V3-V4 Region Research Articles

Characteristics of Mucosa-Associated Microbiota in Ulcerative Colitis Patients with 5-Aminosalicylic Acid Intolerance

Background/Objectives: 5-Aminosalicylic acid (5-ASA) is a first-line therapy for ulcerative colitis (UC). This study examined the mucosa-associated microbiota (MAM) in UC patients, distinguishing between those who were 5-ASA tolerant and intolerant. Methods: Brushing samples were collected from the sigmoid and ileal end of patients with UC during endoscopic procedures. The samples were profiled by using the Illumina MiSeq platform. The V3–V4 regions of the 16S rRNA gene (460 bp) were amplified by using tailed PCR. Results: A total of 15 patients with 5-ASA intolerance, 38 patients with 5-ASA tolerance, and 19 healthy controls were recruited in this study. The α-diversity indices were remarkably different among the three groups in the ileum mucosa but not in the sigmoid colon. In the ileum mucosa, Alistipes, Ruminococcaceae, and Odoribacter were less abundant in the 5-ASA-intolerant group than in the control and 5-ASA-tolerant groups. On the contrary, Merdibacter, Brevundimonas, and Porphyromonas were more abundant in the 5-ASA-intolerant group than in other groups. Conclusions: The present study showed that the changes in MAM were characterized by a decrease in mucoprotective bacteria rather than an increase in harmful bacteria.

Environmental factors that regulate Vibrio spp. abundance and community structure in tropical waters

Vibrio spp. is a group of heterotrophic bacteria that are ubiquitous in marine habitats, with various ecological and clinical importance. This study investigated the environmental factors that regulate Vibrio spp. dynamics in various tropical marine habitats, including nearshore (an estuary and a coastal beach) and offshore transects located northwest and southeast of Peninsular Malaysia, while focusing on the distribution of attached and free-living Vibrio spp., population growth, and community composition. The results showed that > 85% of the Vibrio spp. in nearshore waters occurred in attached form and correlated positively to total suspended solids (TSS) and Chlorophyll a (Chl a) concentrations. On the other hand, Vibrio spp. growth rates were positively correlated to dissolved organic carbon (DOC) concentrations, but negatively correlated to total bacterial counts, likely due to resource competition. In addition, high-throughput sequencing of 16S rRNA V3-V4 region showed that Vibrio spp. in these tropical waters contributed < 1 − 18% of the whole bacterioplankton community, and the six major Vibrio spp. taxa were V. alginolyticus group, V. brasiliensis, V. caribbeanicus, V. hepatarius group, V. splendidus group and V. thalassae. db-RDA (cumulative variance explicated = 93.53%) further revealed the influence of TSS, DOC, and dissolved organic nitrogen (DON) to the Vibrio spp. community profiles. The study highlighted the importance of suspended solids (TSS and Chl a) and dissolved organic nutrients (DOC and DON) towards Vibrio spp. dynamics in tropical marine waters.

Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy.

Children diagnosed with severe tonsillar hypertrophy display discernible craniofacial features distinct from those with adenoid hypertrophy, prompting illuminating considerations regarding microbiota regulation in this non-inflammatory condition. The present study aimed to characterize the salivary microbial profile in children with tonsillar hypertrophy and explore the potential functionality therein. A total of 112 children, with a mean age of 7.79 ± 2.41 years, were enrolled and divided into the tonsillar hypertrophy (TH) group (n = 46, 8.4 ± 2.5 years old), adenoid hypertrophy (AH) group (n = 21, 7.6 ± 2.8 years old), adenotonsillar hypertrophy (ATH) group (n = 23, 7.2 ± 2.1 years old), and control group (n = 22, 8.6 ± 2.1 years old). Unstimulated saliva samples were collected, and microbial profiles were analyzed by 16S rRNA sequencing of V3-V4 regions. Diversity and composition of salivary microbiome and the correlation with parameters of overnight polysomnography and complete blood count were investigated. As a result, children with tonsillar hypertrophy had significantly higher α-diversity indices (P＜0.05). β-diversity based on Bray-Curtis distance revealed that the salivary microbiome of the tonsillar hypertrophy group had a slight separation from the other three groups (P＜0.05). The linear discriminant analysis effect size (LEfSe) analysis indicated that Gemella was most closely related to tonsillar hypertrophy, and higher abundance of Gemella, Parvimonas, Dialister, and Lactobacillus may reflect an active state of immune regulation. Meanwhile, children with different degrees of tonsillar hypertrophy shared similar salivary microbiome diversity. This study demonstrated that the salivary microbiome in pediatric tonsillar hypertrophy patients had different signatures, highlighting that the site of upper airway obstruction primarily influences the salivary microbiome rather than hypertrophy severity.IMPORTANCETonsillar hypertrophy is the most frequent cause of upper airway obstruction and one of the primary risk factors for pediatric obstructive sleep apnea (OSA). Studies have discovered that children with isolated tonsillar hypertrophy exhibit different craniofacial morphology features compared with those with isolated adenoid hypertrophy or adenotonsillar hypertrophy. Furthermore, characteristic salivary microbiota from children with OSA compared with healthy children has been identified in our previous research. However, few studies provided insight into the relationship between the different sites of upper airway obstruction resulting from the enlargement of pharyngeal lymphoid tissue at different sites and the alterations in the microbiome. Here, to investigate the differences in the salivary microbiome of children with tonsillar hypertrophy and/or adenoid hypertrophy, we conducted a cross-sectional study and depicted the unique microbiome profile of pediatric tonsillar hypertrophy, which was mainly characterized by a significantly higher abundance of genera belonging to phyla Firmicutes and certain bacteria involving in the immune response in tonsillar hypertrophy, offering novel perspectives for future related research.

