16S rRNA Gene Sequence Research Articles

Pseudonocardia spirodelae sp. nov., isolated from duckweed and formal proposal to reclassify Pseudonocardia antarctica as a later heterotypic synonym of Pseudonocardia alni and reclassify Pseudonocardia carboxydivorans as Pseudonocardia alni subsp. carboxydivorans.

A novel Pseudonocardia strain DW16-2T, isolated from duckweed (Spirodela polyrhiza), was taxonomically studied in detail. The analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to Pseudonocardia carboxydivorans Y8T (98.8%), followed by Pseudonocardia tropica YIM 61452T (98.7%), Pseudonocardia antarctica DVS 5a1T (98.7%) and Pseudonocardia alni DSM 44104T (98.7%). The average nucleotide identity (ANI) based on blast and digital DNA-DNA hybridization (dDDH) relatedness values between strain DW16-2T and their closest type strains were below the threshold values for identifying a novel species. Morphological, physiological and chemotaxonomic features of strain DW16-2T were typical for the genus Pseudonocardia by forming extensively branched substrate mycelium and aerial mycelium that fragmented into rod-shaped spore, with a smooth surface. The whole-cell hydrolysates of strain DW16-2T contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were arabinose, galactose, glucose and a trace amount of ribose. The polar lipids contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified phospholipids. The menaquinone (MK) was MK-8(H4). The cellular fatty acids (>5 %) were iso-C16 : 0, iso-C16 : 1 H, summed feature 3: C16 : 1 ω7c/C16 : 1 ω6c; C16 : 1 ω6c/C16 : 1 ω7c, C17 : 1 ω8c and anteiso-C17 : 0. Characterization based on chemotaxonomic, phenotypic, genotypic and phylogenetic evidence demonstrated that strain DW16-2T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia spirodelae sp. nov. (type strain DW16-2T = TBRC 16418T = NBRC 115857T) is proprosed. In addition, the comparison of the whole genome sequences suggested that P. alni and P. antarctica belong to the same species and P. carboxydivorans is a subspecies of P. alni. Therefore, it is proposed that P. antarctica Prabahar et al. 2004 is reclassified as a later heterotypic synonym of P. alni (Evtushenko et al. 1989) Warwick et al. 1994, and P. carboxydivorans Park et al. 2008 is proposed as a subspecies of P. alni (Evtushenko et al. 1989) Warwick et al. 1994.

Genome-based reclassification of Suonthocola fibrivorans as a later heterotypic synonym of Diplocloster agilis.

Both the genera Suonthocola and Diplocloster are members of the family Lachnospiraceae. Their type species, both Suonthocola fibrivorans Sanger_33T and Diplocloster agilis ASD5720T, were isolated from human faeces. A comparison of their 16S rRNA gene sequences revealed 100% similarity, suggesting their close relatedness and the possibility of belonging to the same species. To clarify their taxonomic relationship, genome-based analyses were carried out. Overall genomic relatedness indices analyses indicated that S. fibrivorans Sanger_33T shared average amino acid identity and percentage of conserved proteins prediction values higher than the Lachnospiraceae-specific genus-level thresholds with D. agilis ASD5720T, as well as the other two existing species of the genus Diplocloster. Additionally, S. fibrivorans Sanger_33T formed a distinct branch with D. agilis ASD5720T, clustering with the other two species of the genus Diplocloster into the same clade in both the 16S rRNA gene phylogenetic tree and the core-genome phylogenomic tree. Essentially, both the average nucleotide identity and digital DNA-DNA hybridization prediction values between S. fibrivorans Sanger_33T and D. agilis ASD5720T were above the recommended species boundaries. It is thus clear that S. fibrivorans Sanger_33T and D. agilis ASD5720T constitute the same species. On the basis of the earliest valid publication, priority is given to D. agilis Chaplin et al. 2022. Based on this, the orphan species S. fibrivorans Hitch et al. 2022 is reclassified as a later heterotypic synonym of D. agilis Chaplin et al. 2022, along with the reclassification of the genus Suonthocola Hitch et al. 2022 as a later synonym of Diplocloster Chaplin et al. 2022.

Fecal Microbiota Transplantation from Methionine-Restricted Diet Mouse Donors Improves Alzheimer's Learning and Memory Abilities Through Short-Chain Fatty Acids.

