrition are growing concerns, necessitating intervention. Liquid nutrition support offers a practical solution for traditional dietary issues, but it raises a key issue: the potential for post-meal glucose spikes impacting efficacy. This study examined the effects of supplementation of Polygonatum cyrtonema Hua polysaccharide (PCP), konjac glucomannan (KGM) and their combination on acute phase postprandial glycemic response and long-term glucose metabolism in T2DM mice on a complete nutritional liquid diet. KGM was more effective in reducing postprandial glucose response, while PCP was more prominent in ameliorating long-term glucose metabolism. The KGM-PCP combination demonstrated superior outcomes in fasting blood glucose, insulin, and glucose homeostasis. PCP and KGM also influenced the composition and abundance of the gut microbiome, with the H-PCP group showing optimal performance. Moreover, the KGM-PCP combination improved body weight, lipid homeostasis, and liver health the most. PCP potentially regulates glycemia through metabolic pathways, while KGM improves glycemic metabolism by reducing postprandial glucose levels in response to viscous intestinal contents. This research identifies the structure, viscosity properties, and hypoglycemic effects of KGM and PCP in complete nutritional liquid diet fed T2DM mice, enabling their strategic utilization as hypoglycemic components in nutritional administration and glycemic regulation.

RevDate: 2024-03-24

Bijla M, Saini SK, Pathak A, et al (2024)

Microbiome interactions with different risk factors in development of myocardial infarction.

Experimental gerontology pii:S0531-5565(24)00051-2 [Epub ahead of print].

Among all non-communicable diseases, Cardiovascular Diseases (CVDs) stand as the leading global cause of mortality. Within this spectrum, Myocardial Infarction (MI) strikingly accounts for over 15 % of all deaths. The intricate web of risk factors for MI, comprising family history, tobacco use, oral health, hypertension, nutritional pattern, and microbial infections, is firmly influenced by the human gut and oral microbiota, their diversity, richness, and dysbiosis, along with their respective metabolites. Host genetic factors, especially allelic variations in signaling and inflammatory markers, greatly affect the progression or severity of the disease. Despite the established significance of the human microbiome-nutrient-metabolite interplay in associations with CVDs, the unexplored terrain of the gut-heart-oral axis has risen as a critical knowledge gap. Moreover, the pivotal role of the microbiome and the complex interplay with host genetics, compounded by age-related changes, emerges as an area of vital importance in the development of MI. In addition, a distinctive disease susceptibility and severity influenced by gender-based or ancestral differences, adds a crucial insights to the association with increased mortality. Here, we aimed to provide an overview on interactions of microbiome (oral and gut) with major risk factors (tobacco use, alcohol consumption, diet, hypertension host genetics, gender, and aging) in the development of MI and therapeutic regulation.

RevDate: 2024-03-24

Sen P, Fan Y, Schlezinger JJ, et al (2024)

Exposure to environmental toxicants is associated with gut microbiome dysbiosis, insulin resistance and obesity.

Environment international, 186:108569 pii:S0160-4120(24)00155-7 [Epub ahead of print].

Environmental toxicants (ETs) are associated with adverse health outcomes. Here we hypothesized that exposures to ETs are linked with obesity and insulin resistance partly through a dysbiotic gut microbiota and changes in the serum levels of secondary bile acids (BAs). Serum BAs, per- and polyfluoroalkyl substances (PFAS) and additional twenty-seven ETs were measured by mass spectrometry in 264 Danes (121 men and 143 women, aged 56.6 ± 7.3 years, BMI 29.7 ± 6.0 kg/m[2]) using a combination of targeted and suspect screening approaches. Bacterial species were identified based on whole-genome shotgun sequencing (WGS) of DNA extracted from stool samples. Personalized genome-scale metabolic models (GEMs) of gut microbial communities were developed to elucidate regulation of BA pathways. Subsequently, we compared findings from the human study with metabolic implications of exposure to perfluorooctanoic acid (PFOA) in PPARα-humanized mice. Serum levels of twelve ETs were associated with obesity and insulin resistance. High chemical exposure was associated with increased abundance of several bacterial species (spp.) of genus (Anaerotruncus, Alistipes, Bacteroides, Bifidobacterium, Clostridium, Dorea, Eubacterium, Escherichia, Prevotella, Ruminococcus, Roseburia, Subdoligranulum, and Veillonella), particularly in men. Conversely, females in the higher exposure group, showed a decrease abundance of Prevotella copri. High concentrations of ETs were correlated with increased levels of secondary BAs including lithocholic acid (LCA), and decreased levels of ursodeoxycholic acid (UDCA). In silico causal inference analyses suggested that microbiome-derived secondary BAs may act as mediators between ETs and obesity or insulin resistance. Furthermore, these findings were substantiated by the outcome of the murine exposure study. Our combined epidemiological and mechanistic studies suggest that multiple ETs may play a role in the etiology of obesity and insulin resistance. These effects may arise from disruptions in the microbial biosynthesis of secondary BAs.

RevDate: 2024-03-24

Liu YQ, Chen Y, Li YY, et al (2024)

Plant growth-promoting bacteria improve the Cd phytoremediation efficiency of soils contaminated with PE-Cd complex pollution by influencing the rhizosphere microbiome of sorghum.

Journal of hazardous materials, 469:134085 pii:S0304-3894(24)00664-2 [Epub ahead of print].

Composite pollution by microplastics and heavy metals poses a potential threat to the soilplant system and has received increasing attention. Plant growth-promoting bacteria (PGPB) have good application potential for the remediation of combined microplastic and heavy metal pollution, but few related studies exist. The present study employed a pot experiment to investigate the effects of inoculation with the PGPB Bacillus sp. SL-413 and Enterobacter sp. VY-1 on sorghum growth and Cd accumulation under conditions of combined cadmium (Cd) and polyethylene (PE) pollution. Cd+PE composite contamination led to a significant reduction in sorghum length and biomass due to increased toxicity. Inoculation with Bacillus sp. SL-413 and Enterobacter sp. VY-1 alleviated the stress caused by Cd+PE complex pollution, and the dry weight of sorghum increased by 25.7% to 46.1% aboveground and by 12.3% to 45.3% belowground. Bacillus sp. SL-413 and Enterobacter sp. VY-1 inoculation increased the Cd content and accumulation in sorghum and improved the phytoremediation efficiency of Cd. The inoculation treatment effectively alleviated the nutrient stress caused by the reduction in soil mineral nutrients due to Cd+PE composite pollution. The composition of the soil bacterial communities was also affected by the Cd, Cd+PE and bacterial inoculation treatments, which affected the diversity of the soil bacterial communities. Network analyses indicated that bacterial inoculation regulated the interaction of rhizospheric microorganisms and increased the stability of soil bacterial communities. The Mantel test showed that the changes in the soil bacterial community and function due to inoculation with Bacillus sp. SL-413 and Enterobacter sp. VY-1 were important factors influencing sorghum growth and Cd remediation efficiency. The results of this study will provide new evidence for the research on joint plantmicrobe remediation of heavy metal and microplastic composite pollution.

RevDate: 2024-03-24

Ding S, Liang Y, Wang M, et al (2024)

Less is more: A new strategy combining nanomaterials and PGPB to promote plant growth and phytoremediation in contaminated soil.

Journal of hazardous materials, 469:134110 pii:S0304-3894(24)00689-7 [Epub ahead of print].

Novel combination strategies of nanomaterials (NMs) and plant growth-promoting bacteria (PGPB) may facilitate soil remediation and plant growth. However, the efficiency of the NM-PGPB combination and interactions among NMs, PGPB, and plants are still largely unknown. We used multiwalled carbon nanotubes (MWCNTs) and zero-valent iron (nZVI) combined with Bacillus sp. PGP5 to enhance the phytoremediation efficiency of Solanum nigrum on heavy metal (HM)-contaminated soil. The NM-PGPB combination showed the best promoting effect on plant growth, which also had synergistic effects on the bioaccumulation of HMs in S. nigrum. The MWCNT-PGP5 combination increased the Cd, Pb, and Zn removal efficiency of S. nigrum by 62.03%, 69.44%, and 61.31%, respectively. The underlining causes of improved plant growth and phytoremediation by NMs-PGPB combination were further elucidated. NM application promoted PGPB survival in soil. Compared with each single application, the combined application minimized disturbance to plant transcription levels and rhizosphere microbial community, resulting in the best performance on soil remediation and plant growth. The NM-PGPB-induced changes in the microbial community and root gene expression were necessary for plant growth promotion. This work reveals the "less is more" advantage of the NM-PGPB combination in soil remediation, providing a new strategy for soil management.

RevDate: 2024-03-24

Bar-Yoseph H, Metcalfe-Roach A, Cirstea M, et al (2024)

Microbiome changes under enteral deprivation are dynamic and dependent on intestinal location.

JPEN. Journal of parenteral and enteral nutrition [Epub ahead of print].

BACKGROUND: The microbiome has a pivotal role in intestinal health, and nutrition has a major role shaping its structure. Enteral deprivation, in which no oral/enteral nutrition is administered, is common in hospitalized/gastrointestinal patients. The dynamics that enteral deprivation exerts on the microbial community, specifically in the small intestine, are not well understood.

METHODS: Enteral deprivation was modeled with exclusive parenteral nutrition (EPN) mice. Mice were allocated to receive either EPN or saline and chow (control) and euthanized after 0, 2, 4, or 6 days. DNA was extracted from jejunum, ileum, and colon content. 16S sequencing was used to compare changes in microbial communities between groups. Functional pathways were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States.

RESULTS: EPN-treated mice showed community changes throughout the intestine. Beta diversity in colon showed clear separation between the groups (Bray-Curtis, P < 0.001). Time-dependent dynamics were seen in ileal but not jejunal samples. Alpha diversity was lower in the colon of EPN mice compared with control/baseline mice (Chao1, P < 0.01) but not in ileum/jejunum. Progressive loss of single-taxon domination was seen, most notably in the small intestine. This was accompanied by increases/decreases in specific taxa. A clear separation was seen in the functional capacity of the community between fed and enterally deprived mice at the ileum and colon, which was observed early on.

CONCLUSIONS: Enteral deprivation disturbs the microbial community in a spatial and dynamic manner. There should be further focus on studying the effect of these changes on the host.

RevDate: 2024-03-26

Williams JS, Higgins AT, Stott KJ, et al (2024)

Enhanced bacterial cancer therapy delivering therapeutic RNA interference of c-Myc.

Cell & bioscience, 14(1):38.

BACKGROUND: Bacterial cancer therapy was first trialled in patients at the end of the nineteenth century. More recently, tumour-targeting bacteria have been harnessed to deliver plasmid-expressed therapeutic interfering RNA to a range of solid tumours. A major limitation to clinical translation of this is the short-term nature of RNA interference in vivo due to plasmid instability. To overcome this, we sought to develop tumour-targeting attenuated bacteria that stably express shRNA by virtue of integration of an expression cassette within the bacterial chromosome and demonstrate therapeutic efficacy in vitro and in vivo.

RESULTS: The attenuated tumour targeting Salmonella typhimurium SL7207 strain was modified to carry chromosomally integrated shRNA expression cassettes at the xylA locus. The colorectal cancer cell lines SW480, HCT116 and breast cancer cell line MCF7 were used to demonstrate the ability of these modified strains to perform intracellular infection and deliver effective RNA and protein knockdown of the target gene c-Myc. In vivo therapeutic efficacy was demonstrated using the Lgr5creER[T2]Apc[flx/flx] and BlgCreBrca2[flx/fl]p53[flx/flx] orthotopic immunocompetent mouse models of colorectal and breast cancer, respectively. In vitro co-cultures of breast and colorectal cancer cell lines with modified SL7207 demonstrated a significant 50-95% (P < 0.01) reduction in RNA and protein expression with SL7207/c-Myc targeted strains. In vivo, following establishment of tumour tissue, a single intra-peritoneal administration of 1 × 10[6] CFU of SL7207/c-Myc was sufficient to permit tumour colonisation and significantly extend survival with no overt toxicity in control animals.