The Composition and Diversity of Soil Microbial Communities Associated With the Invasive Plant Solidago canadensis Vary Across Locations and Time Since Invasion

ABSTRACTAimPrevious local‐scale research (within plots or landscapes) has shown that invasive plants can alter the composition and diversity of soil microbial communities, with potential feedback effects on their own invasion success. However, the broader ecological patterns of these interactions across different invasion timescales and geographic regions remain poorly understood. This study investigated whether the composition and diversity of soil microbial communities associated with Solidago canadensis (Canada goldenrod) invasion vary across both population residence times and geographic locations.LocationSouth‐eastern China.TaxonSoil fungal and bacterial communities and S. canadensis.MethodsWe collected rhizospheric soil of S. canadensis, nonrhizospheric soil and adjacent uninvaded soil from each of 36 populations of S. canadensis with varying residence times (8–89 years), totalling 108 samples. We extracted DNA from these samples and sequenced the V3–V4 region of the bacterial 16S rRNA gene and the ITS2 region of the fungal rDNA. We analysed the DNA sequences to assess whether variation in α‐diversity, β‐diversity, arbuscular mycorrhizal fungi (AMF) richness and the ratio of AMF to plant pathogens in the soil microbial communities varied with S. canadensis population residence time, latitude and longitude.ResultsThe α‐diversity and β‐diversity of soil fungal and bacterial communities significantly varied with S. canadensis residence times, latitude and longitude. In locations where S. canadensis had been established for longer periods, there was an increase in AMF richness and a decrease in plant pathogens in the rhizospheric soil. Fungal diversity in rhizospheric soils was positively correlated with longitude, while bacterial diversity in rhizospheric and nonrhizospheric soils was positively correlated with both latitude and longitude.Main ConclusionsThese findings indicate that the time since invasion and geographical location can both significantly influence the composition and diversity of soil microbial communities associated with invasive plant species.

PSI-30 Effects of high canola meal diet with acidifiers supplementation on cecal microbiota of nursery pigs

Abstract Inclusion of canola meal (CM) in swine diets is typically limited stemming from the presence of glucosinolates (Gls), which can reduce growth performance and cause thyroid dysfunction in nursery pigs. While certain members of hindgut bacterial communities are capable of degrading dietary Gls, which would mitigate their detrimental effects, they have yet to be identified. Moreover, lowering the pH in the hindgut of the pig can break down Gls into less toxic compounds, potentially reducing harm. Thus, this study aimed to characterize major bacterial species populating the hindgut of nursery pigs fed a high CM diet supplemented with acidifier and encapsulated butyrate. A total of 315 nursery pigs weaned at 21 d old, average body weight (BW) 6.0 ± 1.2 kg, were assigned to one of five dietary treatments with 9 replicate pens (7 pigs/pen) in a randomized complete block design. The dietary treatments included PC: a corn-soybean meal-based diet with 20% CM, NC: a corn-soybean meal-based diet with 40% CM, NC+A: NC diet supplemented with an acidifier at 1,500 ppm, NC+B: NC diet supplemented with encapsulated butyrate at 500 ppm, and NC+A+B: NC diet supplemented with both an acidifier and encapsulated butyrate. All diets were formulated to meet or exceed the nutrient requirements of NRC (2012). At the end of the feeding trial (6 wk), one pig from each pen was euthanized to collect fresh cecal digesta. Samples were analyzed using the 16S rRNA gene through PCR-amplification of the V1-V3 regions from microbial genomic DNA, followed by Illumina MiSeq 2X300 sequencing. A comparative analysis of the highly represented taxonomic groups and operational taxonomic units (OTU) using non-parametric Kruskal-Wallis sum-rank test and Wilcoxon pairwise test identified candidate bacterial groups or species enriched across different diets. Bacillota was the predominant phylum across all diets, ranging from 83.2% to 86.3%. At the genus level, Lachnospiracea incertae sedis was less abundant in the NC diets with acidifier (Acidifier effect, P &amp;lt; 0.05), whereas Dialister was less in the NC diets with encapsulated butyrate (Butyrate effect, P &amp;lt; 0.05). The OTU Ssd-00001 (Lactobacillus amylovorus, 99.6%) tended to be greater in the cecal microbiota of pigs fed the NC diets with acidifier (Acidifier effect, P = 0.09). Interestingly, OTU Ssd-00188 (Agathobacter rectalis, 99.2%) tended to be higher in PC diet than in NC diet (P = 0.06), while its abundance was less in the cecal microbiota of pigs fed the NC diets with acidifier (Acidifier effect, P = 0.09). In conclusion, these results provide valuable insights into the microbiome of pigs fed high CM diets. Understanding the interplay between microbial communities and high CM diet with acidifier supplementation is crucial for optimizing swine diets and mitigating challenges associated with the antinutritional effects of dietary Gls from CM.