Alzheimer's disease (AD) is marked by impaired cognitive functions, particularly in learning and memory, owing to complex and diverse mechanisms. Methionine restriction (MR) has been found to exert a mitigating effect on brain oxidative stress to improve AD. However, the bidirectional crosstalk between the gut and brain through which MR enhances learning and memory in AD, as well as the effects of fecal microbiota transplantation (FMT) from MR mice on AD mice, remains underexplored. In this study, APP/PS1 double transgenic AD mice were used and an FMT experiment was conducted. 16S rRNA gene sequencing, targeted metabolomics, and microbial metabolite short-chain fatty acids (SCFAs) of feces samples were analyzed. The results showed that MR reversed the reduction in SCFAs induced by AD, and further activated the free fatty acid receptors, FFAR2 and FFAR3, as well as the transport protein MCT1, thereby signaling to the brain to mitigate inflammation and enhance the learning and memory capabilities. Furthermore, the FMT experiment from methionine-restricted diet mouse donors showed that mice receiving FMT ameliorated Alzheimer's learning and memory ability through SCFAs. This study offers novel non-pharmaceutical intervention strategies for AD prevention.

Exploring the Mechanism of Clostridium autoethanogenum Protein for Broiler Growth Based on Gut Microbiota and Serum Metabolomics.

Intestinal health is vital for poultry production, and protein plays a key role in intestinal nutrition. The present study used 16S rRNA gene sequencing and serum metabolomics to investigate the effect of CAP on the cecal microflora structure and serum metabolites in 42-day-old broiler chickens. A total of 480 one-day-old Arbor Acres broiler chickens were randomly divided into four treatments with twelve replicates comprising 10 chickens each, evenly divided by sex. The four groups were basal diet group (CAP0), treatment group 1 (CAP2), treatment group 2 (CAP3), and treatment group 3 (CAP4). The broilers in the CAP0 group were fed a basal diet (without CAP), while those in the CAP2, CAP3, and CAP4 groups received diets containing 2%, 3%, and 4% CAP, respectively. Growth performance results showed that dietary CAP supplementation significantly ameliorated the feed conversion rate (FCR) of broilers at 42 days in the CAP3 and CAP4 groups (p < 0.05). Microbial results revealed that CAP did not alter the dominant microorganisms in the cecum at the phylum, family, and genus levels. LEfSe analysis showed significantly higher relative abundances of p_Desulfobacterota, f_Desulfovibrionaceae, and g_Ruminococcus in the CAP3 group compared to the CAP0 and CAP4 groups. Metabolomic analyses indicated that the effect of incorporating CAP into the diet on serum metabolites primarily focused on organic acids and their derivatives, small peptides, amino acid derivatives, and oxidized lipids. The addition of 3% or 4% CAP to the diet can enhance metabolic pathways such as the citrate cycle (TCA cycle) and arginine and proline metabolism. In summary, incorporating CAP into the diet can increase the relative abundance of beneficial bacteria in the cecum and improve the feed conversion efficiency of broilers by enhancing amino acid and energy metabolism.

Adaptation of Archaeal Communities to Summer Hypoxia in the Sediment of Bohai Sea.

Understanding the adaptation of archaea to hypoxia is essential for deciphering the functions and mechanisms of microbes when suffering environmental changes. However, the dynamics and responses of archaea to the sedimentary hypoxia in Bohai Sea are still unclear. In this study, the diversity, composition, and distribution of archaeal community in sediment along an inshore-offshore transect across the oxygen-depleted area in the Bohai Sea were investigated in June, July, and August of 2021 by employing high-throughput sequencing of 16S rRNA gene. Results indicated that the archaeal communities were dominated by Thermoproteota (80.61%), Asgardarchaeota (8.70%), and Thermoplasmatota (5.27%). Dissolved oxygen (DO) and NO3 - were the two key factors shaping the distribution of archaeal communities, accounting for 49.5% and 38.3% of the total variabilities (p < 0.05), respectively. With the intensity of oxygen depletion, the diversity of archaeal communities increased significantly. Microbial networks revealed that Bathyarchaeia played a key role in interacting with both bacteria and other archaeal groups. Furthermore, adaptions to hypoxia of archaea were also displayed by variation in relative abundance of the predicted ecological functions and the metabolic pathways. The enrichment of specific nitrogen transformation enzymes showed the potential for nitrogen fixation and removal, which might contribute to the balance of N budget and thus facilitate the ecological restoration under eutrophication in Bohai Sea. Our results provided a new picture on ecological and metabolic adaptions to hypoxia by archaea, which will be beneficial to further investigations in extreme environments both theoretically and practically.