CONCLUSIONS: In summary we have demonstrated that tumour tropic bacteria can be modified to safely deliver therapeutic levels of gene knockdown. This technology has the potential to specifically target primary and secondary solid tumours with personalised therapeutic payloads, providing new multi-cancer detection and treatment options with minimal off-target effects. Further understanding of the tropism mechanisms and impact on host immunity and microbiome is required to progress to clinical translation.

RevDate: 2024-03-26

Inciuraite R, Gedgaudas R, Lukosevicius R, et al (2024)

Constituents of stable commensal microbiota imply diverse colonic epithelial cell reactivity in patients with ulcerative colitis.

Gut pathogens, 16(1):16.

BACKGROUND: Despite extensive research on microbiome alterations in ulcerative colitis (UC), the role of the constituent stable microbiota remains unclear.

RESULTS: This study, employing 16S rRNA-gene sequencing, uncovers a persistent microbial imbalance in both active and quiescent UC patients compared to healthy controls. Using co-occurrence and differential abundance analysis, the study highlights microbial constituents, featuring Phocaeicola, Collinsella, Roseburia, Holdemanella, and Bacteroides, that are not affected during the course of UC. Co-cultivation experiments, utilizing commensal Escherichia coli and Phocaeicola vulgatus, were conducted with intestinal epithelial organoids derived from active UC patients and controls. These experiments reveal a tendency for a differential response in tight junction formation and maintenance in colonic epithelial cells, without inducing pathogen recognition and stress responses, offering further insights into the roles of these microorganisms in UC pathogenesis. These experiments also uncover high variation in patients' response to the same bacteria, which indicate the need for more comprehensive, stratified analyses with an expanded sample size.

CONCLUSION: This study reveals that a substantial part of the gut microbiota remains stable throughout progression of UC. Functional experiments suggest that members of core microbiota - Escherichia coli and Phocaeicola vulgatus - potentially differentially regulate the expression of tight junction gene in the colonic epithelium of UC patients and healthy individuals.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Thu MS, Pongpirul K, Vongsaisuwon M, et al (2024)

Efficacy and mechanisms of cannabis oil for alleviating side effects of breast cancer chemotherapy (CBC2): protocol for randomized controlled trial.

BMC complementary medicine and therapies, 24(1):130.

BACKGROUND: In a pilot study using both cannabidiol (CBD) and tetrahydrocannabinol (THC) as single agents in advanced cancer patients undergoing palliative care in Thailand, the doses were generally well tolerated, and the outcome measure of total symptom distress scores showed overall symptom benefit. The current study aims to determine the intensity of the symptoms experienced by breast cancer patients, to explore the microbiome profile, cytokines, and bacterial metabolites before and after the treatment with cannabis oil or no cannabis oil, and to study the pharmacokinetics parameters and pharmacogenetics profile of the doses.

METHODS: A randomized, double-blinded, placebo-controlled trial will be conducted on the breast cancer cases who were diagnosed with breast cancer and currently receiving chemotherapy at King Chulalongkorn Memorial Hospital (KCMH), Bangkok, Thailand. Block randomization will be used to allocate the patients into three groups: Ganja Oil (THC 2 mg/ml; THC 0.08 mg/drop, and CBD 0.02 mg/drop), Metta Osot (THC 81 mg/ml; THC 3 mg/drop), and placebo oil. The Edmonton Symptom Assessment System (ESAS), Food Frequency Questionnaires (FFQ), microbiome profile, cytokines, and bacterial metabolites will be assessed before and after the interventions, along with pharmacokinetic and pharmacogenetic profile of the treatment during the intervention.

TRIAL REGISTRATION: TCTR20220809001.

RevDate: 2024-03-26
CmpDate: 2024-03-25

Muller E, Shiryan I, E Borenstein (2024)

Multi-omic integration of microbiome data for identifying disease-associated modules.

Nature communications, 15(1):2621.

Multi-omic studies of the human gut microbiome are crucial for understanding its role in disease across multiple functional layers. Nevertheless, integrating and analyzing such complex datasets poses significant challenges. Most notably, current analysis methods often yield extensive lists of disease-associated features (e.g., species, pathways, or metabolites), without capturing the multi-layered structure of the data. Here, we address this challenge by introducing "MintTea", an intermediate integration-based approach combining canonical correlation analysis extensions, consensus analysis, and an evaluation protocol. MintTea identifies "disease-associated multi-omic modules", comprising features from multiple omics that shift in concord and that collectively associate with the disease. Applied to diverse cohorts, MintTea captures modules with high predictive power, significant cross-omic correlations, and alignment with known microbiome-disease associations. For example, analyzing samples from a metabolic syndrome study, MintTea identifies a module with serum glutamate- and TCA cycle-related metabolites, along with bacterial species linked to insulin resistance. In another dataset, MintTea identifies a module associated with late-stage colorectal cancer, including Peptostreptococcus and Gemella species and fecal amino acids, in line with these species' metabolic activity and their coordinated gradual increase with cancer development. This work demonstrates the potential of advanced integration methods in generating systems-level, multifaceted hypotheses underlying microbiome-disease interactions.

RevDate: 2024-03-23

Mager LF, Krause T, KD McCoy (2024)

Interaction of microbiota, mucosal malignancies, and immunotherapy - mechanistic insights.

Mucosal immunology pii:S1933-0219(24)00026-6 [Epub ahead of print].

The microbiome has emerged as a crucial modulator of host immune interactions and clearly impacts on tumor development and therapy efficacy. The microbiome is a double-edged sword in cancer development and therapy as both pro-tumorigenic and anti-tumorigenic bacterial taxa have been identified. The staggering number of association-based studies in various tumor types has led to an enormous amount of data that makes it difficult to identify bacteria that promote tumor development or modulate therapy efficacy from bystander bacteria. Here we aim at comprehensively summarizing the current knowledge of microbiome-host immunity interactions and cancer therapy in various mucosal tissues to find commonalities and thus identify potential functionally relevant bacterial taxa. Moreover, we also review recent studies identifying specific bacteria and mechanisms through which the microbiome modulates cancer development and therapy efficacy.

RevDate: 2024-03-23

Bejarano E, Domenech-Bendaña A, Avila-Portillo N, et al (2024)

Glycative stress as a cause of macular degeneration.

Progress in retinal and eye research pii:S1350-9462(24)00025-9 [Epub ahead of print].

People are living longer and rates of age-related diseases such as age-related macular degeneration (AMD) are accelerating, placing enormous burdens on patients and health care systems. The quality of carbohydrate foods consumed by an individual impacts health. The glycemic index (GI) is a kinetic measure of the rate at which glucose arrives in the blood stream after consuming various carbohydrates. Consuming diets that favor slowly digested carbohydrates releases sugar into the bloodstream gradually after consuming a meal (low glycemic index). This is associated with reduced risk for major age-related diseases including AMD, cardiovascular disease, and diabetes. In comparison, consuming the same amounts of different carbohydrates in higher GI diets, releases glucose into the blood rapidly, causing glycative stress as well as accumulation of advanced glycation end products (AGEs). Such AGEs are cytotoxic by virtue of their forming abnormal proteins and protein aggregates, as well as inhibiting proteolytic and other protective pathways that might otherwise selectively recognize and remove toxic species. Using in vitro and animal models of glycative stress, we observed that consuming higher GI diets perturbs metabolism and the microbiome, resulting in a shift to more lipid-rich metabolomic profiles. Interactions between aging, diet, eye phenotypes and physiology were observed. A large body of laboratory animal and human clinical epidemiologic data indicates that consuming lower GI diets, or lower glycemia diets, is protective against features of early AMD (AMDf) in mice and AMD prevalence or AMD progression in humans. Drugs may be optimised to diminish the ravages of higher glycemic diets. Human trials are indicated to determine if AMD progression can be retarded using lower GI diets. Here we summarized the current knowledge regarding the pathological role of glycative stress in retinal dysfunction and how dietary strategies might diminish retinal disease.

RevDate: 2024-03-23

Su Y, Shi Q, Li Z, et al (2024)

Rhodopseudomonas palustris shapes bacterial community, reduces Cd bioavailability in Cd contaminated flooding paddy soil, and improves rice performance.

The Science of the total environment pii:S0048-9697(24)01967-3 [Epub ahead of print].

Photosynthetic bacteria (PSB) are suitable to live and remediate cadmium (Cd) in the slightly oxygenated or anaerobic flooding paddy field. However, there is currently limited study on the inhibition of Cd accumulation in rice by PSB, and the relevant mechanisms has yet to be elucidated. In the current study, we firstly used Rhodopseudomonas palustris SC06 (a typical PSB) as research target and combined physiology, biochemistry, microbiome and metabolome to evaluate the mechanisms of remeding Cd pollution in paddy field and inhibiting Cd accumulation in rice. Microbiome analysis results revealed that intensive inoculation with R. palustris SC06 successfully survived and multiplied in flooding paddy soil, and significantly increased the relatively abundance of anaerobic bacteria including Desulfobacterota, Anaerolineaceae, Geobacteraceae, and Gemmatimonadaceae by 46.40 %, 45.00 %, 50.12 %, and 21.30 %, respectively. Simultaneously, the structure of microbial community was regulated to maintain relative stability in the rhizosphere soil of rice under Cd stress. In turn, these bacteria communities reduced bioavailable Cd and enhanced residual Cd in soil, and induced the upregulation of sugar and organic acids in the rice roots, which further inhibited Cd uptake in rice seedlings, and dramatically improved the photosynthetic efficiency in the leaves and the activities of antioxidative enzymes in the roots. Finally, Cd content of the roots, stems, leaves, and grains significantly decreased by 38.14 %, 69.10 %, 83.40 %, and 37.24 % comparing with the control, respectively. This study provides a new strategy for the remediation of Cd-contaminated flooding paddy fields and the safe production of rice.

RevDate: 2024-03-23

Bou Sanayeh E, Tawfik M, Makram M, et al (2024)

Hungatella hathewayi bacteremia due to acute appendicitis: A case report and a narrative review.

Hungatella species, including Hungatella hathewayi and Hungatella effluvii, previously identified as part of the Clostridium genus, are anaerobic bacteria primarily residing in the gut microbiome, with infrequent implications in human infections. This article presents the case of an 87-year-old Asian male admitted for a hyperosmolar hyperglycemic state with septic shock secondary to Hungatella hathewayi bacteremia originating from acute appendicitis. Remarkably, the bacterium was detected in the blood 48 hours before the emergence of clinical and radiographic evidence of acute appendicitis. Additionally, we conducted a literature review to identify all documented human infections caused by Hungatella species. Timely microbial identification in such cases is essential for implementing targeted antibiotic therapy and optimizing clinical outcomes.

RevDate: 2024-03-23

Elms L, Hand B, Skubisz M, et al (2024)

The effect of iron supplements on the gut microbiome of women of reproductive age: A randomized controlled trial.

The Journal of nutrition pii:S0022-3166(24)00163-9 [Epub ahead of print].

BACKGROUND: Iron deficiency is the most common nutritional deficiency worldwide, particularly for young children and women of reproductive age. While oral iron supplements are routinely recommended and generally considered safe, iron supplementation has been shown to alter the fecal microbiota in low-income countries. Little is known about the effect of iron supplementation on the fecal microbiota in high-income settings.

