Differences In Beta Diversity Research Articles

Soil microbial community response to ectomycorrhizal dominance in diverse neotropical montane forests

Ectomycorrhizal (EM) associations can promote the dominance of tree species in otherwise diverse tropical forests. These EM associations between trees and their fungal mutualists have important consequences for soil organic matter cycling, yet the influence of these EM-associated effects on surrounding microbial communities is not well known, particularly in neotropical forests. We examined fungal and prokaryotic community composition in surface soil samples from mixed arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) stands as well as stands dominated by EM-associated Oreomunnea mexicana (Juglandaceae) in four watersheds differing in soil fertility in the Fortuna Forest Reserve, Panama. We hypothesized that EM-dominated stands would support distinct microbial community assemblages relative to the mixed AM-EM stands due to differences in carbon and nitrogen cycling associated with the dominance of EM trees. We expected that this microbiome selection in EM-dominated stands would lead to lower overall microbial community diversity and turnover, with tighter correspondence between general fungal and prokaryotic communities. We measured fungal and prokaryotic community composition via high-throughput Illumina sequencing of the ITS2 (fungi) and 16S rRNA (prokaryotic) gene regions. We analyzed differences in alpha and beta diversity between forest stands associated with different mycorrhizal types, as well as the relative abundance of fungal functional groups and various microbial taxa. We found that fungal and prokaryotic community composition differed based on stand mycorrhizal type. There was lower prokaryotic diversity and lower relative abundance of fungal saprotrophs and pathogens in EM-dominated than AM-EM mixed stands. However, contrary to our prediction, there was lower homogeneity for fungal communities in EM-dominated stands compared to mixed AM-EM stands. Overall, we demonstrate that EM-dominated tropical forest stands have distinct soil microbiomes relative to surrounding diverse forests, suggesting that EM fungi may filter microbial functional groups in ways that could potentially influence plant performance or ecosystem function.

The effects of hydrolyzed protein on macronutrient digestibility, fecal metabolites and microbiota, oxidative stress and inflammatory biomarkers, and skin and coat quality in adult dogs.

Research on protein hydrolysates has observed various properties and functionalities on ingredients depending on the type of hydrolysate. The objective of this study was to evaluate the effects of hydrolyzed chicken protein that was incorporated into diets on digestibility, gut health, skin and coat health, oxidative stress, and intestinal inflammation markers in healthy adult dogs. Five complete and balanced diets were manufactured: (1) CONd: 25% chicken meal diet; (2) 5% CLHd: 5% chicken liver and heart hydrolysate plus 20% chicken meal diet; (3) CLHd: 25% chicken liver and heart hydrolysate diet; (4) 5% CHd: 5% chicken hydrolysate plus 20% chicken meal diet; (5) CHd: 25% chicken hydrolysate diet. A replicated 5 × 5 Latin square design was used which included 10 neutered adult Beagles. Each of the 5 periods consisted of a 7-d washout time and a 28-d treatment period. All diets were well accepted by the dogs. Fecal butyrate concentration was higher while fecal isovalerate and total phenol/indole were lower in dogs fed CLHd than CONd (P < 0.05). Dogs fed CHd had higher fecal immunoglobulin A concentration when compared with CLHd (P < 0.05); however, both groups were comparable to the CONd. There was no difference among groups in serum cytokine concentrations, serum oxidative stress biomarkers, or skin and coat health analyses (P > 0.05). Fecal microbiota was shifted by CLHd with higher abundance in Ruminococcus gauvreauii group as well as lower Clostridium sensu stricto 1, Sutterella, Fusobacterium, and Bacteroides when compared with CONd (P < 0.05). There was also a difference in beta diversity of fecal microbiota between CLHd and CHd (P < 0.05). In conclusion, chicken protein hydrolysate could be incorporated into canine extruded diets as a comparable source of protein to traditional chicken meal. The test chicken protein hydrolysates showed the potential to support gut health by modulating immune response and microbiota; however, functional properties of protein hydrolysates are dependent on inclusion level and source.

Alterations of rumen and fecal microbiome in growing beef and dairy steers fed rumen-protected Capsicum oleoresin.