PSXII-18 Nitrogen balance and ruminal bacterial diversity indexes of Nellore cattle fed with amylolytic and fibrolytic enzymes in feedlot

Abstract This study was carried out to evaluate the use of dietary exogenous enzyme (ENZ) products with amylolytic and fibrolytic activity on nitrogen balance and ruminal alpha and beta diversity of Nellore cattle in feedlot. Rumen cannulated Nellore steers [n = 10; body weigh (BW) = 543 kg ± 28.6 kg] were distributed in a replicate 5 × 5 Latin-square design using individual pens. The treatments consisted of a negative control (CON; without ENZ); Amylase [AML, Amaize, Alltech; 0.5 g/kg of diet dry matter (DM); Xylanase (FBL, Fibrozyme, Alltech; 0.9 g/kg of diet DM]; Half dose (HD; AML 0.25 g/kg of diet DM and FBL 0.45 g/kg of diet DM); and Full dose (FD; AML 0.5 g/kg of diet DM and FBL 0.90 g/kg of diet DM; Table 1). The experimental period lasted 19 d (14 d of adaptation and 5 d of collection). Between d 15 and 18, total urine collection was performed to calculate the nitrogen balance. On d 19 a mixed ruminal sample (6 mL of solid and liquid content) was taken 4 h after feeding and stored at -80 ºC until DNA extraction. Total genomic DNA was extracted using the ZymoBIOMICS DNA Miniprep Kit. The library was prepared using primers for the region V3V4 of the16S rRNA gene; 341F (5’-CCTAYGGGRBGCASCAG-3’) x 806R (5’- GGACTACNNGGGTATCTAAT-3’). The amplicons (~ 470 bp) were sequenced with the Illumina NovaSeq 6000 PE 250 platform. The sequences were analyzed using qiime2 with the SILVA database for the taxonomic assignment. Alpha and beta diversities were calculated in Rstudio using phyloseq. All data were analyzed as orthogonal contrasts assuming treatment as a fixed effect: 1) CON vs. ENZ, 2) AML vs. FBL, 3) HD vs. FD, and 4) AML + FBL vs. HD + FD. Animals that received ENZ had reduced fecal nitrogen excretion (FNE, P = 0.014) and greater efficiency of nitrogen utilization (ENU, P = 0.031) than animals in the CON group. The FBL treatment resulted in greater CP/DOM ratio (P = 0.049), nitrogen balance (P = 0.089), and ENU (P = 0.015) compared with AML treatment. No differences were observed between HD and FD for any nitrogen balance variable (P &amp;gt; 0.10). Animals supplemented with both enzymes (HD + FD) had greater values of N intake (P = 0.018), greater CP/DOM ratio (P = 0.006), and greater FNE (P = 0.002) than animals fed either enzyme alone (AML + FBL). The ENZ supplementation did not impact alpha diversity index or beta diversity (P &amp;gt; 0.10). In conclusion, the addition of exogenous enzymes affected nitrogen balance but not ruminal alpha and beta diversity of Nellore cattle in feedlot.