OBJECTIVE: To assess the effect of oral iron supplementation versus placebo on the gut microbiome in non-pregnant women of reproductive age in a high-income country.

DESIGN: A 21-day prospective parallel design double-blind, randomized control trial conducted in South Australia, Australia. Women (18-45 y) were randomized to either iron (65.7 mg ferrous fumarate) or placebo. Fecal samples were collected prior to commencing supplements and after 21 days of supplementation. The primary outcome was microbiota beta-diversity (paired-sample weighted UniFrac dissimilarity) between treatment and placebo groups after 21 days of supplementation. Exploratory outcomes included changes in the relative abundance of bacterial taxa.

RESULTS: Of 82 women randomized, 80 completed the trial. There was no significant difference between the groups for weighted UniFrac dissimilarity [mean difference: 0.003 (95% confidence interval: -0.007, 0.014); p=0.52] or relative abundance of common bacterial taxa or Escherichia-Shigella (q>0.05).

CONCLUSIONS: Iron supplementation did not affect the microbiome of non-pregnant women of reproductive age in Australia.

NCT05033483 https://www.

CLINICALTRIALS: gov/study/NCT05033483.

RevDate: 2024-03-23

McCoubrey LE, Ferraro F, Seegobin N, et al (2024)

Poly(D,l-lactide-co-glycolide) particles are metabolised by the gut microbiome and elevate short chain fatty acids.

Journal of controlled release : official journal of the Controlled Release Society pii:S0168-3659(24)00192-5 [Epub ahead of print].

The production of short chain fatty acids (SCFAs) by the colonic microbiome has numerous benefits for human health, including maintenance of epithelial barrier function, suppression of colitis, and protection against carcinogenesis. Despite the therapeutic potential, there is currently no optimal approach for elevating the colonic microbiome's synthesis of SCFAs. In this study, poly(D,l-lactide-co-glycolide) (PLGA) was investigated for this application, as it was hypothesised that the colonic microbiota would metabolise PLGA to its lactate monomers, which would promote the resident microbiota's synthesis of SCFAs. Two grades of spray dried PLGA, alongside a lactate bolus control, were screened in an advanced model of the human colon, known as the M-SHIME® system. Whilst the high molecular weight (Mw) grade of PLGA was stable in the presence of the microbiota sourced from three healthy humans, the low Mw PLGA (PLGA 2) was found to be metabolised. This microbial degradation led to sustained release of lactate over 48 h and increased concentrations of the SCFAs propionate and butyrate. Further, microbial synthesis of harmful ammonium was significantly reduced compared to untreated controls. Interestingly, both types of PLGA was found to influence the composition of the luminal and mucosal microbiota in a donor-specific manner. An in vitro model of an inflamed colonic epithelium also showed the polymer to affect the expression of pro- and anti-inflammatory markers, such as interleukins 8 and 10. The findings of this study reveal PLGA's sensitivity to enzymatic metabolism in the gut, which could be harnessed for therapeutic elevation of colonic SCFAs.

RevDate: 2024-03-23

Fall C, Romero-Camacho MP, Olguín MT, et al (2024)

Aerobic digestibility of waste aerobic granular sludge (AGS) assessed by respirometry, physical-chemical analyses, modeling and 16S rRNA gene sequencing.

Journal of environmental management, 356:120639 pii:S0301-4797(24)00625-X [Epub ahead of print].

Research has evolved on aerobic granular sludge (AGS) process, but still there are very few studies on the treatment of excess AGS sludge, with almost none considering its aerobic digestion. Here therefore, the aerobic digestibility of typical AGS sludge was assessed. Granules were produced from acetate-based synthetic wastewater (WW) and were subjected to aerobic digestion for 64 d. The stabilization process was monitored over time through physical-chemical parameters, oxygen uptake rates (OUR) and 16S rRNA gene sequencing. The microbial analyses revealed that the cultivated granules were dominated by slow-growing bacteria, mainly ordinary heterotrophic organisms with potential for polyhydroxyalkanoates (PHA) aerobic storage (PHA-OHOs), polyphosphate and glycogen accumulating organisms (PAOs and GAOs), fermentative anaerobes and nitrifiers (AOB and NOB). Differential abundance analysis of the bacterial data (before versus after digestion) discriminated between the most vulnerable microbiome genera and those most resistant to aerobic digestion. Furthermore, modeling of the stabilization process determined that the endogenous decay rate constant (bH) for the heterotrophs present in the granules was notably low; bH = 0.05 d[-1] (average), four times less than for common activated sludge (AS), which is rated at 0.2 d[-1]. For first time, the research reveals another important feature of AGS sludge, i.e. the slow-decaying character of its bacteria (along with their known slow-growing character). This results in slower stabilization, need of bigger digesters and reconsideration of the specific OUR limits in biosolids regulations (SOUR limit of 1.5 mg/gTSS.h), for waste AGS compared to conventional waste AS. The study suggests that aerobic digestion of waste AGS (fully-granulated) could differ from that of conventional AS. Future work is needed on aerobic digestibility of real AGS sludges from municipal and industrial WWs, compared to synthetic WWs.

RevDate: 2024-03-23

Tony-Odigie A, Dalpke AH, Boutin S, et al (2024)

Airway commensal bacteria in cystic fibrosis inhibit the growth of P. aeruginosa via a released metabolite.

Microbiological research, 283:127680 pii:S0944-5013(24)00081-8 [Epub ahead of print].

In cystic fibrosis (CF), Pseudomonas aeruginosa infection plays a critical role in disease progression. Although multiple studies suggest that airway commensals might be able to interfere with pathogenic bacteria, the role of the distinct commensals in the polymicrobial lung infections is largely unknown. In this study, we aimed to identify airway commensal bacteria that may inhibit the growth of P. aeruginosa. Through a screening study with more than 80 CF commensal strains across 21 species, more than 30 commensal strains from various species have been identified to be able to inhibit the growth of P. aeruginosa. The underlying mechanisms were investigated via genomic, metabolic and functional analysis, revealing that the inhibitory commensals may affect the growth of P. aeruginosa by releasing a large amount of acetic acid. The data provide information about the distinct roles of airway commensals and provide insights into novel strategies for controlling airway infections.

RevDate: 2024-03-23

Karvanen M, O Cars (2024)

The language of antimicrobial and antibiotic resistance is blocking global collective action.

Infectious diseases (London, England) [Epub ahead of print].

Sustainable access to effective antibiotics is a foundational need for functioning health care that is increasingly threatened by antibiotic resistance. Although resistance has been known as long as antibiotics have been in clinical use, there are still multiple gaps in the global and local responses. One often cited cause for this complacency is the language that is used to describe the problem and its consequences. In this paper, we survey some examples of the current discussions around antibiotic resistance and seek to offer a path towards unified and understandable messaging that is relevant both to the public and policymakers by using narratives that highlight the individual and societal consequences of antibiotic resistance. Major shortcomings in the current language that hamper both the understanding of antibiotic resistance and needed behaviour change have been identified in scientific papers and special reports. These shortcomings range from terminology that is difficult to understand, through a lack of personal relevance, to a fragmented response in the policy field. We propose that scientists, including behaviour change experts, and other key stakeholders that are engaged in the issue take lead to agreement on the core scientific facts and to formulate a vision that can be a foundation for creation of consistent global narratives. These narratives must in turn be adapted to local contexts. Development of such narratives should be viewed as an essential component in national action plans on AMR to raise awareness, empower citizens and incentivise societal behaviour change, policy development and implementation of governance structures.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Lin FX, ZP Xu (2024)

Deficient butyrate metabolism in the gut microbiome: an emerging risk factor for recurrent kidney stone disease.

Urolithiasis, 52(1):47.

RevDate: 2024-03-23

Berckx F, Wibberg D, Brachmann A, et al (2024)

Genome analysis and biogeographic distribution of the earliest divergent Frankia clade in the southern hemisphere.

FEMS microbiology ecology pii:7633977 [Epub ahead of print].

Coriariaceae are a small plant family of 14-17 species and subspecies that currently have a global but disjunct distribution. All species can form root nodules in symbiosis with diazotrophic Frankia cluster-2 strains, which form the earliest divergent symbiotic clade within this bacterial genus. Studies on Frankia cluster-2 mostly have focused on strains occurring in the northern hemisphere. Except for one strain from Papua New Guinea, namely Candidatus Frankia meridionalis Cppng1, no complete genome of Frankia associated with Coriaria occurring in the southern hemisphere has been published thus far, yet the majority of the Coriariaceae species occur here. We present field sampling data of novel Frankia cluster-2 strains, representing two novel species, which are associated with Coriaria arborea and Coriaria sarmentosa in New Zealand, and with Coriaria ruscifolia in Patagonia (Argentina), in addition to identifying Ca. F. meridionalis present in New Zealand. The novel Frankia species were found to be closely related to both Ca. F. meridionalis, and a Frankia species occurring in the Philippines, Taiwan, and Japan. Our data suggest that the different Frankia cluster-2 species diverged early after becoming symbiotic circa 100 million years ago.

RevDate: 2024-03-23

Konecny AJ, Huang Y, Setty M, et al (2024)

Signals that control MAIT cell function in healthy and inflamed human tissues.

Immunological reviews [Epub ahead of print].

Mucosal-associated invariant T (MAIT) cells have a semi-invariant T-cell receptor that allows recognition of antigen in the context of the MHC class I-related (MR1) protein. Metabolic intermediates of the riboflavin synthesis pathway have been identified as MR1-restricted antigens with agonist properties. As riboflavin synthesis occurs in many bacterial species, but not human cells, it has been proposed that the main purpose of MAIT cells is antibacterial surveillance and protection. The majority of human MAIT cells secrete interferon-gamma (IFNg) upon activation, while some MAIT cells in tissues can also express IL-17. Given that MAIT cells are present in human barrier tissues colonized by a microbiome, MAIT cells must somehow be able to distinguish colonization from infection to ensure effector functions are only elicited when necessary. Importantly, MAIT cells have additional functional properties, including the potential to contribute to restoring tissue homeostasis by expression of CTLA-4 and secretion of the cytokine IL-22. A recent study provided compelling data indicating that the range of human MAIT cell functional properties is explained by plasticity rather than distinct lineages. This further underscores the necessity to better understand how different signals regulate MAIT cell function. In this review, we highlight what is known in regards to activating and inhibitory signals for MAIT cells with a specific focus on signals relevant to healthy and inflamed tissues. We consider the quantity, quality, and the temporal order of these signals on MAIT cell function and discuss the current limitations of computational tools to extrapolate which signals are received by MAIT cells in human tissues. Using lessons learned from conventional CD8 T cells, we also discuss how TCR signals may integrate with cytokine signals in MAIT cells to elicit distinct functional states.

RevDate: 2024-03-26
CmpDate: 2024-03-25

Zhang Y, Wu X, Li D, et al (2024)

HPV-associated cervicovaginal microbiome and host metabolome characteristics.

BMC microbiology, 24(1):94.

BACKGROUND: Cervicovaginal microbiome plays an important role in the persistence of HPV infection and subsequent disease development. However, cervicovaginal microbiota varied cross populations with different habits and regions. Identification of population-specific biomarkers from cervicovaginal microbiota and host metabolome axis may support early detection or surveillance of HPV-induced cervical disease at all sites. Therefore, in the present study, to identify HPV-specific biomarkers, cervicovaginal secretion and serum samples from HPV-infected patients (HPV group, n = 25) and normal controls (normal group, n = 17) in Xichang, China were collected for microbiome (16S rRNA gene sequencing) and metabolome (UHPLC-MS/MS) analysis, respectively.