The microbiome has been linked to animal health and productivity, and thus, modulating animal microbiomes is becoming of increasing interest. Antimicrobial growth promoters (AGP) were once a common technology used to modulate the microbiome, but regulation and consumer pressure have decreased AGP use in food animals. One alternative to antimicrobial growth promoters are phytotherapeutics, compounds derived from plants. Capsaicin is a compound from the Capsicum genus, which includes chili peppers. Capsaicin has antimicrobial properties and could be used to manipulate the gastrointestinal microbiome of cattle. Both the rumen and fecal microbiomes are essential to cattle health and production, and modulation of either microbiome can affect both cattle health and productivity. We hypothesized that the addition of rumen-protected capsaicin to the diet of cattle would alter the composition of the fecal microbiome, but not the rumen microbiome. To determine the impact of rumen-protected capsaicin in cattle, four Holstein and four Angus steers were fed rumen-protected Capsicum oleoresin at 0 (Control), 5, 10, or 15mg kg-1 diet dry matter. Cattle were fed in treatment groups in a 4 × 4 Latin Square design with a 21-d adaptation phase and a 7-d sample collection phase. Rumen samples were collected on day 22 at 0-, 2-, 6-, 12-, and 18-h post-feeding, and fecal swabs were collected on the last day of sample collection, day 28, within 1h of feeding. Sequencing data of the 16s rRNA gene was analyzed using the dada2 pipeline and taxa were assigned using the SILVA database. No differences were observed in alpha diversity among fecal or rumen samples for either breed (P > 0.08) and no difference between groups was detected for either breed in rumen samples or for Angus steers in fecal samples (P > 0.42). There was a difference in beta diversity between treatments in fecal samples of Holstein steers (P < 0.01), however, a pairwise comparison of the treatment groups suggests no difference between treatments after adjusting for multiple comparisons. Therefore, we were unable to observe substantial overall variation in the rumen or fecal microbiomes of steers due to increasing concentrations of rumen-protected capsaicin. We do, however, see a trend toward increased concentrations of capsaicin influencing the fecal microbiome structure of Holstein steers despite this lack of significance.

Age over sex: evaluating gut microbiota differences in healthy Chinese populations.

Age and gender have been recognized as two pivotal covariates affecting the composition of the gut microbiota. However, their mediated variations in microbiota seem to be inconsistent across different countries and races. In this study, 613 individuals, whom we referred to as the "healthy" population, were selected from 1,018 volunteers through rigorous selection using 16S rRNA sequencing. Three enterotypes were identified, namely, Escherichia-Shigella, mixture (Bacteroides and Faecalibacterium), and Prevotella. Moreover, 11 covariates that explain the differences in microbiota were determined, with age being the predominant factor. Furthermore, age-related differences in alpha diversity, beta diversity, and core genera were observed in our cohort. Remarkably, after adjusting for 10 covariates other than age, abundant genera that differed between age groups were demonstrated. In contrast, minimal differences in alpha diversity, beta diversity, and differentially abundant genera were observed between male and female individuals. Furthermore, we also demonstrated the age trajectories of several well-known beneficial genera, lipopolysaccharide (LPS)-producing genera, and short-chain fatty acids (SCFAs)-producing genera. Overall, our study further elucidated the effects mediated by age and gender on microbiota differences, which are of significant importance for a comprehensive understanding of the gut microbiome spectrum in healthy individuals.

Longitudinal Pilot Evaluation of the Gut Microbiota Comparing Patients With and Without Chronic Kidney Disease

ObjectiveThe gut microbiota contributes to metabolic diseases, such as diabetes and hypertension, but is poorly characterized in chronic kidney disease (CKD). Design and methodsWe enrolled 24 adults within household pairs, in which at least one member had self-reported kidney disease, diabetes, or hypertension. CKD was classified based on estimated glomerular filtration rate (eGFR) <60 ml/min/1.73m2 or urine-albumin-to-creatinine ratio (UACR) of ≥30 mg/g. Participants collected stool and dietary recalls seasonally over a year. Gut microbiota was characterized using 16s rRNA and metagenomic sequencing. Results10 participants had CKD (42%) with a median (IQR) eGFR of 49 (44, 54) ml/min/1.73 m2. By 16s rRNA sequencing, there was moderate to high intra-class correlation (ICC=0.6) for seasonal alpha diversity (Shannon index) within-individuals and modest differences by season (p<0.01). ICC was lower with metagenomics, which has resolution at the species level (ICC=0.2). There were no differences in alpha or beta diversity by CKD with either method. Among 79 genera, Frisingicoccus, Tuzzerella, Faecalitalea, and Lachnoclostridium had lower abundance in CKD, while Collinsella, Lachnospiraceae_ND3007, Veillonella, and Erysipelotrichaceae_UCG_003 were more abundant in CKD (each nominal p<0.05) using 16s rRNA sequencing. Higher Collinsella and Veillonella and lower Lachnoclostridium in CKD were also identified by metagenomics. By metagenomics, Coprococcus catus and Bacteroides stercoris were more and less abundant in CKD, respectively, at false discovery rate corrected p=0.02. ConclusionsWe identified candidate taxa in the gut microbiota associated with CKD. High ICC in individuals with modest seasonal impacts imply that follow up studies may use less frequent sampling.