Exploring local microbial communities in adenoids through 16S rRNA gene sequencing

Objective:To explore the hypothesis of "pathogen storage pool" by analyzing the local microbial community of adenoids. Methods:Under the guidance of a 70° nasal endoscope, sterile swabs were used to collect secretions from the adenoid crypts of the subjects. The samples were sent to the laboratory for DNA extraction and standard bacterial 16S full-length sequencing analysis. Results:At the species level, the top three microbial communities in adenoid crypts were Bacillus subtilis（18.78%）, Fusobacterium pyogenes（11.42%）, and Streptococcus pneumoniae（9.38%）. Conclusion:The local microbial community of adenoids exhibits a high degree of diversity, including microbial communities from the oral cavity and gastrointestinal tract. Our research results support the hypothesis that adenoids act as a " pathogen reservoir".

Isolation and characterization of the midgut microbiota of Aedes albopictus to identify suitable candidates for paratransgenesis.

Aedes albopictus is a widely recognized carrier of various pathogens. Its resilient characteristics enable it to easily spread across diverse climates. The microbiota in the midgut of mosquitoes plays a crucial role in the interactions between the host and pathogens and can either enhance or reduce the ability of the insect to transmit diseases. Hence, determining the microorganisms present in the mosquito's digestive system could be a promising approach to developing an effective method of controlling them. Hence, the aim of this study was to investigate the microbial compositions in the midguts of Ae. albopictus mosquitoes collected from the fields of Sistan and Baluchestan Province. The midguts of 60 female mosquitoes were dissected, and their related bacteria were determined using the culture-dependent method. Different colonies were differentiated using the biochemical tests followed by 16S rRNA gene sequencing. The isolated bacteria were identified as belonging to the Asaia, Delftia, Serratia, Aeromonas, Paracoccus, and Planomicrobium genera based on biochemical and molecular analysis. The findings obtained in this study were largely consistent with earlier studies conducted on mosquitoes gathered from different regions throughout the world. Overall, the findings could enhance our understanding of the microbial diversity in Ae. albopictus and aid in the identification of a potent and widespread bacterium for the development of a paratransgenesis tool to combat Aedes-borne infectious diseases.

Citrus aurantium 'Changshan-huyou' physiological premature fruit drop: A promising prebiotic to tackle obesity.

Presently, the mitigation and governance of obesity have surfaced as significant public health dilemmas on a global scale. A wealth of studies indicated that the host gut microbiota is instrumental in regulating the interplay between high-fat diet (HFD) intake and the pathogenesis of obesity. Physiological premature fruit drop, a major byproduct of citrus, is rich in a variety of bioactive constituents, yet its potential has remained underutilized for an extended period. The objective of this investigation is to examine the chemical constituents of Citrus aurantium'Changshan-huyou' premature fruit drop (HYFD) and investigate its anti-obesity effects, elucidating its potential pathways. Volatile compounds and flavonoids in HYFD were analyzed using chromatographic and mass spectrometric techniques. Furthermore, this study utilized biochemical assays and histopathological examinations to evaluate the effects of HYFD on HFD-fed mice. The impact of HYFD on the gut microbiota of the mice was examined through 16S rRNA gene sequencing, and fecal microbiota transplantation was employed to validate the role of the gut microbial community in host obesity prevention. Concurrently, transcriptome was employed to identify differentially expressed genes, providing further insights into the molecular mechanisms through which HYFD manifests its anti-obesity effects. Our findings demonstrated that HYFD supplementation significantly alleviated adiposity and ameliorated the dysbiosis of gut microbiota in HFD-induced mice. HYFD rectified the HFD-induced gut microbiota dysregulation, enhanced the presence of beneficial microbial taxa linked to lipid metabolism, including Parabacteroides and Alistipes, and elevated concentrations of the anti-obesity short-chain fatty acids, comprising caproic acid and isocaproic acid. Additionally, transcriptomic analyses confirmed that HYFD prevented obesity in mice by enhancing fatty acid catabolism via the activation of the AMPK/PPARα/CPT1a signaling pathway. Our results provided novel insights into the mechanism of citrus physiological premature fruit drop and its potential role in preventing obesity, while sparking greater interest in leveraging more biomass waste.