RESULTS: The results showed that key altered metabolites of 9,10-DiHOME, α-linolenic acid, ethylparaben, glycocholic acid, pipecolic acid, and 9,12,13-trihydroxy-10(E),15(Z)-octadecadienoic acid, correlating with Sneathia (Sneathia_amnii), Lactobacillus (Lactobacillus_iners), Atopobium, Mycoplasma, and Gardnerella, may be potential biomarkers of HPV infection.

CONCLUSION: The results of current study would help to reveal the association of changes in cervicovaginal microbiota and serum metabolome with HPV infections.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Pearman WS, Morales SE, Vaux F, et al (2024)

Host population crashes disrupt the diversity of associated marine microbiomes.

Environmental microbiology, 26(3):e16611.

Host-associated microbial communities are shaped by myriad factors ranging from host conditions, environmental conditions and other microbes. Disentangling the ecological impact of each of these factors can be particularly difficult as many variables are correlated. Here, we leveraged earthquake-induced changes in host population structure to assess the influence of population crashes on marine microbial ecosystems. A large (7.8 magnitude) earthquake in New Zealand in 2016 led to widespread coastal uplift of up to ~6 m, sufficient to locally extirpate some intertidal southern bull kelp populations. These uplifted populations are slowly recovering, but remain at much lower densities than at nearby, less-uplifted sites. By comparing the microbial communities of the hosts from disturbed and relatively undisturbed populations using 16S rRNA gene amplicon sequencing, we observed that disturbed host populations supported higher functional, taxonomic and phylogenetic microbial beta diversity than non-disturbed host populations. Our findings shed light on microbiome ecological assembly processes, particularly highlighting that large-scale disturbances that affect host populations can dramatically influence microbiome structure. We suggest that disturbance-induced changes in host density limit the dispersal opportunities of microbes, with host community connectivity declining with the density of host populations.

RevDate: 2024-03-26
CmpDate: 2024-03-25

Kunasegaran T, Balasubramaniam VRMT, Thirunavuk Arasoo VJ, et al (2024)

Diet, lifestyle and gut microbiota composition among Malaysian women with gestational diabetes mellitus: a prospective cohort study.

Scientific reports, 14(1):6891.

The study addressed a significant gap in the profiling and understanding of the gut microbiota's influence on Malaysian Malay women with gestational diabetes mellitus (GDM). This prospective cohort study aimed to explore the intricate relationship between gut microbiota, dietary choices, and lifestyle factors among Malay women, both with and without GDM. The research specifically focused on participants during the second (T0) and third (T1) trimesters of pregnancy in Johor Bahru, Malaysia. In Part 1 of the study, a diverse pool of pregnant women at T0 was categorized into two groups: those diagnosed with GDM and those without GDM, with a total sample size of 105 individuals. The assessments encompassed demographic, clinical, lifestyle, and dietary factors at the T0 and T1 trimesters. Part 2 of the study delved into microbiome analysis, targeting a better understanding of the gut microbiota among the participants. Stool samples were randomly collected from 50% of the individuals in each group (GDM and non-GDM) at T0 and T1. The collected samples underwent processing, and 16s rRNA metagenomic analysis was employed to study the microbial composition. The results suggested an association between elevated body weight and glucose levels, poor sleep quality, lack of physical activity, greater intake of iron and meat, and reduced fruit consumption among women with GDM compared to non-GDM groups. The microbiome analysis revealed changes in microbial composition over time, with reduced diversity observed in the GDM group during the third trimester. The genera Lactiplantibacillus, Parvibacter, Prevotellaceae UCG001, and Vagococcus positively correlated with physical activity levels in GDM women in the second trimester. Similarly, the genus Victivallis exhibited a strong positive correlation with gravida and parity. On the contrary, the genus Bacteroides and Roseburia showed a negative correlation with omega-3 polyunsaturated fatty acids (PUFAs) in women without GDM in the third trimester. The study highlighted the multifaceted nature of GDM, involving a combination of lifestyle factors, dietary choices, and changes in gut microbiota composition. The findings emphasized the importance of considering these interconnected elements in understanding and managing gestational diabetes among Malaysian Malay women. Further exploration is essential to comprehend the mechanisms underlying this relationship and develop targeted interventions for effective GDM management.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Čaušević S, Dubey M, Morales M, et al (2024)

Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions.

Nature communications, 15(1):2557.

Microbiome engineering - the targeted manipulation of microbial communities - is considered a promising strategy to restore ecosystems, but experimental support and mechanistic understanding are required. Here, we show that bacterial inoculants for soil microbiome engineering may fail to establish because they inadvertently facilitate growth of native resident microbiomes. By generating soil microcosms in presence or absence of standardized soil resident communities, we show how different nutrient availabilities limit outgrowth of focal bacterial inoculants (three Pseudomonads), and how this might be improved by adding an artificial, inoculant-selective nutrient niche. Through random paired interaction assays in agarose micro-beads, we demonstrate that, in addition to direct competition, inoculants lose competitiveness by facilitating growth of resident soil bacteria. Metatranscriptomics experiments with toluene as selective nutrient niche for the inoculant Pseudomonas veronii indicate that this facilitation is due to loss and uptake of excreted metabolites by resident taxa. Generation of selective nutrient niches for inoculants may help to favor their proliferation for the duration of their intended action while limiting their competitive loss.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Liu J, Malekoltojari A, Asokakumar A, et al (2024)

Diindoles produced from commensal microbiota metabolites function as endogenous CAR/Nr1i3 ligands.

Nature communications, 15(1):2563.

Numerous studies have demonstrated the correlation between human gut bacteria and host physiology, mediated primarily via nuclear receptors (NRs). Despite this body of work, the systematic identification and characterization of microbe-derived ligands that regulate NRs remain a considerable challenge. In this study, we discover a series of diindole molecules produced from commensal bacteria metabolites that act as specific agonists for the orphan constitutive androstane receptor (CAR). Using various biophysical analyses we show that their nanomolar affinities are comparable to those of synthetic CAR agonists, and that they can activate both rodent and human CAR orthologues, which established synthetic agonists cannot. We also find that the diindoles, diindolylmethane (DIM) and diindolylethane (DIE) selectively up-regulate bona fide CAR target genes in primary human hepatocytes and mouse liver without causing significant side effects. These findings provide new insights into the complex interplay between the gut microbiome and host physiology, as well as new tools for disease treatment.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Seo YJ, Lim C, Lim B, et al (2024)

Microbial-transcriptome integrative analysis of heat stress effects on amino acid metabolism and lipid peroxidation in poultry jejunum.

Animal biotechnology, 35(1):2331179.

Despite the significant threat of heat stress to livestock animals, only a few studies have considered the potential relationship between broiler chickens and their microbiota. Therefore, this study examined microbial modifications, transcriptional changes and host-microbiome interactions using a predicted metabolome data-based approach to understand the impact of heat stress on poultry. After the analysis, the host functional enrichment analysis revealed that pathways related to lipid and protein metabolism were elevated under heat stress conditions. In contrast, pathways related to the cell cycle were suppressed under normal environmental temperatures. In line with the transcriptome analysis, the microbial analysis results indicate that taxonomic changes affect lipid degradation. Heat stress engendered statistically significant difference in the abundance of 11 microorganisms, including Bacteroides and Peptostreptococcacea. Together, integrative approach analysis suggests that microbiota-induced metabolites affect host fatty acid peroxidation metabolism, which is correlated with the gene families of Acyl-CoA dehydrogenase long chain (ACADL), Acyl-CoA Oxidase (ACOX) and Acetyl-CoA Acyltransferase (ACAA). This integrated approach provides novel insights into heat stress problems and identifies potential biomarkers associated with heat stress.

RevDate: 2024-03-22

Datathon 2022 Consortium:, Jurburg SD, Álvarez Blanco MJ, et al (2024)

Datathons: fostering equitability in data reuse in ecology.

Trends in microbiology pii:S0966-842X(24)00050-7 [Epub ahead of print].

Approaches to rapidly collecting global biodiversity data are increasingly important, but biodiversity blind spots persist. We organized a three-day Datathon event to improve the openness of local biodiversity data and facilitate data reuse by local researchers. The first Datathon, organized among microbial ecologists in Uruguay and Argentina assembled the largest microbiome dataset in the region to date and formed collaborative consortia for microbiome data synthesis.

RevDate: 2024-03-22

Pristner M, Wasinger D, Seki D, et al (2024)

Neuroactive metabolites and bile acids are altered in extremely premature infants with brain injury.

Cell reports. Medicine pii:S2666-3791(24)00126-5 [Epub ahead of print].

The gut microbiome is associated with pathological neurophysiological evolvement in extremely premature infants suffering from brain injury. The exact underlying mechanism and its associated metabolic signatures in infants are not fully understood. To decipher metabolite profiles linked to neonatal brain injury, we investigate the fecal and plasma metabolome of samples obtained from a cohort of 51 extremely premature infants at several time points, using liquid chromatography (LC)-high-resolution mass spectrometry (MS)-based untargeted metabolomics and LC-MS/MS-based targeted analysis for investigating bile acids and amidated bile acid conjugates. The data are integrated with 16S rRNA gene amplicon gut microbiome profiles as well as patient cytokine, growth factor, and T cell profiles. We find an early onset of differentiation in neuroactive metabolites between infants with and without brain injury. We detect several bacterially derived bile acid amino acid conjugates in plasma and feces. These results provide insights into the early-life metabolome of extremely premature infants.

RevDate: 2024-03-22

Shi Y, Du Q, Li Z, et al (2024)

Multiomics profiling of the therapeutic effect of Dan-deng-tong-nao capsule on cerebral ischemia-reperfusion injury.

Phytomedicine : international journal of phytotherapy and phytopharmacology, 128:155335 pii:S0944-7113(23)00693-1 [Epub ahead of print].

BACKGROUND: Stroke is a complex physiological process associated with intestinal flora dysbiosis and metabolic disorders. Dan-deng-tong-nao capsule (DDTN) is a traditional Chinese medicine used clinically to treat cerebral ischemia-reperfusion injury (CIRI) for many years. However, little is known about the effects of DDTN in the treatment of CIRI from the perspective of gut microbiota and metabolites.

PURPOSE: This study aimed to investigate the regulatory roles of DDTN in endogenous metabolism and gut microbiota in CIRI rats, thus providing a basis for clinical rational drug use and discovering natural products with potential physiological activities in DDTN for the treatment of CIRI.

METHODS: The chemical composition of DDTN in vitro and in vivo was investigated using ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLCHRMS), followed by target prediction using reverse molecular docking. Secondly, a biological evaluation of DDTN ameliorating neural damage in CIRI was performed at the whole animal level. Then, an integrated omics approach based on UHPLCHRMS and 16S rRNA sequencing was proposed to reveal the anti-CIRI effect and possible mechanism of DDTN. Finally, exploring the intrinsic link between changes in metabolite profiles, changes in the intestinal flora, and targets of components to reveal DDTN for the treatment of CIRI.

RESULTS: A total of 112 chemical components of DDTN were identified in vitro and 10 absorbed constituents in vivo. The efficacy of DDTN in the treatment of CIRI was confirmed by alleviating cerebral infarction and neurological deficits. After the DDTN intervention, 21 and 26 metabolites were significantly altered in plasma and fecal, respectively. Based on the fecal microbiome, a total of 36 genera were enriched among the different groups. Finally, the results of the network integration analysis showed that the 10 potential active ingredients of DDTN could mediate the differential expression of 24 metabolites and 6 gut microbes by targeting 25 target proteins.

CONCLUSION: This study was the first to outline the landscapes of metabolites as well as gut microbiota regulated by DDTN in CIRI rats using multi-omics data, and comprehensively revealed the systematic relationships among ingredients, targets, metabolites, and gut microbiota, thus providing new perspectives on the mechanism of DDTN in the treatment of CIRI.