Comparison of the fecal microbiota of adult healthy dogs fed a plant-based (vegan) or an animal-based diet.

Pet guardians are increasingly seeking vegan dog foods. However, research on the impact of these diets on gastrointestinal (GI) physiology and health is limited. In humans, vegan diets modify the GI microbiota, increasing beneficial digestive microorganisms. This study aimed to examine the canine fecal microbiota in response to a vegan diet compared to an animal-based diet. Sixty-one client-owned healthy adult dogs completed a randomized, double-blinded longitudinal study. Dogs were randomly assigned into two groups that were fed either a commercial extruded animal-based diet (MEAT, n = 30) or an experimental extruded vegan diet (PLANT, n = 31) for 12 weeks. Fecal collections occurred at the start of the experimental period and after 3 months of exclusively feeding either diet. Bacterial DNA was extracted from the feces, and the V4 region of the 16S rRNA gene was amplified using PCR and sequenced on Illumina MiSeq. Beta-diversity was measured using Jaccard and Bray-Curtis distances, and the PERMANOVA was used to assess for differences in fecal microbiota within and between groups. Alpha-diversity indices for richness, evenness, and diversity, as well as relative abundance, were calculated and compared between groups. Beta-diversity differences occurred between diet groups at exit time-point with differences on Bray-Curtis distances at the family and genus levels (p = 0.007 and p = 0.001, respectively), and for the Jaccard distance at the family and genus level (p = 0.006 and p = 0.011, respectively). Significant differences in alpha-diversity occurred when comparing the PLANT to the MEAT group at the exit time-point with the PLANT group having a lower evenness (p = 0.012), but no significant differences in richness (p = 0.188), or diversity (p = 0.06). At exit-timepoint, compared to the MEAT group, the relative abundance of Fusobacterium, Bacteroides, and Campylobacter was lower in the PLANT group. The relative abundance of Fusobacterium decreased over time in the PLANT group, while no change was observed in the MEAT group. These results indicate that vegan diets may change the canine gut microbiota. Future studies are warranted to confirm our results and determine long-term effects of vegan diets on the canine gut microbiome.

Longitudinal Changes of Ocular Surface Microbiome in Patients Undergoing Hemopoietic Stem Cell Transplant (HSCT).

To evaluate changes in the ocular surface microbiome (OSM) between pre- and post-haemopoietic stem cell transplant (HSCT) in the same patient, and to assess the potential impact of these changes in ocular graft-versus-host disease (o)GVHD development. Lower fornix conjunctival swabs of 24 patients were obtained before and after HSCT and subjected to DNA extraction for amplification and sequencing of the V3-V4 regions of the bacterial 16S rRNA gene. The obtained reads were reconstructed, filtered, and clustered into zero-radius operational taxonomic units (zOTUs) at 97% identity level before taxonomic assignment, and biodiversity indexes were calculated. Transplant characteristics were recorded, and dry eye was diagnosed and staged 1-4 according to the Dry Eye WorkShop (DEWS) score. No significant difference in OSM alpha diversity between pre- and post-transplant was found. A significant difference in beta diversity was observed between patients with a DEWS score of 1 versus 3 (p = 0.035). Increased corneal damage between pre- and post-HSCT was significantly associated with a decrease in alpha diversity. The changes in OSM were not associated with oGVHD, nor with any transplant parameter. This preliminary study is the first study to analyse changes in the OSM before and after HSCT longitudinally. No trend in OSM biodiversity, microbial profile, or overall composition changes before and after HSCT was significant or associated with oGVHD onset. The great variability in the observed OSM profiles seems to suggest the absence of a patient-specific OSM "signature".