The Disturbed Microbial Niches of Itchy Scalp.

Scalp itch without evident cause is an uncomfortable symptom that annoys many people in life but lacks adequate attention in academic. To investigate the relationship between scalp itching and microorganisms, and identify the key microbes and predicted functions associated with scalp itching, furtherly to provide useful targets for scalp itch solution. We performed microbial comparison between 44 normal subjects and 89 subjects having scalp itching problem with un-identified origin based on 16S rRNA gene sequencing and ddPCR (digital droplet PCR), and identified itch relevant microbes and predicted functions. To minimize false positive findings, another 43 itchy subjects were used for independent validation. The three most abundant bacterial genus Cutibacterium, Lawsonella, Staphylococcus and predominant fungi Malassezia were not significantly different between the normal and itchy subjects, but an imbalance between Cutibacterium and Staphylococcus occurred in itchy scalp. As the predominant function contributor in the community, various Cutibacterium ASVs (amplicon sequence variants) were detected in itchy or normal subjects with low abundance and were subject specific. Some non-resident microbes from environment such as Leptolyngbya ANT.L52.2 and Pseudomonas were enhanced in itchy scalp and occupied an important ecological niche. The severity of itch was alleviated when these low abundant and low subject coverage ASVs were reduced or diminished. Our findings raise the attention to (1) the ratio of Cutibacterium to Staphylococcus and (2) the low abundant bacteria on scalp, and provide potential solutions to ease scalp itch.

Exploring the Potential of Microalgae Cocultivation on Bacterial Community Dynamics in a Nile Tilapia and Garlic Aquaponic System

The cocultivation of microalgae in aquaponic systems can improve nutrient removal and enhance water quality. Moreover, it can promote the biological and physicochemical balance in aquaponic ecosystems. However, the bacterial communities in aquaponic systems have not yet been comprehensively characterized and the effects of microalgae cocultivation remain unclear. Using 16S rRNA gene sequencing, we sought to elucidate the effects of a cocultivation of Chlorella vulgaris, Scenedesmus species, and Spirulina platensis cocultivation on the bacterial communities in the rearing tanks and the biofilter of a garlic (Allium sativum L.) and Nile tilapia (Oreochromis niloticus L.) aquaponic system during a 56‐days experiment. Feed intake, weight gain, and survival rates of Nile tilapia significantly improved in experimental groups cocultivated with microalgae compared to the control group, while garlic plant biomass, leaf number, and shoot length were not significantly different from the control. Alpha‐diversity analysis revealed significantly higher richness and evenness in the bacterial communities from the biofilter and rearing tanks of the cocultivated systems when compared with the control system. The cocultivation also had a statistically significant effect on the bacterial composition: nonmetric multidimensional scaling analysis of a Bray–Curtis dissimilarity matrix demonstrated unique clustering patterns, indicating distinct bacterial communities in the biofilter and rearing tank water cocultivated with microalgal strains. We found significantly decreased abundances of the potentially pathogenic bacterial genera Janthinobacterium, Aeromonas, Pseudomonas, and Flavobacterium in aquaponic systems cocultivated with microalgae when compared to the control. Furthermore, the beneficial bacterial genera Fusibacter, Geothrix, Thiobaca, and Treponema were significantly enriched in the microalgae cocultivated systems. The results clearly demonstrate that integrating microalgae into an aquaponic recirculating aquaculture system (RAS), not only improves weight gain and survival rates of Nile tilapia, but also enriches beneficial bacterial genera and reduces potentially pathogenic microorganisms, offering a promising strategy to reduce antibiotic use and enhance water quality in aquaponics, without growth impairments of cocultivated plants.

In vivo mechanism of the interaction between trimethylamine lyase expression and glycolytic pathways.

Recent studies confirmed that host-gut microbiota interactions modulate disease-linked metabolite TMA production via TMA lyase. However, microbial enzyme production mechanisms remain unclear. In the present study, we investigated the impact of dietary and intervention factors on gut microbiota, microbial gene expression, and the interplay between TMA lyase and glycolytic pathways in mice. Using 16S rRNA gene sequencing, metagenomics, and metabolomics, the gut microbiota composition and microbial functional gene expression profiles related to TMA lyase and glycolytic enzymes were determined. The results revealed that distinct diets and intervention factors altered gut microbiota, gene expression, and metabolites linked to glycine metabolism and glycolysis. Notably, an arabinoxylan-rich diet suppressed genes linked to choline, glycine, glycolysis, and TMA lyase, favoring glycine utilization via pyruvate pathways. Glycolytic inhibitors amplified these effects, mainly inhibiting pyruvate kinase. Our findings underscored the crosstalk between TMA lyase and glycolytic pathways, regulating glycine levels, and suggested avenues for targeted interventions and personalized diets to curb choline TMA lyase production.