RevDate: 2024-03-22

Fernandez-Cantos MV, Babu AF, Hanhineva K, et al (2024)

Identification of metabolites produced by six gut commensal Bacteroidales strains using non-targeted LC-MS/MS metabolite profiling.

Microbiological research, 283:127700 pii:S0944-5013(24)00101-0 [Epub ahead of print].

As the most abundant gram-negative bacterial order in the gastrointestinal tract, Bacteroidales bacteria have been extensively studied for their contribution to various aspects of gut health. These bacteria are renowned for their involvement in immunomodulation and their remarkable capacity to break down complex carbohydrates and fibers. However, the human gut microbiota is known to produce many metabolites that ultimately mediate important microbe-host and microbe-microbe interactions. To gain further insights into the metabolites produced by the gut commensal strains of this order, we examined the metabolite composition of their bacterial cell cultures in the stationary phase. Based on their abundance in the gastrointestinal tract and their relevance in health and disease, we selected a total of six bacterial strains from the relevant genera Bacteroides, Phocaeicola, Parabacteroides, and Segatella. We grew these strains in modified Gifu anaerobic medium (mGAM) supplemented with mucin, which resembles the gut microbiota's natural environment. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolite profiling revealed 179 annotated metabolites that had significantly differential abundances between the studied bacterial strains and the control growth medium. Most of them belonged to classes such as amino acids and derivatives, organic acids, and nucleot(s)ides. Of particular interest, Segatella copri DSM 18205 (previously referred to as Prevotella copri) produced substantial quantities of the bioactive metabolites phenylethylamine, tyramine, tryptamine, and ornithine. Parabacteroides merdae CL03T12C32 stood out due to its ability to produce cadaverine, histamine, acetylputrescine, and deoxycarnitine. In addition, we found that strains of the genera Bacteroides, Phocaeicola, and Parabacteroides accumulated considerable amounts of proline-hydroxyproline, a collagen-derived bioactive dipeptide. Collectively, these findings offer a more detailed comprehension of the metabolic potential of these Bacteroidales strains, contributing to a better understanding of their role within the human gut microbiome in health and disease.

RevDate: 2024-03-22

Belotserkovsky I, Stabryla LM, Hunter M, et al (2024)

Standards for fecal microbiota transplant: Tools and therapeutic advances.

Biologicals : journal of the International Association of Biological Standardization, 86:101758 pii:S1045-1056(24)00015-0 [Epub ahead of print].

Fecal microbiota transplantation (FMT) has been demonstrated to be efficacious in preventing recurrent Clostridioides difficile (C. difficile) infections, and is being investigated for treatment of several other diseases including inflammatory bowel disease, cancer, obesity, liver disease, and diabetes. To speed up the translation of FMT into clinical practice as a safe and standardized therapeutic intervention, additional evidence-based technical and regulatory guidance is needed. To this end in May of 2022, the International Alliance for Biological Standardization (IABS) and the BIOASTER Microbiology Technology Institute hosted a second webinar to discuss key issues still impeding the advancement and standardization of FMT. The goal of this two-day webinar was to provide a forum for scientific experts to share and discuss data and key challenges with one another. Discussion included a focus on the evaluation of safety, efficacy, clinical trial design, reproducibility and accuracy in obtained microbiome measurements and data reporting, and the potential for standardization across these areas. It also focused on increasing the application potential and visibility of FMT beyond treating C. difficile infections.

RevDate: 2024-03-22

R Muralitharan R, Nakai ME, Snelson M, et al (2024)

Influence of angiotensin II on the gut microbiome: Modest effects in comparison to experimental factors.

Cardiovascular research pii:7633834 [Epub ahead of print].

INTRODUCTION: Animal models are regularly used to test the role of the gut microbiome in hypertension. Small-scale pre-clinical studies have investigated changes to the gut microbiome in the angiotensin II hypertensive model. However, the gut microbiome is influenced by internal and external experimental factors which are not regularly considered in the study design. Once these factors are accounted for, it is unclear if microbiome signatures are reproduceable. We aimed to determine the influence of angiotensin II treatment on the gut microbiome using a large and diverse cohort of mice and to quantify the magnitude by which other factors contribute to microbiome variations.

METHODS AND RESULTS: We conducted a retrospective study to establish a diverse mouse cohort resembling large human studies. We sequenced the V4 region of the 16S rRNA gene from 538 samples across the gastrointestinal tract of 303 male and female C57BL/6J mice randomised into sham or angiotensin II treatment from different genotypes, diets, animal facilities, and age groups. Analysing over 17 million sequencing reads, we observed that angiotensin II treatment influenced α-diversity (P = 0.0137) and β-diversity (i.e., composition of the microbiome, P < 0.001). Bacterial abundance analysis revealed patterns consistent with a reduction in short-chain fatty acid-producers, microbial metabolites that lower blood pressure. Furthermore, animal facility, genotype, diet, age, sex, intestinal sampling site, and sequencing batch had significant effects on both α- and β-diversity (all P < 0.001). Sampling site (6.8%) and diet (6%) had the largest impact on the microbiome, while angiotensin II and sex had the smallest effect (each 0.4%).

CONCLUSIONS: Our large-scale data confirmed findings from small-scale studies that angiotensin II impacted the gut microbiome. However, this effect was modest relative to most of the other factors studied. Accounting for these factors in future pre-clinical hypertensive studies will increase the likelihood that microbiome findings are replicable and translatable.

RevDate: 2024-03-22

Stuart MK, Motes HC, DA Hudman (2024)

Effect of Phytochemical Compounds on Trichomonas tenax, an Oral Protozoan.

Alternative therapies in health and medicine pii:AT7352 [Epub ahead of print].

Trichomonas tenax is an oral protozoan with an estimated global pooled prevalence of 17% in the human population.1 Observational studies have demonstrated a significant statistical correlation between oral colonization by T. tenax and the progression of periodontal disease.2 Proposed pathogenic mechanisms for this protozoan include the production of tissue-damaging enzymes, induction of apoptosis in human cells, and dysbiosis of the oral microbiome.3 In patients for whom metronidazole (MTZ) is contraindicated, phytochemicals may offer a viable alternative for controlling T. tenax. Various plant extracts have shown promising in vitro activity against other trichomonads, such as T. vaginalis and Tritrichomonas foetus, as reviewed by Friedman et al.4.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Wang Y, Li W, C Ha (2024)

A large-scale causal analysis of gut microbiota and endometriosis associated infertility: A Mendelian randomization study.

Medicine, 103(12):e37383.

Endometriosis is a prevalent condition with notable impacts on fertility. Recent studies have implicated gut microbiota in the development of endometriosis associated infertility (EAI). This study employs Mendelian randomization (MR) to elucidate the causal relationship between specific gut microbes and EAI. Using MR, we selected single nucleotide polymorphisms associated with 211 gut microbiota taxa from large-scale genome-wide association studies summary data. We applied statistical methods including inverse variance weighting, weighted median, and MR-Egger for analysis. Outliers were identified through the leave-one-out method. MR-Egger intercept tests were conducted to address horizontal pleiotropy, while Cochran Q and P values assessed heterogeneity. The false discovery rate method was used for multiple testing correction. Sensitivity analysis and F statistics evaluated the reliability and potential biases of our results. The inverse variance weighting method indicated a significant association of the genus Actinomyces (OR = 1.657, 95% CI: 1.187-2.312, P = .00298) with an increased risk of EAI. Conversely, genera Holdemania (OR = 0.630, 95% CI: 0.444-0.894, P = .00969) and Ruminococcaceae NK4A214 group (OR = 0.689, 95% CI: 0.481-0.999, P = .0439) appeared as protective factors. MR-PRESSO global test and MR-Egger regression indicated no significant horizontal pleiotropy (P > .05). Leave-one-out analysis confirmed the robustness of these findings. Our study provides evidence of a causal relationship between specific gut microbiome taxa and EAI. These findings offer novel insights and may guide the development of new preventive and therapeutic strategies for managing EAI.

RevDate: 2024-03-22

Griffiths JA, Yoo BB, Thuy-Boun P, et al (2024)

Peripheral neuronal activation shapes the microbiome and alters gut physiology.

Cell reports, 43(4):113953 pii:S2211-1247(24)00281-X [Epub ahead of print].

The gastrointestinal (GI) tract is innervated by intrinsic neurons of the enteric nervous system (ENS) and extrinsic neurons of the central nervous system and peripheral ganglia. The GI tract also harbors a diverse microbiome, but interactions between the ENS and the microbiome remain poorly understood. Here, we activate choline acetyltransferase (ChAT)-expressing or tyrosine hydroxylase (TH)-expressing gut-associated neurons in mice to determine effects on intestinal microbial communities and their metabolites as well as on host physiology. The resulting multi-omics datasets support broad roles for discrete peripheral neuronal subtypes in shaping microbiome structure, including modulating bile acid profiles and fungal colonization. Physiologically, activation of either ChAT[+] or TH[+] neurons increases fecal output, while only ChAT[+] activation results in increased colonic contractility and diarrhea-like fluid secretion. These findings suggest that specific subsets of peripherally activated neurons differentially regulate the gut microbiome and GI physiology in mice without involvement of signals from the brain.

RevDate: 2024-03-26

Brady MV, EC Farrer (2024)

The soil microbiome affects patterns of local adaptation in an alpine plant under moisture stress.

American journal of botany, 111(3):e16304.

PREMISE: The soil microbiome plays a role in plant trait expression and fitness, and plants may be locally adapted or maladapted to their soil microbiota. However, few studies of local adaptation in plants have incorporated a microbial treatment separate from manipulations of the abiotic environment, so our understanding of microbes in plant adaptation is limited.

METHODS: Here we tested microbial effects on local adaptation in four paired populations of an abundant alpine plant from two community types, dry and moist meadow. In a 5-month greenhouse experiment, we manipulated source population, soil moisture, and soil microbiome and measured plant survival and biomass to assess treatment effects.

RESULTS: Dry meadow populations had higher biomass than moist meadow populations at low moisture, demonstrating evidence of local adaptation to soil moisture in the absence of microbes. In the presence of microbes, dry meadow populations had greater survival than moist meadow populations when grown with dry meadow microbes regardless of moisture. Moist meadow populations showed no signs of adaptation or maladaptation.

CONCLUSIONS: Our research highlights the importance of microbial mutualists in local adaptation, particularly in dry environments with higher abiotic stress. Plant populations from environments with greater abiotic stress exhibit different patterns of adaptation when grown with soil microbes versus without, while plant populations from less abiotically stressful environments do not. Improving our understanding of the role microbes play in plant adaptation will require further studies incorporating microbial manipulations.

RevDate: 2024-03-22

Paulay A, Grimaud GM, Caballero R, et al (2024)

Design of a proteolytic module for improved metabolic modeling of Bacteroides caccae.

mSystems [Epub ahead of print].