Impact of dietary inflammatory index on gingival health.

Periodontal disease is a biofilm-dependent chronic inflammatory condition triggered by a host response. Several factors impact systemic inflammation and could lead to changes in disease pathogenesis. Recently, studies have assessed the influence of nutritional patterns on the development of periodontitis. In the present cross-sectional study, we evaluated the dietary inflammatory profile on periodontal conditions, focusing on clinical, subgingival microbial, and cytokine assessment of individuals with periodontal health or gingivitis. One hundred patients with periodontal health or gingivitis were included. Plaque index (PI), Bleeding on probing (BoP), the probing depth (PD), and the clinical attachment level (CAL) for each patient were assessed. Nutritional data and the Dietary Inflammatory Index (DII) were recorded by two 24-h food recalls on non-consecutive days. Biofilm and gingival crevicular fluid (GCF) to assess the microbiome profile and inflammatory biomarkers were collected. Multiple regressions focused on the DII, age, and sex as predictors of periodontal conditions were done. Age and moderate DII scores increased the risk of gingivitis by 1.64 and 3.94 times, respectively. Males with an elevated DII score had 27.15 times higher odds of being diagnosed with gingivitis and BoP (β=6.54; p=0.03). Elderly patients with a moderate or high DII score were less prone to gingivitis and increased BoP (p<0.04) compared with younger subjects. Considering the DII, there were no differences in microbial alpha and beta diversity; however, distinct species abundance and a higher concentration of monocyte-chemoattractant protein-1 and interleukin 33 were seen in patients with a higher DII. A pro-inflammatory diet significantly contributes to periodontal inflammation, modulating inflammatory biomarkers and affecting the subgingival microbial community in healthy individuals.

Characteristics of gut microbiota in captive Asian elephants (Elephas maximus) from infant to elderly

Gut microbiota play an important role in the health and disease of Asian elephants, however, its characteristics at each stage of life have not been thoroughly investigated in maintaining and regulating health of elephants. This study, therefore, aimed to characterize the profiles of the gut microbiota of captive Asian elephants from infants to the elderly. Gut microbiota were identified by 16S rRNA sequencing from the feces of captive Asian elephants with varying age groups, including infant calves, suckling calves, weaned calves, subadult and adult elephants, and geriatric elephants. The diversity of the gut microbiota was lowest in infants, stable during adulthood, and slightly decreased in the geriatric period. The gut microbiota of the infant elephants was dominated by milk-fermenting taxa including genus Bifidobacterium of family Bifidobacteriaceae together with genus Akkermansia. The fiber-fermenting taxa such as Lachnospiraceae_NK3A20_group were found to be increased in suckling elephants in differential abundance analysis by Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC). The gut microbiota profiles after weaning until the adult period has been uniform as indicated by no significant differences in beta diversity between groups. However, the composition of the gut microbiota was found to change again in geriatric elephants. Understanding of the composition of the gut microbiota of captive Asian elephants at various life stages could be beneficial for promoting good health throughout their lifespan, as well as ensuring the welfare of captive elephants.

Duodenal and pancreatic tissue microbiome profiles of PPI users and non-users

Factors that influence the pancreas microbiome are not well understood. Regular proton pump inhibitor (PPI) use induces significant alterations in the gut microbiome, including an increase in the abundance of Streptococcus, and may be associated with pancreatic cancer risk. The aim of this study was to examine whether PPI use is associated with pancreatic and duodenal tissue microbiomes. We compared 16S rRNA microbiome profiles of normal pancreatic and duodenal tissue from 103 patients undergoing pancreatic surgery for non-malignant indications, including 34 patients on PPIs, accounting for factors including age, smoking, body mass index and the presence of main pancreatic duct dilation. Histologically normal tissue from the pancreatic head had higher alpha diversity and enrichment of Firmicutes by phylum-level analysis and Streptococcus species compared to normal pancreas body/tail tissues (16.8 % vs 8.8 %, P = .02, and 5.9 % vs 1.4 %, P = .03, respectively). Measures of beta diversity differed significantly between the pancreas and the duodenum, but in subjects with main pancreatic duct dilation, beta diversity of pancreatic head tissue was more similar to normal duodenal tissue than those without pancreatic duct dilation. Duodenal tissue of PPI users had significant enrichment of Firmicute phyla (34.7 % vs. 14.1 %, P = .01) and Streptococcus genera (19.5 % vs. 5.2 %, P = .01) compared to non-users; these differences were not evident in pancreas tissues. By multivariate analysis, PPI use was associated with alpha diversity in the duodenum, but not in the pancreas. However, some differences in pancreas tissue beta diversity were observed between PPI users and non-users. In summary, we find differences in the microbiome profiles of the pancreas head versus the pancreatic body/tail and we find PPI use is associated with alterations in duodenal and pancreatic tissue microbiome profiles.