Preventive effects of kefir on colon tumor development in Wistar rats: gut microbiota critical role.

To clarify the effects of kefir in critical periods of development in adult diseases, we study the effects of kefir intake during early life on gut microbiota and prevention of colorectal carcinogenesis in adulthood. Lactating Wistar rats were divided into three groups: control (C), kefir lactation (KL), and kefir puberty (KP) groups. The C and KP groups received 1 mL of water/day; KL dams received kefir milk daily (108 CFU/mL) during lactation. After weaning (postnatal day 21), KP pups received kefir treatment until 60 days. At 67 days old, colorectal carcinogenesis was induced through intraperitoneal injection of 1, 2-dimethylhydrazine. The gut microbiota composition were analyzed by 16S rRNA gene sequencing and DESeq2 (differential abundance method), revealing significant differences in bacterial abundances between the kefir consumption periods. Maternal kefir intake strong anticancer power, suppressed tumors in adult offspring and reduced the relative risk of offspring tumor development. The gut microbiota in cecal samples of the KL group was enriched with Lactobacillus, Romboutsia, and Blautia. In contrast, control animals were enriched with Acinetobacter. The administration of kefir during critical periods of development, with emphasis on lactation, affected the gut microbial community structure to promote host benefits. Pearson analysis indicated positive correlation between tumor number with IL-1 levels. Therefore, the probiotic fermented food intake in early life may be effective as chemopreventive potential against colon tumor development, especially in lactation period.

Gut microbiome associated with PARP inhibitor efficacy in patients with ovarian cancer.

To investigate an association between the gut microbiome and efficacy of poly(ADP-ribose) polymerase inhibitors (PARPi) in ovarian cancer. This study conducted fecal microbiome analysis (16S rRNA gene sequencing) and circulating tumor DNA (ctDNA) profiling for ovarian cancer patients who underwent PARPi maintenance therapy. Fecal and blood samples were collected at the baseline and the progressive disease (PD) or last follow-up. The relative abundance of gut microbes and progression-free survival (PFS) were analyzed using linear discriminant analysis of effect size and the Cox proportional hazard model according to BRCA1/2 mutation (BRCA1/2mut) status detected by ctDNA sequencing. Baseline samples were available from 23 BRCA1/2mut-positive patients and 33 BRCA1/2mut-negative patients. The microbes enriched in the baseline samples with long PFS were Bifidobacterium, Roseburia, Dialister, Butyricicoccus, and Bilophila for BRCA1/2mut-positive patients and Phascolarctobacterium for BRCA1/2mut-negative patients. In multivariate analyses dividing patients by the median values of relative abundances, no bacteria were associated with PFS in BRCA1/2mut-positive patients, whereas high Phascolarctobacterium abundances (≥1.11%) was significantly associated with longer PFS in BRCA1/2mut-negative patients (median 14.0 vs. 5.9 months, hazard ratio=0.28; 95% confidence interval=0.11-0.69; p=0.014). In the last samples, the relative abundances of Phascolarctobacterium were significantly higher in patients without PD (n=5) than those with PD (n=15) (median 1.25% vs. 0.06%; p=0.016). High fecal composition of Phascolarctobacterium was associated with prolonged PFS in patients with BRCA1/2mut-negative ovarian cancer receiving PARPi therapy. Our results would provide new insights for future research.

Pseudomonas retamae sp. nov., a novel endophytic bacterium with plant growth-promoting potential, isolated from root nodules of Retama monosperma in Northwestern Algeria.

A thorough polyphasic taxonomic study, integrating genome-based taxonomic approaches, was carried out to characterize the RB5T strain isolated from root nodules of Retama monosperma growing on the coastal dunes of Bousfer Beach (Oran, Algeria). The 16S rRNA gene sequence analysis revealed that strain RB5T had the highest similarity to Pseudomonas granadensis LMG27940T (98.94%) and Pseudomonas gozinkensis IzPS32dT (98.73%). Phylogenetic studies, including both 16S rRNA gene sequence and multilocus sequence analysis using 16S rRNA, gyrB and rpoD housekeeping genes, positioned RB5T in a distinct branch alongside its closest relative, P. granadensis LMG27940T. Phylogenomic analysis using the Bac120 marker set and Type (Strain) Genome Server confirmed the unique position of RB5T and its close relationship with P. granadensis LMG27940T. Similarly, genomic comparisons using average nucleotide identity based on blast (ANIb) and digital DNA-DNA hybridization (dDDH) revealed values of 92.85 and 59.3%, respectively, when compared with its closest relative, P. granadensis LMG27940T. Both values fall below the established species delimitation thresholds of 95-96% for ANIb and 70% for dDDH, providing strong genomic evidence that strain RB5T represents a novel species. Further average nucleotide identity comparisons with unclassified Pseudomonas spp. (384 genomes) and metagenomic-derived genomes from the Genome Taxonomy Database (GTDB) showed values between 84.27 and 89.2%, indicating that strain RB5T belongs to a unique evolutionary line. The genome of RB5T, with a size of 6 311 310 bp and a G+C content of 60%, harbours several key genes associated with plant growth-promoting traits, making it a promising candidate for sustainable agriculture. Phenotypically, RB5T strain is an aerobic, rod-shaped, Gram-negative, non-spore-forming bacterium that is motile with a single polar flagellum. It grows under a wide range of temperature (4-42 °C) and pH (5-10) conditions and tolerates up to 6% (w/v) NaCl. The main cellular fatty acid composition of RB5T includes C16:0, C17:0 cyclo and the summed features 3 consisting of C16:1 ω7c/C16:1 ω6c. Based on the phylogenetic, phenotypic, chemotaxonomic and genome comparison analyses, strain RB5T was identified as a novel species of the genus Pseudomonas, for which the name Pseudomonas retamae sp. nov. is proposed. The type strain is RB5T (=DSM 117471T=LMG 33633T=CIP 112482T).

Oral Tributyrin Treatment affects Short-Chain Fatty Acid Transport, Mucosal Health, and Microbiome in a Mouse Model of Inflammatory Diarrhea.

Butyrate may decrease intestinal inflammation and diarrhea. This study investigates the impact of oral application of sodium butyrate (NaB) and tributyrin (TB) on colonic butyrate concentration, SCFA transporter expression, colonic absorptive function, barrier properties, inflammation, and microbial composition in the colon of slc26a3-/- mice, a mouse model for inflammatory diarrhea. In vivo fluid absorption and bicarbonate secretory rates were evaluated in the cecum and mid-colon of slc26a3+/+ and slc26a3-/- mice before and during luminal perfusion of NaB-containing saline and were significantly stimulated in both slc26a3+/+ and slc26a3-/- colon by NaB. Age-matched slc26a3+/+ and slc26a3-/- mice were either fed chow containing 5% NaB or gavaged twice daily with TB for 21 days. Food and water intake, weight, and stool water content were assessed daily. Stool and tissues were collected for further analysis of SCFA production, barrier integrity, mucosal inflammation, and microbiome analysis by 16S rRNA gene sequencing. 5% NaB diet did not exert a significant impact on SCFA levels, mucus barrier, or inflammatory markers, but significantly increased oral water intake. TB gavage treatment increased the expression of SCFA transporters Mct1 and Smct1, mucus content and microbial diversity, and decreased the neutrophil marker Lipocalin 2, Phospholipase A2, and the antimicrobial peptide Reg3b in the slc26a3-/- cecum. However, TB treatment also resulted in an increase in inflammatory markers such as TNFα, Il-1β and CD3e in the wildtype mucosa. While there are some benefits with TB ingestion for barrier properties and microbial composition in the diseased cecum, potentially detrimental effects were noted in the healthy colon.

Distribution and environmental dissemination of antibiotic resistance genes in poultry farms and surrounding ecosystems.