The gut microbiota plays a crucial role in health and is significantly modulated by human diets. In addition to Western diets which are rich in proteins, high-protein diets are used for specific populations or indications, mainly weight loss. In this study, we investigated the effect of protein supplementation on Bacteroides caccae, a Gram-negative gut symbiont. The supplementation with whey proteins led to a significant increase in growth rate, final biomass, and short-chain fatty acids production. A comprehensive genomic analysis revealed that B. caccae possesses a set of 156 proteases with putative intracellular and extracellular localization and allowed to identify amino acid transporters and metabolic pathways. We developed a fully curated genome-scale metabolic model of B. caccae that incorporated its proteolytic activity and simulated its growth and production of fermentation-related metabolites in response to the different growth media. We validated the model by comparing the predicted phenotype to experimental data. The model accurately predicted B. caccae's growth and metabolite production (R[2] = 0.92 for the training set and R[2] = 0.89 for the validation set). We found that accounting for both ATP consumption related to proteolysis, and whey protein accessibility is necessary for accurate predictions of metabolites production. These results provide insights into B. caccae's adaptation to a high-protein diet and its ability to utilize proteins as a source of nutrition. The proposed model provides a useful tool for understanding the feeding mechanism of B. caccae in the gut microbiome.IMPORTANCEMicrobial proteolysis is understudied despite the availability of dietary proteins for the gut microbiota. Here, the proteolytic potential of the gut symbiont Bacteroides caccae was analyzed for the first time using pan-genomics. This sketches a well-equipped bacteria for protein breakdown, capable of producing 156 different proteases with a broad spectrum of cleavage targets. This functional potential was confirmed by the enhancement of growth and metabolic activities at high protein levels. Proteolysis was included in a B. caccae metabolic model which was fitted with the experiments and validated on external data. This model pinpoints the links between protein availability and short-chain fatty acids production, and the importance for B. caccae to gain access to glutamate and asparagine to promote growth. This integrated approach can be generalized to other symbionts and upscaled to complex microbiota to get insights into the ecological impact of proteins on the gut microbiota.

RevDate: 2024-03-22

Dong S, Zeng Q, He W, et al (2024)

Effect of Lactobacillus plantarum BFS1243 on a female frailty model induced by fecal microbiota transplantation in germ-free mice.

Food & function [Epub ahead of print].

Frailty, a complex geriatric syndrome, significantly impedes the goal of achieving 'healthy aging'. Increasing evidence suggests a connection between gut microbiota, systemic inflammation, and disease. However, it remains to be determined whether interventions targeting the intestinal flora can effectively ameliorate frailty. Our research involved fecal microbiota transplantation (FMT) experiments on germ-free (GF) mice, dividing these mice into three groups: a group receiving transplants from healthy elderly individuals (HF group), a group of frailty patients (FF group), and the FF group supplemented with Lactobacillus plantarum BFS1243 (FFL group). Our findings indicated a significant shift in the gut microbiota of the FF group, in contrast to the HF group, characterized by decreased Akkermansia and increased Enterocloster, Parabacteroides, and Eisenbergiella. Concurrently, there was a reduction in amino acids and SCFAs, with BFS1243 partially mitigating these changes. The FF group exhibited an upregulation of inflammatory markers, including PGE2, CRP, and TNF-α, and a downregulation of irisin, all of which were moderated by BFS1243 treatment. Furthermore, BFS1243 improved intestinal barrier integrity and physical endurance in the FF mice. Correlation analysis revealed a negative association between SCFA-producing species and metabolites like lysine and butyric acid with pro-inflammatory factors. In conclusion, our study conclusively demonstrated that alterations in the gut microbiota of elderly individuals can lead to physical frailty, likely due to detrimental effects on the intestinal barrier and a pro-inflammatory state. These findings underscore the potential of gut microbiome modulation as a clinical strategy for treating frailty.

RevDate: 2024-03-22

Han L, Chang ZM, Ren CS, et al (2024)

Colony performance of three native bumblebee species from South China and association with their gut microbiome.

Insect science [Epub ahead of print].

Bumblebees play an important ecological economic role as pollinators in nature and agriculture. For reasons of biosecurity, many countries promote the cultivation of native bumblebee species for crop pollination instead of importing "alien" species. In South China, a few bumblebee species are considered useful in this way, particularly, Bombus atripes, Bombus bicoloratus and Bombus breviceps. However, whether they are suitable for artificial rearing and forming healthy colonies for pollination, remains unknown. In this project, queens from the 3 native species of Guizhou Province were collected and colonies were started under standardized conditions. The colonies were scored based on 19 parameters, including the stage of colony development, number and weight of offspring, and diet consumed. The data revealed that B. breviceps had the best performance, produced more workers and consumed the smallest diet. Next, we performed 16S rDNA sequencing of the bacterial communities found in the guts of offspring workers, and then a correlation analysis between colony performance and gut bacteria was conducted. Here, B. breviceps showed the highest diversity in gut bacterial composition, dominated by the bacteria Gilliamella, Snodgrassella, Enterobacter, and Lactobacillus Firm5. The higher the abundance of Snodgrassella, the better the performance of the colony in the foundation stage, and later Lactobacillus Firm5, Apibacter and Bifidobacterium were beneficial during the stages of rapid growth and colony decline. Although we do not understand all of the interactions yet, these correlations explain why B. breviceps demonstrated better colony performance. Our data provide valuable information for breeding local Bombus species and will contribute to developing strong colonies for crop pollination.

RevDate: 2024-03-23

Vidal-Gallardo A, Méndez Benítez JE, Flores Rios L, et al (2024)

The Role of Gut Microbiome in the Pathogenesis and the Treatment of Inflammatory Bowel Diseases.

Cureus, 16(2):e54569.

Inflammatory bowel disease (IBD), which includes ulcerative colitis and Crohn's disease, is a chronic condition characterized by inflammation of the gastrointestinal tract. Its exact cause is unknown, but it's thought to result from a dysregulated immune response influenced by various factors, including changes in the intestinal microbiota, diet, lifestyle, and genetics. The gut microbiome, consisting of diverse microorganisms, plays a crucial role in maintaining physiological balance, with its disruption leading to inflammatory responses typical of IBD. Treatments primarily aim at symptom control, employing immunomodulators, corticosteroids, and newer approaches like probiotics, prebiotics, fecal transplants, and dietary modifications, all focusing on leveraging the microbiota's potential in disease management. These strategies aim to restore the delicate balance of the gut microbiome, typically altered in IBD, marked by a decrease in beneficial bacteria and an increase in harmful pathogens. This review underscores the importance of the gut microbiome in the pathogenesis and treatment of IBD, highlighting the shift towards personalized medicine and the necessity for further research in understanding the complex interactions between the gut microbiota, immune system, and genetics in IBD. It points to the potential of emerging treatments and the importance of a multifaceted approach in managing this complex and challenging disease.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Qiu T, D Yan (2024)

Editorial: Benefits and risks of drug combination therapy for chronic metabolic diseases.

Frontiers in endocrinology, 15:1390248.

RevDate: 2024-03-23

Caputi V, Hill L, Figueiredo M, et al (2024)

Functional contribution of the intestinal microbiome in autism spectrum disorder, attention deficit hyperactivity disorder, and Rett syndrome: a systematic review of pediatric and adult studies.

Frontiers in neuroscience, 18:1341656.

INTRODUCTION: Critical phases of neurodevelopment and gut microbiota diversification occur in early life and both processes are impacted by genetic and environmental factors. Recent studies have shown the presence of gut microbiota alterations in neurodevelopmental disorders. Here we performed a systematic review of alterations of the intestinal microbiota composition and function in pediatric and adult patients affected by autism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD), and Rett syndrome (RETT).

METHODS: We searched selected keywords in the online databases of PubMed, Cochrane, and OVID (January 1980 to December 2021) with secondary review of references of eligible articles. Two reviewers independently performed critical appraisals on the included articles using the Critical Appraisal Skills Program for each study design.

RESULTS: Our systematic review identified 18, 7, and 3 original articles describing intestinal microbiota profiles in ASD, ADHD, and RETT, respectively. Decreased Firmicutes and increased Bacteroidetes were observed in the gut microbiota of individuals affected by ASD and ADHD. Proinflammatory cytokines, short-chain fatty acids and neurotransmitter levels were altered in ASD and RETT. Constipation and visceral pain were related to changes in the gut microbiota in patients affected by ASD and RETT. Hyperactivity and impulsivity were negatively correlated with Faecalibacterium (phylum Firmicutes) and positively correlated with Bacteroides sp. (phylum Bacteroidetes) in ADHD subjects. Five studies explored microbiota-or diet-targeted interventions in ASD and ADHD. Probiotic treatments with Lactobacillus sp. and fecal microbiota transplantation from healthy donors reduced constipation and ameliorated ASD symptoms in affected children. Perinatal administration of Lactobacillus sp. prevented the onset of Asperger and ADHD symptoms in adolescence. Micronutrient supplementation improved disease symptomatology in ADHD without causing significant changes in microbiota communities' composition.

DISCUSSION: Several discrepancies were found among the included studies, primarily due to sample size, variations in dietary practices, and a high prevalence of functional gastrointestinal symptoms. Further studies employing longitudinal study designs, larger sample sizes and multi-omics technologies are warranted to identify the functional contribution of the intestinal microbiota in developmental trajectories of the human brain and neurobehavior.

https://clinicaltrials.gov/, CRD42020158734.

RevDate: 2024-03-23

Hui X, Yang J, Sun J, et al (2024)

MCSS: microbial community simulator based on structure.

Frontiers in microbiology, 15:1358257.

De novo assembly plays a pivotal role in metagenomic analysis, and the incorporation of third-generation sequencing technology can significantly improve the integrity and accuracy of assembly results. Recently, with advancements in sequencing technology (Hi-Fi, ultra-long), several long-read-based bioinformatic tools have been developed. However, the validation of the performance and reliability of these tools is a crucial concern. To address this gap, we present MCSS (microbial community simulator based on structure), which has the capability to generate simulated microbial community and sequencing datasets based on the structure attributes of real microbiome communities. The evaluation results indicate that it can generate simulated communities that exhibit both diversity and similarity to actual community structures. Additionally, MCSS generates synthetic PacBio Hi-Fi and Oxford Nanopore Technologies (ONT) long reads for the species within the simulated community. This innovative tool provides a valuable resource for benchmarking and refining metagenomic analysis methods. Code available at: https://github.com/panlab-bio/mcss.

RevDate: 2024-03-22

Zou S, Chen Z, Tan Y, et al (2024)

Microbiomes detected by cerebrospinal fluid metagenomic next-generation sequencing among patients with and without HIV with suspected central nervous system infection.

HIV medicine [Epub ahead of print].

BACKGROUND: Opportunistic infections in the central nervous system (CNS) can be a serious threat to people living with HIV. Early aetiological diagnosis and targeted treatment are crucial but difficult. Metagenomic next-generation sequencing (mNGS) has significant advantages over traditional detection methods. However, differences in the cerebrospinal fluid (CSF) microbiome profiles of patients living with and without HIV with suspected CNS infections using mNGS and conventional testing methods have not yet been adequately evaluated.

METHODS: We conducted a retrospective cohort study in the first hospital of Changsha between January 2019 and June 2022 to investigate the microbiomes detected using mNGS of the CSF of patients living with and without HIV with suspected CNS infections. The pathogens causing CNS infections were concurrently identified using both mNGS and traditional detection methods. The spectrum of pathogens identified was compared between the two groups.

RESULTS: Overall, 173 patients (140 with and 33 without HIV) with suspected CNS infection were enrolled in our study. In total, 106 (75.7%) patients with and 16 (48.5%) patients without HIV tested positive with mNGS (p = 0.002). Among the enrolled patients, 71 (50.7%) with HIV and five (15.2%) without HIV tested positive for two or more pathogens (p < 0.001). Patients with HIV had significantly higher proportions of fungus (20.7% vs. 3.0%, p = 0.016) and DNA virus (59.3% vs. 21.2%, p < 0.001) than those without HIV. Epstein-Barr virus (33.6%) was the most commonly identified potential pathogen in the CSF of patients living with HIV using mNGS, followed by cytomegalovirus (20.7%) and torque teno virus (13.8%). The top three causative pathogens identified in patients without HIV were Streptococcus (18.2%), Epstein-Barr virus (12.1%), and Mycobacterium tuberculosis (9.1%). In total, 113 patients living with HIV were diagnosed as having CNS infections. The rate of pathogen detection in people living with HIV with a CNS infection was significantly higher with mNGS than with conventional methods (93.8% vs. 15.0%, p < 0.001).