Effects of early postnatal gastric and colonic microbiota transplantation on piglet gut health

BackgroundDiarrhea is a major cause of reduced growth and mortality in piglets during the suckling and weaning periods and poses a major threat to the global pig industry. Diarrhea and gut dysbiosis may in part be prevented via improved early postnatal microbial colonization of the gut. To secure better postnatal gut colonization, we hypothesized that transplantation of colonic or gastric content from healthy donors to newborn recipients would prevent diarrhea in the recipients in the post-weaning period. Our objective was to examine the impact of transplanting colonic or gastric content on health and growth parameters and paraclinical parameters in recipient single-housed piglets exposed to a weaning transition and challenged with enterotoxigenic Escherichia coli (ETEC).MethodsSeventy-two 1-day-old piglets were randomized to four groups: colonic microbiota transplantation (CMT, n = 18), colonic content filtrate transplantation (CcFT, n = 18), gastric microbiota transplantation (GMT, n = 18), or saline (CON, n = 18). Inoculations were given on d 2 and 3 of life, and all piglets were milk-fed until weaning (d 20) and shortly after challenged with ETEC (d 24). We assessed growth, diarrhea prevalence, ETEC concentration, organ weight, blood parameters, small intestinal morphology and histology, gut mucosal function, and microbiota composition and diversity.ResultsEpisodes of diarrhea were seen in all groups during both the milk- and the solid-feeding phase, possibly due to stress associated with single housing. However, CcFT showed lower diarrhea prevalence on d 27, 28, and 29 compared to CON (all P < 0.05). CcFT also showed a lower ETEC prevalence on d 27 (P < 0.05). CMT showed a higher alpha diversity and a difference in beta diversity compared to CON (P < 0.05). Growth and other paraclinical endpoints were similar across groups.ConclusionIn conclusion, only CcFT reduced ETEC-related post-weaning diarrhea. However, the protective effect was marginal, suggesting that higher doses, more effective modalities of administration, longer treatment periods, and better donor quality should be explored by future research to optimize the protective effects of transplantation.

Herpesvirus reactivation in respiratory tract is associated with increased mortality of severe pneumonia patients and their respiratory microbiome dysbiosis.

Severe pneumonia (SP) is a respiratory tract disease that seriously threatens human health. The herpesvirus detected in patients, especially with severe and immunodeficient diseases, is gradually attracting the attention of clinical doctors. However, little is known about the effect of herpesvirus on the prognosis of SP patients and the pulmonary microbial community. Here, we retrospectively analyzed respiratory samples from 45 SP patients detected by metagenomic next-generation sequencing (mNGS). A total of five types of herpesviruses were detected, with Human alphaherpesvirus 1 (HHV-1) in 19 patients, Human betaherpesvirus 5 (CMV) in 7 patients, Human betaherpesvirus 7 (HHV-7) in 6 patients, Human alphaherpesvirus 2 (HHV-2) in 5 patients, and Human gammaherpesvirus 4 (EBV) in 4 patients. Further analysis showed that the mortality of the herpesvirus-positive group was significantly higher than that of the negative group. The results also showed that HHV-1 was significantly associated with the prognosis of SP patients, while the other herpesviruses did not have a significant difference in patient mortality. A comparison of the microbial community characteristics of SP patients showed a significant difference in beta-diversity between herpesvirus-positive and negative groups. Species difference analysis showed that the herpesvirus-positive group was related to more conditional pathogens, such as Pneumocystis jirovecii and Burkholderia cepacia. In summary, our results suggest that the presence of herpesvirus is associated with the mortality of SP patients. Furthermore, enrichment of conditional pathogens in the respiratory tract of herpesvirus-positive SP patients may be a potential reason for the increased mortality.

The preliminary evidence on the association of the gut microbiota with stroke risk stratification in South Chinese population.