Antibiotic resistance poses a significant threat to human and animal health worldwide, with farms serving as crucial reservoirs of Antibiotic Resistance Genes (ARGs) and Antibiotic-resistant bacteria. However, the distribution of ARGs in poultry farms and their transmission patterns in the environment remain poorly understood. This study collected samples of aerosol microorganisms, cloacal matter, soil, and vegetables from poultry farms and surrounding environments at three different distances. We used 16S rRNA gene sequencing and HT-qPCR to analyze the characteristics of aerosol microbial communities and the abundance of ARGs. At the phylum level, Proteobacteria, Firmicutes, and Bacteroidetes were dominant in cloacal samples, aerosol samples, and vegetable samples, while Proteobacteria Actinobacteriota and Acidobacteria dominated soil. Pseudomonas was dominant in cloacal samples at the genus level, whereas Fusobacterium was prevalent in soil. The diversity and richness of bacterial communities were more similar between cloacal samples than those observed between either sample type compared with soil. Our results showed that tetracycline and aminoglycoside ARG relative abundance was high across all sample types but significantly increased within feces/air compared to soils/vegetables. Association analysis revealed five potential host genera for ARG/MGE presence among various microbiota populations studied here. Our findings confirm that farms are important sources for the environmental dissemination of pathogens and ARGs.

Collection and Processing of Samples for Next-Generation Sequencing to Study the Gut Microbiome.

16S rRNA gene sequencing is commonly used for identification and quantitation of microorganisms in complex biological mixtures, such as the human gut microbiome. The 16S rRNA gene is an excellent target gene for sequencing DNA in a heterogenous sample, as it is a highly conserved part of the transcriptional machinery. Universal PCR primers are used to amplify the conserved regions of 16S. Thus, it is possible to amplify the gene in a wide range of different microorganisms from a single sample. As the 16S rRNA gene consists of both conserved and variable regions, sequencing of the variable regions can be used to differentiate between different bacterial species.

GUT, VAGINAL AND URINARY MICROBIOTA AS POTENTIAL BIOMARKERS OF SENSITIZATION IN WOMEN WITH CHRONIC PELVIC PAIN.

A subgroup of patients with chronic pelvic pain (CPP) exhibit organ sensitization, whose origin and mechanism remains largely unknown. Changes in microbiota composition in pelvic organs have been found to be associated with various pelvic pathological conditions. Therefore, a comprehensive analysis of the gut and genito-urinary microbiota composition and interactions in women with CPP may be key to understanding their involvement in the sensitization processes. To identify pelvic organ microbiota signatures that are associated with organ hypersensitivity in CPP patients. This study involved women with high (S-CPP, n=14) and low (NS-CPP, n=14) pelvic sensitization scores according to the Convergences PP criteria. Pelvic organ sensitivity was assessed by rectal barostat, and noninvasive bladder, muscular and vulvar sensory tests. Quality of life, pelvic symptoms and psychological state were assessed. Using 16S rRNA gene sequencing, the gut, vaginal and urinary microbiota diversity and composition were analyzed and compared between S-CPP and NS-CPP women. Differentially abundant bacterial amplicon sequence variants (ASVs) between groups were associated with clinical characteristics and organ sensitivity. System biology approaches using Weighted Gene Correlation Network Analysis (WGCNA) were used to identify bacterial ASV modules associated with functional and clinical parameters. Pain pressure thresholds were significantly decreased in S-CPP women for the vulva and for the rectum, the bladder and the perineal muscles as compared to NS-CPP. However, pain intensity felt at rectal, muscular and bladder pain thresholds was significantly increased in S-CPP women. After stimulation, S-CPP women presented increased and prolonged pain in perineal muscles and bladder compared to NS-CPP women. Alpha and β-diversities were significantly increased in S-CPP women in vaginal and urinary but not in gut microbiota. Using, differential abundance analysis, we showed that 13 ASVs in the gut, 6 in the vagina and 2 in the bladder were differentially expressed between S-CPP and NS-CPP patients. More specifically, in vaginal microbiota, a significant increase of Streptococcus and Prevotella genera was observed in S-CPP as compared to NS-CPP. A significant increase in Clostridium sensu stricto 1 ASV was observed in urinary microbiota of S-CPP as compared to NS-CPP patients. Next, we found that 4 gut microbiota ASVs (belonging to Akkermansia, Desulfovibrio, Faecalibacterium and CAG-352) were correlated with pain intensity at maximal rectal distension threshold. We also identified an ASV (Blautia) which is increased in NS-CPP as being inversely correlated to several gut sensitization markers. In the vaginal microbiota, the Lactobacillus jensenii ASV was associated with less dysmenorrhea and an increased bladder capacity. Furthermore, we identified two vaginal ASVs belonging to Prevotella which are increased in S-CPP as being associated with dysmenorrhea. Finally, using WGCNA analysis methods, we identified vaginal and urinary tract ASVs modules driven by Peptostreptococcales-Tissierellales Peptoniphilus which were strongly correlated with rectal, muscular and bladder poststimulation pain. We also identified a gut ASVs module driven by Christensenellaceae_R-7 that significantly associated with anxiety, gastro-intestinal symptoms and rectal sensitivity. This work identified specific bacterial signatures of specific pelvic organs and their association with organ sensitization, which are potential therapeutic targets in CPP women.