CONCLUSION: CSF microbiome profiles differ between patients living with and without HIV with suspected CNS infection. mNGS is a powerful tool for the diagnosis of CNS infection among people living with HIV, especially in those with mixed infections.

RevDate: 2024-03-22

Włodarczyk R, Drzewińska-Chańko J, Kamiński M, et al (2024)

Stopover habitat selection drives variation in the gut microbiome composition and pathogen acquisition by migrating shorebirds.

FEMS microbiology ecology pii:7633434 [Epub ahead of print].

Long-distance host movements play a major regulatory role in shaping microbial communities of their digestive tract. Here, we studied gut microbiota composition during seasonal migration in five shorebird species (Charadriiformes) that use different migratory (stopover) habitats. Our analyses revealed significant interspecific variation in both composition and diversity of gut microbiome, but the effect of host identity was weak. A strong variation in gut microbiota was observed between coastal and inland (dam reservoir and river valley) stopover habitats within species. Comparisons between host age classes provided support for an increasing alpha diversity of gut microbiota during ontogeny and an age-related remodeling of microbiome composition. There was, however, no correlation between microbiome and diet composition across study species. Finally, we detected high prevalence of avian pathogens, which may cause zoonotic disease in humans (e.g. Vibrio cholerae) and we identified stopover habitat as one of the major axes of variation in the bacterial pathogen exposure risk in shorebirds. Our study not only sheds new light on ecological processes that shape avian gut microbiota, but also has implications for our better understanding of host-pathogen interface and the role of birds in long-distance transmission of pathogens.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Phimister FD, Anderson RC, Thomas DG, et al (2024)

Using meta-analysis to understand the impacts of dietary protein and fat content on the composition of fecal microbiota of domestic dogs (Canis lupus familiaris): A pilot study.

MicrobiologyOpen, 13(2):e1404.

The interplay between diet and fecal microbiota composition is garnering increased interest across various host species, including domestic dogs. While the influence of dietary macronutrients and their associated microbial communities have been extensively reviewed, these reviews are descriptive and do not account for differences in microbial community analysis, nor do they standardize macronutrient content across studies. To address this, a meta-analysis was performed to assess the impact of dietary crude protein ("protein") and dietary crude fat ("fat") on the fecal microbiota composition in healthy dogs. Sixteen publications met the eligibility criteria for the meta-analysis, yielding a final data set of 314 dogs. Diets were classed as low, moderate, high, or supra in terms of protein or fat content. Sequence data from each publication were retrieved from public databases and reanalyzed using consistent bioinformatic pipelines. Analysis of community diversity indices and unsupervised clustering of the data with principal coordinate analysis revealed a small effect size and complete overlap between protein and fat levels at the overall community level. Supervised clustering through random forest analysis and partial least squares-discriminant analysis indicated alterations in the fecal microbiota composition at a more individual taxonomic level, corresponding to the levels of protein or fat. The Prevotellaceae Ga6A1 group and Enterococcus were associated with increasing levels of protein, while Allobaculum and Clostridium sensu stricto 13 were associated with increasing levels of fat. Interestingly, the random forest analyses revealed that Sharpea, despite its low relative abundance in the dog's fecal microbiome, was primarily responsible for the separation of the microbiome for both protein and fat. Future research should focus on validating and understanding the functional roles of these relatively low-abundant genera.

RevDate: 2024-03-25

Zhou Y, Qin Y, Ma J, et al (2024)

Heat-killed Prevotella intermedia promotes the progression of oral squamous cell carcinoma by inhibiting the expression of tumor suppressors and affecting the tumor microenvironment.

Experimental hematology & oncology, 13(1):33.

BACKGROUND: Oral microbial dysbiosis contributes to the development of oral squamous cell carcinoma (OSCC). Our previous study showed that Prevotella intermedia (P. intermedia) were enriched in the oral mucosal surface, plaque, and saliva of patients with OSCC. Intratumoral microbiome could reshape the immune system and influence the development of various tumors. However, the invasion status of human OSCC tissues by P. intermedia and the pathway through which intratumoral P. intermedia potentiates tumor progression remain unexplored.

METHODS: P. intermedia in human OSCC or normal tissues was detected by FISH. A mouse OSCC cell line SCC7 was adopted to investigate the effects of heat-killed P. intermedia treatment on cell proliferation, invasion, and cytokine release by using CCK-8 assay, transwell invasion assay and ELISA. Moreover, we established a mouse transplanted tumor model by using SCC7 cells, injected heat-killed P. intermedia into tumor tissues, and investigated the effects of heat-killed P. intermedia on tumor growth, invasion, cytokine levels, immune cell infiltrations, and expression levels by using gross observation, H&E staining, ELISA, immunohistochemistry, mRNA sequencing, and transcriptomic analysis.

RESULTS: Our results indicated that P. intermedia were abundant in OSCC and surrounding muscle tissues. Heat-killed P. intermedia promoted SCC7 cell proliferation, invasion and proinflammatory cytokine secretions, accelerated transplanted tumor growth in mice, exacerbate muscle and perineural invasion of OSCC, elevated the serum levels of IL-17A, IL-6, TNF-α, IFN-γ, and PD-L1, induced Treg cells M2 type macrophages in mouse transplanted tumors. The data of transcriptomic analysis revealed that heat-killed P. intermedia increased the expression levels of inflammatory cytokines and chemokines while reduced the expression levels of some tumor suppressor genes in mouse transplanted tumors. Additionally, IL-17 signaling pathway was upregulated whereas GABAergic system was downregulated by heat-killed P. intermedia treatment.

CONCLUSIONS: Taken together, our results suggest that P. intermedia could inhibit the expression of tumor suppressors, alter the tumor microenvironment, and promote the progression of OSCC.

RevDate: 2024-03-25
CmpDate: 2024-03-25

van de Wouw M, Wang Y, Workentine ML, et al (2024)

Cluster-specific associations between the gut microbiota and behavioral outcomes in preschool-aged children.

Microbiome, 12(1):60.

BACKGROUND: The gut microbiota is recognized as a regulator of brain development and behavioral outcomes during childhood. Nonetheless, associations between the gut microbiota and behavior are often inconsistent among studies in humans, perhaps because many host-microbe relationships vary widely between individuals. This study aims to stratify children based on their gut microbiota composition (i.e., clusters) and to identify novel gut microbiome cluster-specific associations between the stool metabolomic pathways and child behavioral outcomes.

METHODS: Stool samples were collected from a community sample of 248 typically developing children (3-5 years). The gut microbiota was analyzed using 16S sequencing while LC-MS/MS was used for untargeted metabolomics. Parent-reported behavioral outcomes (i.e., Adaptive Skills, Internalizing, Externalizing, Behavioral Symptoms, Developmental Social Disorders) were assessed using the Behavior Assessment System for Children (BASC-2). Children were grouped based on their gut microbiota composition using the Dirichlet multinomial method, after which differences in the metabolome and behavioral outcomes were investigated.

RESULTS: Four different gut microbiota clusters were identified, where the cluster enriched in both Bacteroides and Bifidobacterium (Ba2) had the most distinct stool metabolome. The cluster characterized by high Bifidobacterium abundance (Bif), as well as cluster Ba2, were associated with lower Adaptive Skill scores and its subcomponent Social Skills. Cluster Ba2 also had significantly lower stool histidine to urocanate turnover, which in turn was associated with lower Social Skill scores in a cluster-dependent manner. Finally, cluster Ba2 had increased levels of compounds involved in Galactose metabolism (i.e., stachyose, raffinose, alpha-D-glucose), where alpha-D-glucose was associated with the Adaptive Skill subcomponent Daily Living scores (i.e., ability to perform basic everyday tasks) in a cluster-dependent manner.

CONCLUSIONS: These data show novel associations between the gut microbiota, its metabolites, and behavioral outcomes in typically developing preschool-aged children. Our results support the concept that cluster-based groupings could be used to develop more personalized interventions to support child behavioral outcomes. Video Abstract.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Du J, Khemmani M, Halverson T, et al (2024)

Cataloging the phylogenetic diversity of human bladder bacterial isolates.

Genome biology, 25(1):75.

BACKGROUND: Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge of the microbiota of other anatomical sites, such as the gut and oral cavity.

RESULTS: To facilitate genomic, functional, and experimental analyses of the human bladder microbiota, we present a bladder-specific bacterial isolate reference collection comprising 1134 genomes, primarily from adult females. These genomes were culled from bacterial isolates obtained by a metaculturomic method from bladder urine collected by transurethral catheterization. This bladder-specific bacterial isolate reference collection includes 196 different species, including representatives of major aerobes and facultative anaerobes, as well as some anaerobes. It captures 72.2% of the genera found when re-examining previously published 16S rRNA gene sequencing of 392 adult female bladder urine samples. Comparative genomic analysis finds that the taxonomies and functions of the bladder microbiota share more similarities with the vaginal microbiota than the gut microbiota. Whole-genome phylogenetic and functional analyses of 186 bladder Escherichia coli isolates and 387 gut Escherichia coli isolates support the hypothesis that phylogroup distribution and functions of Escherichia coli strains differ dramatically between these two very different niches.

CONCLUSIONS: This bladder-specific bacterial isolate reference collection is a unique resource that will enable bladder microbiota research and comparison to isolates from other anatomical sites.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Tang Y, Nie H, Zhang Y, et al (2024)

Effects of Sjogren's syndrome and high sugar diet on oral microbiome in patients with rampant caries: a clinical study.

BMC oral health, 24(1):361.

OBJECTIVE: The purpose of this study was to assess the composition of the oral microbial flora of adults with rampant caries in China to provide guidance for treatment.

PATIENTS AND METHODS: Sixty human salivary and supragingival plaque samples were collected. They were characterized into four groups: patients with rampant caries with Sjogren's syndrome (RC-SS) or high-sugar diet (RC-HD), common dental caries (DC), and healthy individuals (HP). The 16S rRNA V3-V4 region of the bacterial DNA was detected by Illumina sequencing. PCoA based on OTU with Bray-Curtis algorithm, the abundance of each level, LEfSe analysis, network analysis, and PICRUSt analysis were carried out between the four groups and two sample types. Clinical and demographic data were compared using analysis of variance (ANOVA) or the nonparametric Kruskal-Wallis rank-sum test, depending on the normality of the data, using GraphPad Prism 8 (P < 0.05).

RESULTS: OTU principal component analysis revealed a significant difference between healthy individuals and those with RC-SS. In the saliva of patients with rampant caries, the relative abundance of Firmicutes increased significantly at the phylum level. Further, Streptocpccus, Veillonella, Prevotella, and Dialister increased, while Neisseria and Haemophilus decreased at the genus level. Veillonella increased in the plaque samples of patients with rampant caries.

CONCLUSION: Both salivary and dental plaque composition were significantly different between healthy individuals and patients with rampant caries. This study provides a microbiological basis for exploring the etiology of rampant caries.

CLINICAL RELEVANCE: This study provides basic information on the flora of the oral cavity in adults with rampant caries in China. These findings could serve as a reference for the treatment of this disease.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Hogue T, Hampton-Marcell J, Carroll IM, et al (2024)

Gut microbiota are differentially correlated with blood pressure status in African American collegiate athletes: A pilot study.

Physiological reports, 12(6):e15982.