This study aimed to investigate the association between the gut microbiota and the risk of stroke. Faecal samples from 60 participants in South China, including 45 individuals with risk factors for stroke and 15 healthy controls, were collected and subjected to 16S rRNA sequencing. A bioinformatics analysis was performed to characterise the gut microbial diversity and taxonomic compositions at different risk levels (low, moderate, and high) of stroke. Functional prediction and correlation analyses between the microbiota and laboratory markers were performed to explore the potential mechanisms. A significant difference in beta diversity was observed between the participants from the stroke risk and healthy control groups. Linear discriminant effect size analysis revealed a large number of vascular beneficial bacteria enriched in the participants from the healthy control and low-risk groups, but a few vascular harmful bacteria were more abundant in the participants from the high-risk group than in those from the other groups. In addition, Anaerostipes, Clostridium_XlVb, and Flavonifractor, all of which belonged to the Firmicutes phylum, were enriched in the participants from the low-risk group, and their relative abundances gradually decreased as the stroke risk increased. Spearman's analysis revealed that these outstanding microbiota correlated with the levels of triglycerides, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, white blood cells, neutrophils, and carotid intima-media thickness. The preliminary evidence suggests that gut microbiota is associated with stroke risk. It potentially ameliorates atherosclerosis by targeting lipid metabolism and inflammation. This provides novel insights into the early screening of stroke risk and primary prevention.

Comparative analysis of fasting effects on the cecum microbiome in three guinea pig breeds: Andina, Inti, and Peru.

Guinea pigs have historically been used as a food source and are also an important model for studying the human intestines. Fasting is the act of temporarily stopping the intake of food. This process can alter the microbiota of various animals. This study is the first to investigate the impact of fasting on the cecum microbiome of three guinea pig breeds. We investigated the impact of fasting on the microbiome population structure in the cecum of three guinea pig breeds. This was done by sequencing and analyzing the V4 hypervariable region of the 16S rRNA gene in bacterial communities found in cecum mucosa samples. To achieve this, we established two treatment groups (fasting and fed), for each of the three guinea pig breeds: Andina, Inti, and Peru. The study involved twenty-eight guinea pigs, which were divided into the following groups: Andina-fed (five), Andina-fasting (five), Inti-fed (four), Inti-fasting (five), Peru-fed (five), and Peru-fasting (four). The results indicated a significant difference in beta diversity between the treatment groups for the Peru breed (P-value = 0.049), but not for the treatment groups of the Andina and Inti breeds. The dominant phyla across all groups were Firmicutes and Bacteroidetes. We observed variations in the abundance of different taxa in the cecum microbiota when comparing the treatment groups for each breed. Additionally, there was a higher number of unique taxa observed in the fasting groups compared to the fed groups. We discovered that the genus Victivallis was the only one present in all fasting groups across all breeds. Despite the findings, the resilience of the gut microbiome was not challenged in all three breeds, which can lead to disruptive changes that may affect the overall maintenance of the cecum microbiome. Based on the observed differences in the treatment groups of the Peru breed, it can be suggested that fasting has a greater impact on this particular breed.

Characterization of the semen microbiota of healthy stud dogs using 16S RNA sequencing

The reproductive microbiota of male dogs has never been investigated using culture-independent sequencing techniques. The purpose of the present study was to get seminal knowledge on the microbiota of the ejaculate. Specifically, factors as the fraction of the ejaculate, the sperm quality (normospermia, teratozoospermia), and the living environment were evaluated. The sperm-rich and the prostatic fractions of the ejaculate were collected from healthy stud dogs. Following the sperm analysis, samples from twenty animals (normospermic n = 10 and teratozoospermic n = 10) were stored at – 80 °C until further processing including DNA extraction and 16S rRNA sequencing. Alpha- (Shannon index) and beta- (Bray-Curtis, Unweighted UniFrac) diversities were assessed and compared (PERMANOVA) based on the group of samples (biological samples from the ejaculate and controls), the fraction of the ejaculate (sperm-rich and prostatic fractions), the animal group (normospermia and teratozoospermia), and the living environment of the animal (kennel or pet living in-house). The most abundant bacterial phyla in canine semen samples were Proteobacteria, Firmicutes, and Actinobacteria. Overall, the dominant bacterial family was that of Pasteurellaceae The genus Mycoplasma was never detected. No differences in terms of bacterial composition were found based on the fraction of the ejaculate and based on the animal group (P > 0.05). On the other hand, differences in alpha and beta diversities were highlighted based on the living environment (P = 0.001).Overall, the results of the present study provide preliminary insights on dog semen microbiota, opening a new chapter in the field of canine andrology. Our results suggest that the environment may play a role in influencing the reproductive microbiota of male dogs and that the prostatic fraction of the ejaculate can be used for further research as a representative of the semen microbiota.