Flavobacterium magnesitis sp. nov. and Flavobacterium zubiriense sp. nov., two novel Flavobacterium species isolated from alkaline magnesite residues.

Three bacterial strains, designated FZUC8N2.13T, FBOR7N2.3T and FZUR7N2.5, were isolated from distinct magnesite residues in Spain. Phylogenetic and phylogenomic analysis places them within the genus Flavobacterium. Strains FBOR7N2.3T and FZUR7N2.5 share 100% of similarity in the 16S rRNA gene sequence, and both are most closely related to Flavobacterium cellulosilyticum AR-3-4T with which they share 97.5% of 16S rRNA gene similarity. Strain FZUC8N2.13T forms a distinct lineage most closely related to Flavobacterium lacustre IMCC36792T with 97.7% 16S rRNA gene similarity. The closest phylogenomic neighbours of these three strains are Flavobacterium flevense DSM 1076T, 'Flavobacterium undicola' BBQ-18T and Flavobacterium commune PK15T. The average nucleotide identity and digital DNA-DNA hybridization values between the three strains and closest members of the genus Flavobacterium are below the threshold values of 95% and 70%, respectively. Strains FZUC8N2.13T, FBOR7N2.3T and FZUR7N2.5 stain Gram-negative, are rod-shaped and form yellow colonies. Optimum growth occurs at 25 °C and pH 7. The genomic G+C contents are 33.4 mol% for strain FZUC8N2.13T and 33.2 mol% for strains FBOR7N2.3T and FZUR7N2.5. The major isoprenoid quinone is menaquinone 6. The major fatty acids are summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) (22.6-31.1%), iso-C15 : 0 (13.6-16.2 %) and anteiso-C15 : 0 (8.7-10.5%). The polar lipids consist of two aminolipids, two aminophospholipids and one glycolipid. The phylogenetic, phylogenomic, phenotypic and chemotaxonomic data indicate that FZUC8N2.13T, FBOR7N2.3T and FZUR7N2.5 are distinct from the described species of Flavobacterium and should be classified as novel species, for which we propose the names Flavobacterium zubiriense for strain FZUC8N2.13T (=UCCCB 179T=CECT 30977T) and Flavobacterium magnesitis for strains FBOR7N2.3T (=UCCCB 178T=CECT 30976T) and FZUR7N2.5 (=UCCCB 216=CECT 31036).

Antibiotic resistance of Salmonella from raw chicken meat at retail markets in Vinh Long Province

Salmonellosis is one of the most prevalent foodborne illnesses worldwide. This study aimed to evaluate the prevalence and antibiotic susceptibility of Salmonella isolates derived from raw chicken meat sold at various retail markets in Vinh Long Province, Vietnam. The results indicated that 100% of the chicken meat samples contained high densities of Salmonella spp. A total of 21 Salmonella isolates were obtained from these samples during this investigation. Using PCR techniques and 16S rRNA gene sequencing, three bacterial strains (SP5_7, SP8_8, and SP9_9) were identified as Salmonella spp., with similarities of 95.31%, 97.89%, and 93.60%, respectively. The antibiogram results revealed that the Salmonella isolates were highly sensitive to ampicillin-sulbactam (90%), sulfamethoxazole-trimethoprim (67%), and doxycycline (52%), and were completely sensitive to gentamicin. Conversely, significant resistance was observed against ampicillin (86%), tetracycline (71%), amoxicillin (62%), and ciprofloxacin (57%). Notably, 86% of the strains exhibited multiresistance to three to ten antibiotics, with the highest proportion (19%) showing resistance to three antibiotics. Furthermore, 18 out of the 21 strains presented a multiple antibiotic resistance (MAR) index &gt;0.2, indicating frequent exposure to antibiotics. These findings underscore the necessity for stricter control measures in the sale of fresh chicken in markets to mitigate the spread of Salmonella in the environment.