Dietary regulation of gut bacteria in the Pacific oyster Magallana gigas and Mediterranean mussel Mytilus galloprovincialis

Feed composition affects the gut bacterial community in aquatic species, but little is known about how diet type impacts gut microbiota in molluscan bivalves. This study investigates the impact of feed composition on the gut bacterial community in two commercially important bivalves: Pacific oyster Magallana gigas and Mediterranean mussel Mytilus galloprovincialis. Oysters and mussels were fed with two types of marine algae, live Isochrysis galbana (microalgae) and the dried seaweed powder Ulva sp. (macroalgae) under a laboratory condition for two months. The V1–V2 region of the 16S rDNA was sequenced through an Illumina MiSeq platform to compare the gut bacterial community of oysters and mussels at the start and the end of the feeding trial. Feed composition directly impacted both alpha and beta diversities of gut microbiota, but the degree of the impact differed between bivalve species. The difference in the gut bacterial assemblages of oysters and mussels in the pre- and post-feeding trials indicated that the diet type and host species shape the composition of gut bacteria. Spirochaeta was absent in mussel guts during the pre- and post-feeding trials but was present in oysters, revealing host specificity in colonizing gut bacteria. The results suggest that the diet type and host species can significantly impact the gut bacterial community structure. This study confirms that diet can modulate gut microbial composition in marine filter-feeding organisms, but the extent of dietary modulation depends on feed type and host species.

Comparative analysis of the gut microbiome of ungulate species from Qinghai-Xizang plateau.

Several studies have investigated the gut bacterial composition of wild ungulates in the Qinghai-Xizang Plateau. However, the relationship between their gut microbiome dendrograms and their phylogenetic tree remains unclear. In this study, we analyzed 45 amplicons (V3-V4 region of the 16S rRNA gene) from five wild ungulates-Pseudois nayaur, Pantholops hodgsonii, Gazella subgutturosa, Bos grunniens, and Equus kiang-from the Qinghai-Xizang Plateau to clarify the relationship between their phylogenies and gut microbiome dendrograms. The unweighted pair group method with arithmetic mean analysis and hierarchical clustering analysis indicated that G. subgutturosa is closely related to P. nayaur; however, these results were inconsistent with their phylogenetic trees. Additionally, the indicator genera in the microbiome of each wild ungulate showed strong associations with the diets and habitats of their host. Thus, diet and space niche differentiation may primarily account for the differences between the gut microbiome characteristics of these wild ungulates and their phylogeny. In summary, our research provides insights into the evolutionary factors influencing the gut microbiome of wild ungulates in the Qinghai-Xizang Plateau.

O88 REDUCTION IN SYSTOLIC BLOOD PRESSURE FOLLOWING DIETARY FIBRE INTERVENTION IS DEPENDENT ON BASELINE GUT MICROBIOTA COMPOSITION

Background/Objective: Dietary interventions high in fibre have been shown to lower blood pressure (BP). This effect is via the gut microbiota, via fermentation of fibre and production of metabolites called short-chain fatty acids (SCFAs). Not all patients respond to dietary fibre interventions for unclear reasons. We aimed to determine if we can identify fibre-responders based on their gut microbiota and production of SCFAs. Methods: We performed a phase II cross-over placebo-controlled randomised clinical trial in untreated hypertensive patients. Twenty treatment-naive participants with hypertension received 40 g per day of fermentable fibre delivered as acetylated and butyrylated high amylose maize starch (HAMSAB) or the placebo for 3 weeks. Blood pressure was monitored at baseline and endpoint by ambulatory BP monitoring, with those experiencing a reduction of ≥2 mmHg in systolic BP classified as responders. The microbiota was determined by sequencing the V4-V5 region of the 16S rRNA gene in baseline stool samples. The relationship between baseline gut microbiota and response to dietary intervention was assessed with the MaAsLin2 package. Plasma SCFAs levels were quantified by mass spectrometry. Results: We observed a placebo-subtracted mean 24-hour systolic BP of –6.1 mmHg (p=0.03, reported in Jama et al., 2023 Nature Cardiovascular Research), with 14 (70%) individuals classified as responders and 6 (30%) as non-responders. Genera significantly enriched in responders included Dialister (β=1.29, q=1.921x10-134), Coprococcus (β=1.26, q=3.282x10-121), Bifidobacterium (β=1.67, q=1.11x10-81), Ruminococcus (β=0.161, q=1.11x10-8), and Roseburia (β=0.82, q=4.275x10-2). Responders also produced higher levels of the SCFAs butyrate (mean±SEM, non-responders 4.95±2.4 vs responders 51.15±14.7, p=0.0096), but no difference in other SCFAs. Conclusions: Participants who experienced a decrease in systolic BP following a dietary fibre intervention had increased bacterial genera known to contain species that produce SCFAs (Bifidobacterium, Roseburia, Ruminococcus) at baseline, and were able to produce more butyrate. These data suggest that baseline microbiota composition contributes to the response to dietary fibre intervention trials in people with hypertension, likely via increased capacity to produce butyrate.

Hidden in the blow - a matrix to characterise cetaceans’ respiratory microbiome: short-finned pilot whale as case study

Cetaceans are key sentinel species of marine ecosystems and ocean health, being a strategic taxonomic group that evaluates the well-being of aquatic habitats and detects harmful environmental trends. Respiratory diseases are amongst the main causes of death in these animals, so identifying the microbiome community in their exhaled breath condensates (EBC), i.e. blow, has been proposed as a key biomarker for assessing respiratory health. Yet, to characterise microbiomes related to these animals’ respiratory tract and use them as a proxy for health status, it is necessary to develop baseline data on the microorganisms associated with cetaceans. Here, the short-finned pilot whale (SFPW, Globicephala macrorhynchus) was used as a case study to validate the most suitable primer set to explore the prokaryotic diversity of the cetaceans’ respiratory tract. DNA extracted from blow samples (n = 12) of animals off Madeira Island was sequenced to amplify both V3-V4 and V4-V5 hypervariable regions of the 16S rRNA gene, using the same sequencing platform (Illumina MiSeq). Independently of the primer set used, all blows shared Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria phyla in their composition. V3-V4 resulted in a higher diversity of taxa with relative abundance above 1%, whereas the V4-V5 primers captured a higher number of microbial Amplicon Sequence Variants, detecting the rare microbial biosphere with pathogen potential. Additionally, it captured the core microbiome more efficiently. Thus, this study provides a detailed characterisation of SFPW respiratory-associated microbial communities, strengthening the idea of sociality influencing microbiome composition in the respiratory tract. Moreover, it supports the use of blow as a relevant biomarker for the physiological state of the airways in free-ranging cetaceans.

Metagenomic insights into bacterial dynamics and niche partitioning in response to varying oxygen gradients in the Arabian Sea oxygen minimum zone (OMZ)

This study investigates the impact of oxygen gradients on bacterial diversity and community composition within the Arabian Sea oxygen minimum zone (OMZ), providing insight into their ecology in this unique environment. Vertical profiling of physicochemical parameters and bacterial community composition was conducted at two stations within the OMZ using Illumina sequencing of the V3-V4 regions of the 16S rRNA gene. The oxygen levels in the water column of the study locations varied from oxic to hypoxic and Station-I exhibited intense anoxic conditions. Bacterial diversity analyses revealed a rich assemblage of 24 bacterial phyla dominated by Proteobacteria, with significant presence of Actinobacteria and Planctomycetes. SIMPER (Similarity percentage) analysis highlights taxa such as Synechococcophycideae, Flavobacteriia in oxic water and Phycisphaerae as significant contributors to community dissimilarity in oxygen-deficient water, emphasizing their ecological roles in nutrient cycling and the impact of oxygen availability on marine biodiversity. Canonical Correspondence Analysis (CCA) further elucidates the relationships between bacterial communities and environmental variables, with oxygen, temperature, and nutrient concentrations playing crucial roles in shaping bacterial community distributions. This research enhances our understanding of microbial ecology in the Arabian Sea OMZ by revealing how microbial communities respond to changing oxygen conditions, providing insights into the ecological dynamics of the region. Furthermore, these findings underscore the need for continued research to predict and mitigate the effects of environmental changes on marine ecosystems, particularly in the context of expanding OMZs and global biogeochemical cycles.

Examination of sex-specific interactions between gut microbiota and host metabolism after 12-week combined polyphenol supplementation in individuals with overweight or obesity

ABSTRACT Polyphenols exert beneficial effects on host metabolism, which may be mediated by the gut microbiota. We investigated sex-specific differences in microbiota composition and interactions with cardiometabolic parameters after polyphenol supplementation in individuals with overweight/obesity. In a double-blind, randomized, placebo-controlled trial, 19 women and 18 men with normal glucose tolerance and body mass index >25 kg/m2 received epigallocatechin-3-gallate and resveratrol (EGCG+RES, 282 + 80 mg/d) or placebo supplements for 12 weeks. Fecal microbiota composition (16S rRNA gene amplicon sequencing, V3-V4 region), in vivo whole-body fat oxidation (indirect calorimetry), and mitochondrial respiration in permeabilized skeletal muscle fibers (SkM-Ox; ex vivo respirometry) were determined pre- and post-intervention. Overall, EGCG+RES supplementation did not affect gut microbiota composition. Akkermansia, Ruminococcaceae UCG-002, Subdoligranulum, and Lachnospiraceae UCG-004 were more abundant, while Veillonella, Tyzzerella 4, Clostridium innocuum group, Ruminococcus gnavus group, Escherichia-Shigella, and an uncultured Ruminococcaceae family genus were less abundant in women compared to men. In women, only baseline Eubacterium ventriosum group abundance correlated with EGCG+RES-induced changes in SkM-Ox. In men, low Dorea, Barnsiella, Anaerotruncus, Ruminococcus, Subdoligranulum, Coprococcus, Eubacterium ventriosum group, Ruminococcaceae UCG-003, and a Ruminococcaceae family genus abundance, and high Blautia abundance at baseline were associated with improvements in SkM-Ox. Changes in whole-body fat oxidation were not associated with gut microbiota features. We conclude that baseline microbiota composition predicts changes in SkM-Ox as a result of EGCG+RES supplementation in men but not in women. Men may be more prone to diet-induced, gut microbiota-related improvements in cardiometabolic health. These sex-differences should be further investigated in future precision-based intervention studies.

Assessing oral and toothbrush microbial profiles among high-altitude individuals with and without periodontal disease: a case-control study

BackgroundPeriodontitis is the sixth-most common disease worldwide. The oral microbiome composition and its association with Periodontal disease (PD) have been largely explored; however, limited studies have explored the microbial profiles of both oral and toothbrushes in patients with PD. Thus, this study aimed to ascertain the oral and toothbrushes microbial composition in high-altitude populations, hypothesizing that their correlation with periodontal health would differ from those at lower altitudes, potentially indicating links between environmental factors, microbial colonization patterns, and periodontal health in distinct geographic contexts.MethodsIn the present study, we enrolled 35 individuals including 21 healthy and 14 diagnosed with PD from the Lhasa region of Tibet, China. Saliva and toothbrush samples were collected from each participant to assess the association between toothbrush usage and oral microbiome with PD using 16 S rRNA gene-specific V3-V4 regions sequencing. To assess the oral and toothbrush microbiome composition and diversity and its possible link to PD.ResultsSignificantly higher Alpha diversity (Shannon index) was observed between the PD group and PD toothbrushes (p = 0.00021) and between the PD group and Healthy toothbrushes (p = 0.00041). The predominant species were Proteobacteria, Bacteroidota, Firmicutes, Actinobacteria, and Fusobacteria, with genera Pseudomonas, Veillonella, Neisseria, Acinetobacter, and Haemophilus. In addition, PICRUST2 analysis unveiled 44 significant pathways differentiating the disease and healthy groups, along with 29 pathways showing significant differences between their respective toothbrush microbial profiles. The distinct oral and toothbrush microbial composition among high-altitude populations suggests potential adaptations to the challenges of high-altitude environments.ConclusionThis study emphasizes the importance of tailored dental care strategies, accounting for altitude and racial factors, to effectively manage periodontal health in these communities. Further research is warranted to investigate the specific microbial mechanisms and develop targeted interventions for optimizing oral health in populations across varying altitudes.

Comparison and characterization of the bacterial microbiota and SIgA production in different gastrointestinal segments in horses.

In the gastrointestinal mucosa, there is a close cooperation between secretory immunoglobulin A (SIgA) and the composition of the microbiota, which aims to maintain homeostasis as well as act as a protective barrier. The purpose of this study was to determine the composition of microbiota and SIgA production in different parts of the digestive tract (small intestine, cecum, colon and rectum) of nine healthy horses and its reflection in the feces. For this purpose, we determined: the composition of the microbiome (by next-generation Sequencing of Hypervariable Regions V3-V4 and V7-V9 of the 16S rRNA gene analysis), the amount of SIgA in the intestinal content samples (by ELISA), as well as the number of IgA-producing cells (IgA+) in the tissue samples (by immohistochemical analysis). Significant differences were observed between the small intestine and the large colon in the composition and diversity of the microbiome, as well as the number of IgA + cells in the mucosal lamina propria and the abundance of SIgA in the intestinal lumen. The small intestine in relation to the large colon is characterised by fewer IgA + cells, more SIgA in the intestinal contents and a less diverse microbiome. However, the cecum appears to be the third separate ecosystem, with a high number of IgA + cells and a diverse microbiome. The fecal sample reflects the current state of the large colon, both in terms of the microbiome and SIgA content; however, it is not known to what extent it may be influenced by dysbiosis in other parts of the digestive tract.

Identification and comparison of intestinal microbial diversity in patients at different stages of hepatic cystic echinococcosis

There is a significant focus on the role of the host microbiome in different outcomes of human parasitic diseases, including cystic echinococcosis (CE). This study was conducted to identify the intestinal microbiome of patients with CE at different stages of hydatid cyst compared to healthy individuals. Stool samples from CE patients as well as healthy individuals were collected. The samples were divided into three groups representing various stages of hepatic hydatid cyst: active (CE1 and CE2), transitional (CE3), and inactive (CE4 and CE5). One family member from each group was selected to serve as a control. The gut microbiome of patients with different stages of hydatid cysts was investigated using metagenomic next-generation amplicon sequencing of the V3–V4 region of the 16S rRNA gene. In this study, we identified 4862 Operational Taxonomic Units from three stages of hydatid cysts in CE patients and healthy individuals with a combined frequency of 2,955,291. The most abundant genera observed in all the subjects were Blautia, Agathobacter, Faecalibacterium, Bacteroides, Bifidobacterium, and Prevotella. The highest microbial frequency was related to inactive forms of CE, and the lowest frequency was observed in the group with active forms. However, the lowest OTU diversity was found in patients with inactive cysts compared with those with active and transitional cyst stages. The genus Agatobacter had the highest OTU frequency. Pseudomonas, Gemella, and Ligilactobacillus showed significant differences among the patients with different stages of hydatid cysts. Additionally, Anaerostipes and Candidatus showed significantly different reads in CE patients compared to healthy individuals. Our findings indicate that several bacterial genera can play a role in the fate of hydatid cysts in patients at different stages of the disease.

Maternal cafeteria diet programs fecal microbiota and modulates serum fatty acid and amino acid levels in adulthood rats

Maternal food environment can program fecal microbiota in offspring mediated by the imprint of intrauterine conditions. Gut bacteria play a role in host fatty acid and amino acid metabolism. This study aimed to determine the effects of maternal diet on fecal microbiota, and the impact on fatty acid and amino acid metabolism in male offspring rats. Ten male pups from dams fed standard diet (C-C, n = 5) and cafeteria diet (Caf-C, n = 5) were fed standard chow diet for twenty-three weeks. Fresh fecal samples were collected at three and twenty-six weeks of age for fecal microbiota analysis by metagenomic sequencing of the V3-V4 region of the 16S rRNA gene. At the end of the study, serum samples were collected to analyse fatty acids from phospholipid and cholesterol ester fractions by gas chromatography and free amino acids by liquid chromatography. The bacterial abundance from the Actinobacteria and Proteobacteria phyla significantly decreased over time for both groups. Additionally, significant differences were found between C-C and Caf-C groups in these bacterial phyla. In the Caf-C group, Firmicutes and Elusimicrobia phyla increased, while Bacteroidetes decreases in adulthood samples. At the genus level, the abundance of Bacteroides decreased, while Elusimicrobium, Lactobacillus, Turicibacter, Blautia, and Veillonella increased in the Caf-C group. Several metabolites including PL-MCFAs (caprylic acid and capric acid), CE-MUFAs (palmitoleic acid and heptadecenoic acid), and free amino acids aspartate, glutamic acid, and cysteine were significantly higher in Caf-C group. This study underscores the putative programming of offspring fecal microbiota by maternal diet impact. These changes led to alterations fatty acids and amino acids metabolism in adult male offspring rats.

Stratified Effects of Tillage and Crop Rotations on Soil Microbes in Carbon and Nitrogen Cycles at Different Soil Depths in Long-Term Corn, Soybean, and Wheat Cultivation.

Understanding the soil bacterial communities involved in carbon (C) and nitrogen (N) cycling can inform beneficial tillage and crop rotation practices for sustainability and crop production. This study evaluated soil bacterial diversity, compositional structure, and functions associated with C-N cycling at two soil depths (0-15 cm and 15-30 cm) under long-term tillage (conventional tillage [CT] and no-till [NT]) and crop rotation (monocultures of corn, soybean, and wheat and corn-soybean-wheat rotation) systems. The soil microbial communities were characterized by metabarcoding the 16S rRNA gene V4-V5 regions using Illumina MiSeq. The results showed that long-term NT reduced the soil bacterial diversity at 15-30 cm compared to CT, while no significant differences were found at 0-15 cm. The bacterial communities differed significantly at the two soil depths under NT but not under CT. Notably, over 70% of the tillage-responding KEGG orthologs (KOs) associated with C fixation (primarily in the reductive citric acid cycle) were more abundant under NT than under CT at both depths. The tillage practices significantly affected bacteria involved in biological nitrogen (N2) fixation at the 0-15 cm soil depth, as well as bacteria involved in denitrification at both soil depths. The crop type and rotation regimes had limited effects on bacterial diversity and structure but significantly affected specific C-N-cycling genes. For instance, three KOs associated with the Calvin-Benson cycle for C fixation and four KOs related to various N-cycling processes were more abundant in the soil of wheat than in that of corn or soybean. These findings indicate that the long-term tillage practices had a greater influence than crop rotation on the soil bacterial communities, particularly in the C- and N-cycling processes. Integrated management practices that consider the combined effects of tillage, crop rotation, and crop types on soil bacterial functional groups are essential for sustainable agriculture.