Bacteroides is increased in an autism cohort and induces autism-relevant behavioral changes in mice in a sex-dependent manner

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition which is defined by decreased social communication and the presence of repetitive or stereotypic behaviors. Recent evidence has suggested that the gut-brain axis may be important in neurodevelopment in general and may play a role in ASD in particular. Here, we present a study of the gut microbiome in 96 individuals diagnosed with ASD in Israel, compared to 42 neurotypical individuals. We determined differences in alpha and beta diversity in the microbiome of individuals with ASD and demonstrated that the phylum Bacteroidetes and genus Bacteroides were the most significantly over-represented in individuals with ASD. To understand the possible functional significance of these changes, we treated newborn mice with Bacteroides fragilis at birth. B. fragilis-treated male mice displayed social behavior dysfunction, increased repetitive behaviors, and gene expression dysregulation in the prefrontal cortex, while female mice did not display behavioral deficits. These findings suggest that overabundance of Bacteroides, particularly in early life, may have functional consequences for individuals with ASD.

Characteristics of the gut microbiome of Swiss elite athletes with a spinal cord injury: An exploratory study

Objectives To illustrate and explore associations between the gut microbiome and spinal cord injury (SCI) characteristics, physical training, dietary intake, body composition, and blood biomarkers of elite Swiss athletes. Design and setting Baseline data analysis of athletes with SCI who participated in a pilot trial (NCT04659408) in the Swiss Paraplegic Center, Nottwil, Switzerland. Participants Elite athletes, five males, and six females, with SCI who competed internationally. Outcome measures We conducted a differential abundance analysis and measured the alpha and beta diversity of the gut microbiome. Results The athletes’ median age was 34.5 years. Six had traumatic SCI and five had a spina bifida. The athletes competed in para-cycling (5), wheelchair athletics (3), and wheelchair tennis (3). A higher duration of training per week was positively associated with Akkermansia and Akkermansiaceae but negatively associated with Prevotellaceae. Muribaculaceae was negatively associated with the average number of trainings per week. Waist circumference is negatively associated with Butyricimonas. Significant differences in the alpha diversity were found with sex, gastrointestinal quality of life index (GIQLI) scores, total caloric intake, total fat intake, total carbohydrate intake, and high-sensitivity C-reactive protein (hs-CRP). Beta diversity differences were found with impairment of the sympathetic nervous system of the gut at the genus level and HbA1c at the family level. Conclusions This study provides insight into the gut microbiome of athletes with SCI. Our results were similar to those found in athletes without SCI. Further replication is needed to confirm the relationships of organisms observed in the gut of athletes with SCI.

The impacts of reduced connectivity on multiple facets of aquatic insect diversity in floodplain wetlands, Northeast China

River-floodplain ecosystems are highly complex and dynamic systems that are subjected to human disturbance, such as the construction of levees. Aquatic insects are among the most widely used indicators to assess human impacts on floodplain wetlands. Most studies are still based on taxonomic biodiversity. However, trait-based approaches remain limited, which could impede the development of effective management strategies. Here, we investigated aquatic insect assemblages in eleven pairs of wetlands along the Wusuli River in two seasons (Spring and Autumn) and assessed their responses to the impact of levee construction, considering taxonomic and functional diversity. We found that pooled species richness (73 taxa) in river-connected wetlands was almost twice of that in levee-blocked wetlands (37 taxa). Six and one indicator taxa for river-connected wetlands were identified in May and October, respectively, while no indicator taxon for the levee-blocked wetlands was identified. Moreover, taxonomic and functional alpha diversity in river-connected wetlands was much higher than in levee-blocked wetlands, but beta diversity showed a contrasting pattern. Additionally, multivariate dispersion analysis indicated a more evident difference in beta diversity between river-connected and levee-blocked wetlands in May than in October, likely due to the temporary lateral connection in summer (i.e., water flowed over levees during flood events). Our results revealed that anthropogenic impacts (e.g., levee construction and agricultural activity) weakened the connectivity of floodplain wetland ecosystems, leading to decreased taxonomic and functional diversity of aquatic insects in isolated wetlands. Our study highlights the importance of combining taxonomic and trait-based approaches in biomonitoring programs of floodplain wetland ecosystems. It also underscores the necessity of restoring habitat connectivity of wetland ecosystems (e.g., river-floodplain connectivity and connections between different wetlands) to facilitate biodiversity recovery and enhance ecological functions and services supported by these valuable ecosystems.

