Search Results (102)

CrAssphage, a bacteriophage that infects human gut-associated Bacteroides spp., has emerged as a potential anthropogenic fecal pollution indicator in environmental matrices. This study investigated the presence and concentration of crAssphages in bivalve mollusks (oysters and mussels) marketed in three cities in the state of Rio de Janeiro, Brazil, sampled from January to December 2022. CrAssphages were detected during the study period in 66.7% (48/72) of sampled oysters and 54.8% (34/62) of sampled mussels, at median concentrations of 1.9 × 10⁴ and 4.2 × 10⁴ genome copies (GC)/g, respectively. These levels were 1–2 log₁₀ higher than those observed for major human enteric viruses, including norovirus genogroups GI and GII, sapovirus, human mastadenovirus (HAdV), rotavirus A, human astrovirus (HAstV), and hepatitis A virus. CrAssphage specificity and sensitivity were calculated for all viruses. Moderate correlations between crAssphage (log₁₀ GC/g) and norovirus GI and GII, HAdV, SaV, and HAstV (Spearman’s rho = 0.581–0.464, p < 0.001) were observed in mussels. Altogether, the data support the use of crAssphage as a molecular indicator of human viral contamination in shellfish, with potential application in routine environmental and food safety monitoring in production areas. Full article

FP is a detrimental behavior for chickens, ducks, and geese associated with numerous physiological and neurobiological characteristics, which have been identified in many species as regulated by the gut microbiota. However, it is unknown whether and how gut microbiota influences FP by regulating neurotransmitter systems in geese. This study aimed to investigate the phenotypic correlation between feather pecking and changes in physiological, neurobiological, and gut microbiota profiles in gosling. Three behavioral phenotypes were observed in goslings, including severe feather peckers (SFPs), victims of SFPs, and non-peckers (NFPs). The significantly lower feather scores and body weights were observed in victims compared to both SFPs and NFPs (p < 0.05). Regarding the physiological phenotype, victims had higher dopamine (DA) levels than NFPs, and SFPs had lower 5-hydroxytryptamine (5-HT) in the serum than NFPs (p < 0.001), with intermediate 5-HT levels in victims. Victims had lower glutathione peroxidase (GSH-Px) compared to SFPs and NFPs (p < 0.05). Moreover, higher mRNA expression levels of HTR1A, SLC6A4, and TPH2 in the 5-HT metabolic pathway were detected in NFPs than those in SFPs and victims (p < 0.05). In addition, regarding gut microbiota measured by 16S rRNA sequencing, SFPs had lower diversity and comparable cecal microbiota compared to victims and NFPs. Proteobacteria, Verrucomicrobia, Ruminococcus spp., and Bilophila spp. were enriched in SFPs, while Bacteroides and Parabacteroides were enriched in NFPs. From the predicted bacterial functional genes, the cAMP signaling pathway, cGMP–PKG signaling pathway, and pyruvate metabolism were activated in SFPs. The correlation analysis revealed that the genera Bacteroides spp. were associated with differences in 5-HT metabolism between the SFPs and NFPs. In summary, differences in the cecal microbiota profile and 5-HT metabolism drive FP phenotypes, which could be associated with the reduced gut abundance of the genera Bacteroides spp. Full article

Background and Objectives: Rectal cancer management increasingly relies on watch-and-wait strategies after neoadjuvant chemoradiotherapy (nCRT). Accurate, non-invasive prediction of pathological complete response (pCR) remains elusive. Emerging evidence suggests that gut-microbiome composition modulates radio-chemosensitivity. We systematically reviewed primary studies that correlated baseline or on-treatment gut-microbiome features with nCRT response in locally advanced rectal cancer (LARC). Methods: MEDLINE, Embase and PubMed were searched from inception to 30 April 2025. Eligibility required (i) prospective or retrospective human studies of LARC, (ii) faecal or mucosal microbiome profiling by 16S, metagenomics, or metatranscriptomics, and (iii) response assessment using tumour-regression grade or pCR. Narrative synthesis and random-effects proportion meta-analysis were performed where data were homogeneous. Results: Twelve studies (n = 1354 unique patients, median sample = 73, range 22–735) met inclusion. Four independent machine-learning models achieved an Area Under the Receiver Operating Characteristic curve AUROC ≥ 0.85 for pCR prediction. Consistently enriched taxa in responders included Lachnospiraceae bacterium, Blautia wexlerae, Roseburia spp., and Intestinimonas butyriciproducens. Non-responders showed over-representation of Fusobacterium nucleatum, Bacteroides fragilis, and Prevotella spp. Two studies linked butyrate-producing modules to radiosensitivity, whereas nucleotide-biosynthesis pathways conferred resistance. Pooled pCR rate in patients with a “butyrate-rich” baseline profile was 44% (95% CI 35–54) versus 21% (95% CI 15–29) in controls (I² = 18%). Conclusions: Despite heterogeneity, convergent functional and taxonomic signals underpin a microbiome-based radiosensitivity axis in LARC. Multi-centre validation cohorts and intervention trials manipulating these taxa, such as prebiotics or live-biotherapeutics, are warranted before clinical deployment. Full article