Microbiological and molecular profile of furcation defects in a population with untreated periodontitis.

To describe the microbiological composition of subgingival dental plaque and molecular profile of gingival crevicular fluid (GCF) of periodontal furcation-involved defects. Fifty-seven participants with periodontitis contributed with a degree II-III furcation involvement (FI), a non-furcation (NF) periodontal defect and a periodontally healthy site (HS). Subgingival plaque was analysed by sequencing the V3-V4 region of the 16S rRNA gene, and a multiplex bead immunoassay was carried out to estimate the GCF levels of 18 GCF biomarkers. Aiming to explore inherent patterns and the intrinsic structure of data, an AI-clustering method was also applied. In total, 171 subgingival plaque and 84 GCF samples were analysed. Four microbiome clusters were identified and associated with FI, NF and HS. A reduced aerobic microbiota (p = .01) was detected in FI compared with NF; IL-6, MMP-3, MMP-8, BMP-2, SOST, EGF and TIMP-1 levels were increased in the GCF of FI compared with NF. This is the first study to profile periodontal furcation defects from a microbiological and inflammatory standpoint using conventional and AI-based analyses. A reduced aerobic microbial biofilm and an increase of several inflammatory, connective tissue degradation and repair markers were detected compared with other periodontal defects.

Associations of upper respiratory mucosa microbiota with Rheumatoid arthritis, autoantibodies, and disease activity.

The lung is recognized as a site for initiating the formation of self-antigen and autoimmune responses in rheumatoid arthritis (RA). We aimed to investigate the association of upper respiratory microbiota with RA, autoantibody production, and disease activity. Forty-six patients with RA and 17 controls were examined. Nasopharyngeal swab samples were sequenced for microbiome profiling using the V3-V4 region of the 16S rRNA gene. The microbial diversity and relative abundance were compared between RA patients and controls. Correlation analyses were conducted to evaluate the relationship between microbial abundance and clinical markers such as autoantibodies and disease activity. Microbial diversity analysis revealed no major differences between RA patients and healthy controls. However, beta diversity analysis indicated a subtle distinction in microbial composition (unweighted UniFrac distance) between the two groups (P = 0.03), hinting at a minor subset of microbiota associated with disease status. Differential abundance analysis uncovered specific taxa at various taxonomic levels, including Saccharibacteria (TM7) [O-1] (PFDR = 2.53 × 10-2), TM7 [F-1] (PFDR = 5.20 × 10-3), Microbacterium (PFDR = 3.37 × 10-4), and Stenotrophomonas (PFDR = 2.57 × 10-3). The relative abundance of ten genera correlated significantly with anti-cyclic citrullinated peptide (anti-CCP) antibody levels (PFDR < 0.05) and 11 genera were significantly associated with disease activity markers, including ESR, CRP, DAS28-ESR, and DAS-CRP (PFDR < 0.05). In particular, Saccharibacteria TM7 [G-3] and Peptostreptococcaceae [XI] [G-1] were correlated with all disease activity biomarkers. Dysbiosis in the upper respiratory mucosa is associated with RA, anti-CCP antibody levels, and disease activity.

The comparison of gut microbiota between wild and captive Asian badgers (Meles leucurus) under different seasons

The gut microbiota plays an important role in the immunology, physiology and growth and development of animals. However, currently, there is a lack of available sequencing data on the gut microbiota of Asian badgers. Studying the gut microbiota of Asian badgers could provide fundamental data for enhancing productivity and immunity of badgers’ breeding, as well as for the protection of wild animals. In this study, we first characterized the composition and structure of the gut microbiota in the large intestines of wild and captive Asian badgers during summer and winter by sequencing the V3-V4 region of the 16S ribosomal RNA gene. A total of 9 dominant phyla and 12 genera among the bacterial communities of the large intestines exhibited significant differences. Our results showed that Firmicutes and Proteobacteria were the most predominant in both wild and captive badgers, regardless of the season. Romboutsia, Streptococcus and Enterococcus may represent potential sources of zoonoses, warranting further attention and study. Our findings indicated that the diversity and availability of food resources were the most important influencing factors on the gut microbiota of Asian badgers, providing fundamental data for the protection and conservation of wild animals. Variation in the gut microbiota due to season, age and sex in both wild and captive Asian badgers should be considered in future research directions. Furthermore, combined multi-omics studies could provide more information for wild animal conservation, and enhancing our understanding of the molecular mechanism between the microbiota and host.