Novel Multi-Strain E3 Probiotic Formulation Improved Mental Health Symptoms and Sleep Quality in Hong Kong Chinese.

Mental health issues have emerged as a significant concern in public health, given their association with physical and psychological comorbidities and the resultant socioeconomic burdens. Recent studies have highlighted the interplay between gut microbes and brain functions through the gut-brain axis. To investigate this further, we conducted a targeted 16S rRNA sequencing and comprehensive bioinformatic analysis among Southern Chinese individuals to explore the role of the gut microbiome in depression, anxiety, and sleep disturbance. We analyzed the differences in the gut microbiome profile of 68 participants with sleep disturbance and mood symptoms before and after an 8-week course of a novel oral E3 multi-strain probiotics formula. The results revealed a significant improvement in subjective sleep quality (PSQI: mean 8.79 at baseline vs. 7.10 at week 8, p < 0.001), depressive symptoms (PHQ9: mean 6.17 at baseline vs. 4.76 at week 8, p < 0.001), and anxious symptoms (GAD7: mean 4.90 at baseline vs. 3.76 at week 8, p < 0.001). Additionally, there were notable differences in beta diversity (weighted UniFrac; p = 0.045) and increased Firmicutes/Bacteroidetes (F/B) ratio (p = 4 × 10-4) were observed in the gut microbiome analysis. Furthermore, the relative abundance of Bifidobacterium bifidum (p < 0.001), Lactobacillus acidophilus (p < 0.001), Lactobacillus helveticus (p < 0.001) and Lactobacillus plantarum (p < 0.001) were significantly increased after the 8-week probiotic supplementation. Our study suggests that the gut microbial landscape varies between responders and non-responders at multiple levels, including genera, species, functional, and network interaction. Notably, the use of probiotics in populations with depressive or anxious symptoms and poor sleeping quality remodeled the gut microbiome and demonstrated improved mood and sleep quality.

Changes in bacterial community structure and root metabolites in Themeda japonica habitat under slight and strong karst rocky desertification

Microorganisms can quickly respond to vegetation succession, and plants also regulate the structure of microbial community through root exudates or by affecting soil nutrients. Themeda japonica is a dominant plant species in karst rocky desertification (KRD) regions, but it is currently unclear the role of soil bacterial communities, interact with T. japonica during the KRD process. The purpose of this study is to explore the variation of soil metal element content, soil enzyme activity, soil bacterial communities and soil environment factor/root metabolites of T. japonica, and the relationship between soil bacterial communities and root metabolites in different degrees of KRD. Our results showed that the significant changes was found in soil metal element content and soil enzyme activity from slight KRD to strong KRD. Metabolic analysis demonstrated that the strong KRD environment increased the organic acid content of T. japonica roots, decreased the amino acids and sugars content. The specific metabolic pathways of Citrate cycle (TCA cycle), carbon fixation in photosynthetic organisms, glyoxylate and dicarboxylate metabolism and pyruvate metabolism were altered to help T. japonica adapt to the harsh environment. In addition, there was significant difference in beta diversity among bulk soil, rhizosphere and root endophytic bacterial community. With the aggravation of KRD, the abundance of Proteobacteria was decreased, while the abundance of Actinobacteria was increased. KRD also enhanced positive interactions between bacterial communities, and made the inter species associations of endophytic bacteria more sensitive. Mantel analysis showed that potassium (K), magnesium (Mg), cadmium (Cd) lead (Pb) and invertase (Inv), alkaline phosphatase (Alp), catalase (Cat), and aconitic acid, alanine, fructose, glucose, L-malic acid, palmitic acid, saccharic acid and serine significantly influence bacterial communities in bulk soil and rhizosphere. These results implied that root metabolites and soil characteristics might jointly affect the bacterial community in KRD area during the process of T. japonica in adapting to different rocky desertification.