Background/Objectives: Emerging evidence suggests that gut microbiota composition is influenced by both age and sex and may contribute to dementia-related brain pathologies. However, comprehensive microbiome-based biomarker discovery stratified by these factors remains limited. Methods: We performed a metagenomic analysis of the gut microbiota of participants stratified by sex (female vs. male) and age (<75 vs. ≥75 years). Alpha diversity (observed operational taxonomic unit, Chao1, Shannon, and Simpson) and linear discriminant analysis effect size analyses were conducted to identify dominant taxa associated with Alzheimer’s pathology, vascular pathology, and dementia-related structural brain changes. Results: Females and non-elderly participants (aged < 75 years) exhibited higher gut microbial diversity, characterized by an increased abundance of Bifidobacterium spp. and Blautia spp., whereas males and elderly participants (aged ≥ 75 years) exhibited increased levels of Bacteroides spp. and Bacteroidia, which have been associated with inflammation and dysbiosis. Several taxa, including Bifidobacterium spp. were consistently identified as potential protective biomarkers, while Bacteroides spp. was linked to a higher risk of dementia-related brain pathologies. Conclusions: Our findings demonstrate distinct age- and sex-specific differences in gut microbiota composition that may be closely associated with the pathophysiology of dementia-related brain pathologies. These results demonstrate that gut microbiota may serve as potential biomarkers for monitoring cerebrovascular conditions, potentially contributing to the development of personalized therapeutic strategies. Full article

Background/Objectives: Antibiotics have a significant impact on the gut microbiota, and we hypothesized that human milk oligosaccharides may alleviate antibiotic-induced gut microbiota dysbiosis. Methods: Six groups of eight mice were administered drinking water with or without ampicillin for one week. We then introduced the human milk oligosaccharide 2′-fucosyllactose (2′FL), either alone or in combination with difucosyl-lactose (DFL), for two weeks after the termination of ampicillin treatment. Results: Ampicillin reduced microbiota diversity and the abundance of specific bacteria. One week after the termination of ampicillin treatment, the 2′FL + DFL mixture counteracted the ampicillin-induced reduction in diversity, although this effect was not sustained. Over the subsequent two weeks, the 2′FL + DFL mixture had a significant impact on the relative abundances of Lactobacillus spp. and Bacteroides spp. Ampicillin also reduced caecal propionate levels, downregulated the gene Gzmb for Granzyme B, and upregulated the gene Reg3a for Regenerating islet-derived protein 3 alpha, all of which were counteracted by the 2′FL + DFL mixture. Ampicillin had a minor impact on ileal cytokine levels. The 2′FL + DFL mixture showed a cytokine effect indicating reduced adaptive and innate inflammation. Ampicillin reduced water intake and growth in the mice. The oligosaccharides did not affect water intake, but the 2′FL + DFL mixture slightly reduced body weight. Conclusions: The 2′FL + DFL mixture appears to hold potential for counteracting some of the side effects of ampicillin treatment. Full article

Protein hydrolysates positively affect intestinal function in both humans and animals, but their impact on gut health and the gut microbial profile in cats has not been thoroughly investigated. In this study, a total of 30 adult cats were randomly assigned to one of three dietary treatments for a 60-day feeding trial. The three dietary treatments were as follows: (1) basal diet (CON), (2) diet containing 15% powdered chicken protein hydrolysate (HP15%), and (3) diet containing 15% liquid chicken protein hydrolysate (HL15%). Compared to the CON group, the HP15% group had a decreased calprotectin levels and fecal gases emissions (p < 0.05). A higher abundance of Bacteroidota, Veillonellaceae, and Bacteroidaceae, while a lower abundance of Firmicutes was showed in the HL15% group than that in the CON group (p < 0.05). At the genus level, compared with the CON group, an increased abundance of Bacteroides spp. and Bifidobacterium spp. was showed, whereas a reduced abundance of Alloprevotella spp. was presented in the HP15% and HL15% groups (p < 0.05). The metabolomic analysis revealed 1405 distinct metabolites between the HP15% and CON groups (p < 0.05, VIP-pred-OPLS-DA > 1), and the level of cholic acid decreased while the level of isodeoxycholic acid increased in the HP15% group (p < 0.05). The metabolomic analysis revealed 1910 distinct metabolites between the HL15% and CON groups (p < 0.05, VIP-pred-OPLS-DA > 1), and the levels of 4-coumaryl alcohol and enterolactone increased in the HL15% group (p < 0.05). In summary, this study suggested that partially replacing chicken meat with chicken protein hydrolysate in the diet of cats helps regulate the gut microbial community and metabolite profile and improves intestinal health. Full article

The effects of high-dose glucocorticoids on the gastrointestinal microbiota of healthy dogs are unknown. This study’s aim was to investigate the effects of immunosuppressive doses of prednisone on the fecal microbiota and the gastric and duodenal mucosal microbiota in healthy dogs. Twelve healthy adult dogs were enrolled into a randomized, double-blinded, placebo-controlled trial. Dogs were evaluated on days 0, 14, and 28 following treatments with either prednisone (2 mg/kg/d) or placebo. Outcome measures included (1) composition and abundance of the fecal microbiota (via high-throughput sequencing of the 16S rRNA gene and qPCR-based dysbiosis index [DI]) and (2) spatial distribution of the gastric and duodenal mucosal microbiota using fluorescence in situ hybridization (FISH). No significant difference in alpha and beta diversity or amplicon sequence variants of the fecal microbiota was observed between treatment groups. Blautia spp. concentrations via qPCR were significantly decreased between prednisone group timepoints 2 and 3. Compared to placebo group dogs, prednisone group dogs showed significantly increased gastric mucosal helicobacters and increased mucosal-associated total bacteria and Bacteroides in duodenal biopsies over the treatment period. The results indicate that immunosuppressive dosages of prednisone alter the mucosal microbiota of healthy dogs in a time-dependent manner, which may disrupt mucosal homeostasis. This report is significant, since it addresses a knowledge gap in our understanding of the effects of glucocorticoids on the gastrointestinal mucosal microbiota of healthy dogs. Full article

Background: Previous work has shown that the mostly beneficial modulation of intestinal microbiota generally found with legume-based diets is likely to be due, at least in part, to their constituent protein components. Objectives: The faecal microbiota composition was studied in rats fed diets differing only in their constituent proteins. Methods: Rats (n = 10/group) were fed for 28 days diets based in milk [(lactalbumin (LA), casein (CAS)], or white lupin (Lupinus albus) protein isolate (LPI). Results: Significant differences among the three groups in bacteria composition and functionality were found by both qPCR and Illumina sequencing analysis. Significant (p < 0.01) differences were found by ANOSIM and Discriminant Analysis among groups at the family, genus and species levels in both microbiota composition and functionality. A number of groups able to explain the differences between animal (casein, lactalbumin) and lupin proteins were revealed by LEfSe and PCA analysis. Specifically, feeding the CAS diet resulted in lower Bifidobacteria and Lactobacilli compared to the other diets, and the LPI diet gave place to lower Enterobacteria than CAS, and lower Escherichia/Shigella than LA and CAS. Differences in the LA group were attributable to Bifidobacterium spp., Collinsella spp. (in particular C. stercoris), Bacteroides spp., Eubacterium spp. (in particular E. dolichum), Roseburia spp. (in particular R. faecis), and Oscillospira spp. In the case of the CAS group, the organisms were Parabacteroides spp., Blautia spp., Enterobacteriaceae spp., Turicibacter spp., species from Christenellaceae, species from Alphaproteobacteria and Mogibacteriaceae, Coprobacillus spp. and Dorea spp. In the case of the LPI group, the organisms were Lactobacillus spp. (Lactobacillus spp. and L. reuteri), species from Clostridiaceae, species from Peptostreptococcaceae, species from Erysipelotrichaceae, and Adlercreutzia spp. Conclusions: Based on the results obtained, LPI is likely to beneficially modulate the intestinal microbiota composition in rats. Additionally, LA-based diet was associated to a healthier microbiota composition than CAS, although the CAS diet also modulated the intestinal microbiota to a composition compatible with improved bowel movement frequency and lipid metabolism. Full article

Ruminants rely on the rumen for the anaerobic fermentation of fibrous plant materials, facilitated by a complex microbial community of bacteria, archaea, fungi, and ciliates. Among them, ruminal ciliates significantly influence ruminal fermentation, methane production, nitrogen utilization efficiency, and microbial interactions. This study examined the impact of ciliate inoculation on ruminal fermentation, microbial composition, and functional profiles in fauna-free conditions. Six treatments were tested: control (no ciliates), small entodinia, Epidinium spp., isotrichids, Ophryoscolex spp., and a mixed inoculum. Using QIIME2 to analyze 16S rRNA gene sequences, the study revealed group-specific effects on methane production, volatile fatty acids (VFAs), and microbial diversity. Small entodinia inoculation increased Streptococcus abundance, while isotrichids enriched Megasphaera, enhancing butyrate production. Alpha diversity indices indicated reduced richness in the ciliate-inoculated groups, reflecting predation on prokaryotes. Beta diversity showed distinct microbial and functional profiles among the treatments. Functional analysis highlighted elevated glycerolipid metabolism in isotrichid groups, associated with Bacteroides and Megasphaera, suggesting roles in lipid metabolism and oxidative stress resistance. Despite limited ciliate cell counts, the study emphasizes ciliate-specific interactions and the role of lactic acid-associated bacteria in shaping ruminal fermentation. Full article

Severe COVID-19 and MIS-C are rare but serious outcomes associated with SARS-CoV-2 infection. The onset of MIS-C often involves the gastrointestinal system, suggesting a potential connection with gut microbiota. This study aims to compare the gut microbiota of children with severe COVID-19 and those with MIS-C using various biomolecular approaches. Gut microbiota composition and specific microbial modulations were analyzed using fecal samples collected at hospital admission. The study included hospitalized patients (mean age 6 ± 5 years) diagnosed with severe COVID-19 (37 patients) or MIS-C (37 patients). Microbial differences were assessed using both NGS and qRT-PCR methodologies. In 75% of cases, pharmacological treatments included antibiotics and corticosteroids, which influenced the microbiota composition. Early age was found to have the most significant impact on microbiota diversity. Significant differences in alpha and beta diversity were observed between COVID-19 and MIS-C patients, particularly concerning low-abundance species. Levels of Bacteroides spp., Bifidobacterium spp., and Akkermansia muciniphila were comparable between groups, while an increased activity of Bifidobacterium spp. was noted in children with positive fecal samples (p = 0.019). An in-depth evaluation of lesser-known gut species may be key to reducing the risk of severe outcomes and developing microbiota-based biomarkers for the early diagnosis of MIS-C. Full article

The progression of chronic obstructive pulmonary disease (COPD) is characterized by functional changes in the airways. The lung–gut axis and gut microbiota (GM) have been linked to the pathophysiology of airway diseases. Regarding COPD, studies have shown that GM alterations could be related the stages of this disease. However, the relationship between GM and clinical, biochemical and immunological parameters in patients with COPD are not well understood. The aim of this study was to compare the relative abundance of specific groups of beneficial gut bacteria between COPD patients and healthy controls (CTLs) in order to evaluate relationships with metabolic and inflammatory markers in COPD. Methods: We included 16 stable COPD patients and 16 healthy volunteer CTLs. The relative abundances of Bifidobacterium spp. (Bf) and Akkermansia muciniphila (Akk) bacteria and the Bacteroidetes and Firmicutes phyla were assessed by qPCR. Pulmonary function was evaluated by spirometry, biochemical parameters by colorimetric methods and plasma cytokine levels by cytometric bead array analysis. Results: The Firmicutes/Bacteroides ratio was related to emergency hospital visits and six-minute walk test (6MWT) results. Furthermore, the relative abundance of Bf was associated with plasma concentrations of glucose, triglycerides, HDL-C and IL-10. In addition, Firmicutes levels and the Firmicutes/Bacteroidetes ratio were associated with the IL-12/IL-10 ratio, while Akk abundance was linked to IL-12 levels. Conclusions: The present findings suggest that the abundance of beneficial bacteria in the GM could influence clinical presentation and immunoregulation in COPD. Full article

Periodontitis is a serious gum infection that damages the soft tissue and destroys the bone supporting the teeth. The aim of the study was to investigate the microbiota using traditional microbiology plating and metagenomic sequencing of extracted tooth alveoli in dogs with severe periodontitis. Isolation of culturable microorganisms was performed as part of bacteriological testing to provide bacteriological diagnosis to veterinary surgeons. Metagenomic sequencing was performed using shotgun sequencing on the Illumina HiSeq system platform. The most prevalent species at sites of periodontal infection detected by metagenomic sequencing were Porphyromonas gulae, Prevotella spp., Tannerella forsythia, Porphyromonas crevioricanis, Porphyromonas cangingivalis, and Bacteroides heparinolyticus. Pasteurella, Streptococcus, and Neisseria were the most frequently isolated culturable bacteria from infected sites detected by traditional microbiologic methods. Metagenomic data revealed that these three genera accounted for only 1.6% of all microbiota at the sites of infection. Antimicrobial resistance patterns of the isolated bacteria included resistance to ampicillin, doxycycline, sulfamethoxazole-trimethoprim, ciprofloxacin, colistin, cefotaxime, and chloramphenicol. Antimicrobial-resistant genes detected using shotgun sequencing also showed resistance to aminoglycosides and macrolides. Dogs with periodontal infections carry bacteria that can cause bite infections in humans as well as multi-resistant isolates. Therefore, treatment and prophylaxis or periodontal disease of dogs is important from a One Health perspective. Full article

Ethanol extracts obtained from 13 poplar propolis samples originating from various European countries by traditional maceration were tested for total polyphenols, flavonoid content, and antioxidant activity. Moreover, the content of 18 polyphenolic compounds (from the group of phenolic acids and flavonoids) was determined using the HPLC method. The inhibitory effect of six selected extracts with the highest activity was assessed by well-diffusion method against five strains (Bifidobacterium spp., L. rhamnosus, L. acidophilus, E. coli, and Bacteroides spp.) of intestinal bacteria self-isolated from the faeces of obese probands with the use of selective media. It was found that the antioxidant activity of propolis varied depending on geographical origin and even among samples from the same region, which indicates that some other factors also influence propolis quality. The samples of different geographical origin varied mainly in the share of individual phenolic compounds, and it was not possible to find a characteristic marker of origin, excluding the galangin present in the Polish samples only. Assessing the inhibitory activity of propolis (in the range of 70 mg to 10 µg per mL) indicated that the concentration of 100 µg/mL was found as being safe for tested fecal bacteria (Bifidobacterium spp., L. rhamnosus, L. acidophilus, E. coli, and Bacteroides spp.). As no negative effect of low doses of propolis on the intestinal microflora was found, it can be suggested that its use in recommended doses brings only beneficial effects to the body. Full article

In the present study, four Bacteroides species that could degrade Fuzhuan brick tea polysaccharide-3 (FBTPS-3) were isolated from human feces and identified to be Bacteroides ovatus, B. uniformis, B. fragilis and B. thetaiotaomicron. The four Bacteroides species showed growth on FBTPS-3 as the carbon source, and B. ovatus showed the best capability for utilizing FBTPS-3 among the four species since B. ovatus could utilize more FBTPS-3 during 24 h fermentation. Moreover, the four Bacteroides species could metabolize FBTPS-3 and promote the production of acetic, propionic and isovaleric acids. Transcriptome analysis of B. ovatus revealed that 602 genes were up-regulated by FBTPS-3, including two carbohydrate-active enzyme clusters and four polysaccharide utilization loci (PULs). The PUL 1 contained GH28 family that could hydrolyze rhamnogalacturonan and other pectic substrates, which was in line with our previous work that rhamnose and galacturonic acid were the main component monosaccharides of FBTPS-3. Collectively, the results suggested that FBTPS-3 could be utilized by Bacteroides spp., and it might be developed as a promising prebiotic targeting Bacteroidetes in intestinal environment. Full article

The effects of gut microbiota on the association between carbohydrate intake during pregnancy and neonatal low birth weight (LBW) were investigated. A prospective cohort study was conducted with 257 singleton-born mother–child pairs in Taiwan, and maternal dietary intake was estimated using a questionnaire, with each macronutrient being classified as low, medium, or high. Maternal fecal samples were collected between 24 and 28 weeks of gestation, and gut microbiota composition and diversity were profiled using 16S rRNA amplicon gene sequencing. Carbohydrates were the major source of total energy (56.61%), followed by fat (27.92%) and protein (15.46%). The rate of infant LBW was 7.8%, which was positively correlated with maternal carbohydrate intake. In the pregnancy gut microbiota, Bacteroides ovatus and Dorea spp. were indirectly and directly negatively associated with fetal growth, respectively; Rosenburia faecis was directly positively associated with neonatal birth weight. Maternal hypertension during pregnancy altered the microbiota features and was associated with poor fetal growth. Microbiota-accessible carbohydrates can modify the composition and function of the pregnancy gut microbiota, thus providing a potential marker to modulate deviations from dietary patterns, particularly in women at risk of hypertension during pregnancy, to prevent neonatal LBW. Full article