Hypertension (HTN) is common among athletes and the most recent epidemiologic data reports that cardiovascular (CV) sudden death is significantly greater in African Americans (AAs). Gut microbial dysbiosis (a poorly diverse stool microbial profile) has been associated with HTN in sedentary people but microbial characteristics of athletes with HTN are unknown. Our purpose was to differentiate microbiome characteristics associated with BP status in AA collegiate athletes. Thirty AA collegiate athletes were stratified by normal BP (systolic BP (SBP) ≤130 mmHg; n = 15) and HTN (SBP ≥130 mmHg; n = 15). 16S rRNA gene sequencing was performed on stool samples to identify microbes at the genus level. We did not observe any significant differences in alpha diversity, but beta diversity was different between groups. Principal coordinate analysis was significantly different (PERMANOVA, p < 0.05, R = 0.235) between groups. Spearman rank correlations showed a significant (p < 0.05) correlation between systolic BP and abundances for Adlercreutzia (R = 0.64), Coprococcus (R = 0.49), Granulicatella (R = 0.63), and Veillonella (R = 0.41). Gut microbial characteristics were associated with differentially abundant microbial genus' and BP status. These results will direct future studies to define the functions of these microbes associated with BP in athletes.

RevDate: 2024-03-22

He X, Wang D, Jiang Y, et al (2024)

Heritable microbiome variation is correlated with source environment in locally adapted maize varieties.

Nature plants [Epub ahead of print].

Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbiota interactions in the face of environmental stresses. Here we surveyed 3,168 root and rhizosphere microbiome samples from 129 accessions of locally adapted Zea, sourced from diverse habitats and grown under control and different stress conditions. We quantified stress treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome abundance. Genome-wide association analysis identified host genetic variants linked to both rhizosphere microbiome abundance and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone bacterium Massilia in our controlled experiments and total soil nitrogen in the source environment. Isolation and controlled inoculation of Massilia alone can contribute to root development, whole-plant biomass production and adaptation to low nitrogen availability. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.

RevDate: 2024-03-22

Shen J, Wang M, E Wang (2024)

Exploitation of the microbiome for crop breeding.

Nature plants [Epub ahead of print].

RevDate: 2024-03-25
CmpDate: 2024-03-25

Liu J, Yan Q, Li S, et al (2024)

Integrative metagenomic and metabolomic analyses reveal the potential of gut microbiota to exacerbate acute pancreatitis.

NPJ biofilms and microbiomes, 10(1):29.

Early dysbiosis in the gut microbiota may contribute to the severity of acute pancreatitis (AP), however, a comprehensive understanding of the gut microbiome, potential pathobionts, and host metabolome in individuals with AP remains elusive. Hence, we employed fecal whole-metagenome shotgun sequencing in 82 AP patients and 115 matched healthy controls, complemented by untargeted serum metabolome and lipidome profiling in a subset of participants. Analyses of the gut microbiome in AP patients revealed reduced diversity, disrupted microbial functions, and altered abundance of 77 species, influenced by both etiology and severity. AP-enriched species, mostly potential pathobionts, correlated positively with host liver function and serum lipid indicators. Conversely, many AP-depleted species were short-chain fatty acid producers. Gut microflora changes were accompanied by shifts in the serum metabolome and lipidome. Specifically, certain gut species, like enriched Bilophila wadsworthia and depleted Bifidobacterium spp., appeared to contribute to elevated triglyceride levels in biliary or hyperlipidemic AP patients. Through culturing and whole-genome sequencing of bacterial isolates, we identified virulence factors and clinically relevant antibiotic resistance in patient-derived strains, suggesting a predisposition to opportunistic infections. Finally, our study demonstrated that gavage of specific pathobionts could exacerbate pancreatitis in a caerulein-treated mouse model. In conclusion, our comprehensive analysis sheds light on the gut microbiome and serum metabolome in AP, elucidating the role of pathobionts in disease progression. These insights offer valuable perspectives for etiologic diagnosis, prevention, and intervention in AP and related conditions.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Joseph A, Anton L, Guan Y, et al (2024)

Extracellular vesicles from vaginal Gardnerella vaginalis and Mobiluncus mulieris contain distinct proteomic cargo and induce inflammatory pathways.

NPJ biofilms and microbiomes, 10(1):28.

Colonization of the vaginal space with bacteria such as Gardnerella vaginalis and Mobiluncus mulieris is associated with increased risk for STIs, bacterial vaginosis, and preterm birth, while Lactobacillus crispatus is associated with optimal reproductive health. Although host-microbe interactions are hypothesized to contribute to reproductive health and disease, the bacterial mediators that are critical to this response remain unclear. Bacterial extracellular vesicles (bEVs) are proposed to participate in host-microbe communication by providing protection of bacterial cargo, delivery to intracellular targets, and ultimately induction of immune responses from the host. We evaluated the proteome of bEVs produced in vitro from G. vaginalis, M. mulieris, and L. crispatus, identifying specific proteins of immunologic interest. We found that bEVs from each bacterial species internalize within cervical and vaginal epithelial cells, and that epithelial and immune cells express a multi-cytokine response when exposed to bEVs from G. vaginalis and M. mulieris but not L. crispatus. Further, we demonstrate that the inflammatory response induced by G. vaginalis and M. mulieris bEVs is TLR2-specific. Our results provide evidence that vaginal bacteria communicate with host cells through secreted bEVs, revealing a mechanism by which bacteria lead to adverse reproductive outcomes associated with inflammation. Elucidating host-microbe interactions in the cervicovaginal space will provide further insight into the mechanisms contributing to microbiome-mediated adverse outcomes and may reveal new therapeutic targets.

RevDate: 2024-03-25
CmpDate: 2024-03-25

Maki KA, Crayton CB, Butera G, et al (2024)

Examining the relationship between the oral microbiome, alcohol intake and alcohol-comorbid neuropsychological disorders: protocol for a scoping review.

BMJ open, 14(3):e079823 pii:bmjopen-2023-079823.

INTRODUCTION: Heavy alcohol use and alcohol use disorder (AUD) continues to rise as a public health problem and increases the risk for disease. Elevated rates of anxiety, depression, sleep disruption and stress are associated with alcohol use. Symptoms may progress to diagnosed neurophysiological conditions and increase risk for relapse if abstinence is attempted. Research on mechanisms connecting the gastrointestinal microbiome to neuropsychological disorders through the gut-brain axis is well-established. Less is known how the oral microbiome and oral microbial-associated biomarkers may signal to the brain. Therefore, a synthesis of research studying relationships between alcohol intake, alcohol-associated neurophysiological symptoms and the oral microbiome is needed to understand the state of the current science. In this paper, we outline our protocol to collect, evaluate and synthesise research focused on associations between alcohol intake and AUD-related neuropsychological disorders with the oral microbiome.

METHODS AND ANALYSIS: The search strategy was developed and will be executed in collaboration with a medical research librarian. Studies will be screened by two independent investigators according to the aim of the scoping review, along with the outlined exclusion and inclusion criteria. After screening, data will be extracted and synthesised from the included papers according to predefined demographic, clinical and microbiome methodology metrics.

ETHICS AND DISSEMINATION: A scoping review of primary sources is needed to synthesise the data on relationships between alcohol use, neuropsychological conditions associated with AUD and the oral microbiome. The proposed scoping review is based on the data from publicly available databases and does not require ethical approval. We expect the results of this synthesis will identify gaps in the growing literature and highlight potential mechanisms linking the oral-brain axis to addiction and other associated neuropsychological conditions. The study findings and results will be disseminated through journals and conferences related to psychology, neuroscience, dentistry and the microbiome.

RevDate: 2024-03-24

Morgan AE, MT Mc Auley (2024)

Vascular dementia: From pathobiology to emerging perspectives.

Ageing research reviews, 96:102278 pii:S1568-1637(24)00096-5 [Epub ahead of print].

Vascular dementia (VaD) is the second most common type of dementia. VaD is synonymous with ageing, and its symptoms place a significant burden on the health and wellbeing of older people. Despite the identification of a substantial number of risk factors for VaD, the pathological mechanisms underpinning this disease remain to be fully elucidated. Consequently, a biogerontological imperative exists to highlight the modifiable lifestyle factors which can mitigate against the risk of developing VaD. This review will critically examine some of the factors which have been revealed to modulate VaD risk. The survey commences by providing an overview of the putative mechanisms which are associated with the pathobiology of VaD. Next, the factors which influence the risk of developing VaD are examined. Finally, emerging treatment avenues including epigenetics, the gut microbiome, and pro-longevity pharmaceuticals are discussed. By drawing this key evidence together, it is our hope that it can be used to inform future experimental investigations in this field.

RevDate: 2024-03-21

Wang Z, Bergemann CM, Simonin M, et al (2024)

Interactions shape aquatic microbiome responses to Cu and Au nanoparticle treatments in wetland manipulation experiments.

Environmental research pii:S0013-9351(24)00507-3 [Epub ahead of print].

In natural systems, organisms are embedded in complex networks where their physiology and community composition is shaped by both biotic and abiotic factors. Therefore, to assess the ecosystem-level effects of contaminants, we must pair complex, multi-trophic field studies with more targeted hypothesis-driven approaches to explore specific actors and mechanisms. Here, we examine aquatic microbiome responses to long-term additions of commercially-available metallic nanoparticles [copper-based (CuNPs) or gold (AuNPs)] and/or nutrients in complex, wetland mesocosms over 9 months, allowing for a full growth cycle of the aquatic plants. We found that both CuNPs and AuNPs (but not nutrient) treatments showed shifts in microbial communities and populations largely at the end of the experiment, as the aquatic plant community senesced. we examine aquatic microbiomes under chronic dosing of NPs and nutrients Simplified microbe-only or microbe + plant incubations revealed that direct effects of AuNPs on aquatic microbiomes can be buffered by plants (regardless of seasonal As mesocosms were dosed weekly, the absence of water column accumulation indicates the partitioning of both metals into other environmental compartments, mainly the floc and aquatic plants photosynthetically-derived organic matter. Overall, this study identifies the potential for NP environmental impacts to be either suppressed by or propagated across trophic levels via the presence of primary producers, highlighting the importance of organismal interactions in mediating emerging contaminants' ecosystem-wide impacts.

RevDate: 2024-03-21

Kim TS, Ikeuchi T, Theofilou VI, et al (2024)

Epithelial-derived interleukin-23 promotes oral mucosal immunopathology.

Immunity pii:S1074-7613(24)00096-7 [Epub ahead of print].

At mucosal surfaces, epithelial cells provide a structural barrier and an immune defense system. However, dysregulated epithelial responses can contribute to disease states. Here, we demonstrated that epithelial cell-intrinsic production of interleukin-23 (IL-23) triggers an inflammatory loop in the prevalent oral disease periodontitis. Epithelial IL-23 expression localized to areas proximal to the disease-associated microbiome and was evident in experimental models and patients with common and genetic forms of disease. Mechanistically, flagellated microbial species of the periodontitis microbiome triggered epithelial IL-23 induction in a TLR5 receptor-dependent manner. Therefore, unlike other Th17-driven diseases, non-hematopoietic-cell-derived IL-23 served as an initiator of pathogenic inflammation in periodontitis. Beyond periodontitis, analysis of publicly available datasets revealed the expression of epithelial IL-23 in settings of infection, malignancy, and autoimmunity, suggesting a broader role for epithelial-intrinsic IL-23 in human disease. Collectively, this work highlights an important role for the barrier epithelium in the induction of IL-23-mediated inflammation.

LOAD NEXT 100 CITATIONS

ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @ gmail.com

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin and even a collection of poetry — Chicago Poems by Carl Sandburg.

Timelines

ESP now offers a large collection of user-selected side-by-side timelines (e.g., all science vs. all other categories, or arts and culture vs. world history), designed to provide a comparative context for appreciating world events.

Biographies

Biographical information about many key scientists (e.g., Walter Sutton).

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )