Changes In Β-diversity Research Articles

P1311 Mucosal Microbiome Signatures Associated with Postoperative Endoscopic Recurrence in Paediatric Crohn’s Disease

Abstract Background Following ileocecal resection (ICR) for Crohn’s disease (CD), recurrence is frequent even in the biologic era. Gut microbiota is involved in this setting and a few adult studies have suggested that bacterial recolonization after surgery may predict recurrence. Given the inherent risk of postoperative recurrence associated with age and disease duration, studies investigating the role of the gut microbiota in predicting relapse in children undergoing ICR appears critical. We aimed to identify changes in the mucosal microbiome associated with, and predictive of, endoscopic CD recurrence within the first year post-ICR in a paediatric population. Methods Microbiota composition (16S rDNA sequencing) was assessed from ileal and colonic mucosa at the time of ICR and later during endoscopic evaluation from above and below the surgical anastomosis in 33 patients (26 with paired samples) prospectively recruited at a tertiary care paediatric IBD center. Results The study included 33 children (mean age 16±2.7 years) undergoing ICR. At the time of ileo-colonoscopy, 9 (35%) patients had endoscopic recurrence (Rutgeerts’ score≥ i2). ICR strongly modified the gut mucosal microbiota composition with significant changes in β-diversity (R2= 0.03, PERMANOVA test, p=0.01). Bacterial recolonization post-ICR differed according to recurrence status (Figure 1). Post-operatively, recurrence was associated with an increase in Fusobacterium, Dialister genera and in members of the Lachnospiraceae family, and a decrease in Faecalibacterium, Lactobacillus genera and members of the Streptococcaceae family. Microbiota colonizing the neoterminal ileum and subanastomotic colon differed in children with recurrence and showed, compared to remission, elevated and reduced bacterial abundance of the Enterobacter (q=0.1) and Ruminococcaceae (q=0.05) families in colonic samples respectively while the ileal mucosa exhibited profound depletion in Faecalibacterium (q=0.01). Postoperative colonic mucosal relative abundance of Enterobacteriaceae (q=0.06) and Ruminococcaceae (q=0.06) correlated positively and negatively with length of intestinal resection. At the time of surgery, several bacterial taxa able to predict relapse were identified (Figure 2). Conclusion Predicting postoperative CD relapse remains challenging, although several clinical risk factors of recurrence have been identified. Our study demonstrates that bacterial recolonization following ICR might pave the way towards remission or recurrence. Our results highlight, for the first time in a paediatric population, target species that may help clinicians to better define patients at risk of relapse and allow precise modulations of the overall microbial ecosystem towards remission pattern.

Rust Disease Changes the Abundance and Composition of Bacterial Community in Iris lactea Rhizosphere

The microbial community plays a vital role in root–environment interactions, which affect plant performance under biotic stress. Rust disease significantly affects plant growth, which may also affect rhizosphere microbial community. However, there is a scarcity of studies investigating the microbial community of rhizosphere under rust disease stress. Iris lactea is a widely utilized plant in gardening and landscaping due to its versatility and ornamental value, but it is often susceptible to rust disease in landscape settings. In this study, we compared the bacterial communities between bulk soil (non-cultivated control), rhizosphere soil of healthy Iris lactea plants, and rhizosphere soil of Iris lactea plants infected with rust disease (rhizosphere-R). Results revealed significant alterations in the abundance and composition of bacterial communities associated with rust disease infection. Specifically, the rhizosphere-R samples exhibited a decreased Shannon index at 1.9% compared to bulk soil and the relative abundance of Proteobacteria was increased at 31.65%. Moreover, distinct changes in β-diversity were shown between bulk soil and rhizosphere samples. Notably, potentially pathogenic bacteria increased in abundance under rust disease stress, while beneficial bacterial taxa decreased. Overall, our results show that rust disease affects the rhizosphere microbial community, which emphasizes the ecological implications of plant–microbe interactions under biotic stress and implications for developing targeted rhizobacterial-based biocontrol strategies.

The importance of species addition 'versus' replacement varies over succession in plant communities after glacier retreat.

The mechanisms underlying plant succession remain highly debated. Due to the local scope of most studies, we lack a global quantification of the relative importance of species addition 'versus' replacement. We assessed the role of these processes in the variation (β-diversity) of plant communities colonizing the forelands of 46 retreating glaciers worldwide, using both environmental DNA and traditional surveys. Our findings indicate that addition and replacement concur in determining community changes in deglaciated sites, but their relative importance varied over time. Taxa addition dominated immediately after glacier retreat, as expected in harsh environments, while replacement became more important for late-successional communities. These changes were aligned with total β-diversity changes, which were more pronounced between early-successional communities than between late-successional communities (>50 yr since glacier retreat). Despite the complexity of community assembly during plant succession, the observed global pattern suggests a generalized shift from the dominance of facilitation and/or stochastic processes in early-successional communities to a predominance of competition later on.

Взаимосвязь синдрома хронической усталости и состояния кишечного микробиома

Chronic fatigue syndrome / myalgic encephalomyelitis (ME/CFS) is a heterogeneous disease with multiple manifestations. The intestinal microbiome is receiving increasing attention in various refractory diseases, including ME/CFS. This study aims to advance our understanding of the relationship between the intestinal microbiome and ME/CFS by analyzing data from various clinical studies. We searched the literature published in 4 databases (PubMed, Cochrane Library, Web of Science, and Google Scholar) prior to May 31, 2023. Our analysis included 11 clinical studies involving 553 patients with ME/CFS and 480 healthy controls. Comparative metadata analysis revealed a significant reduction in α-diversity and a marked change in β-diversity in the gut microbiome of ME/CFS patients compared to healthy controls. The ratio of Firmicutes to Bacteroides decreased by 2.3-fold, and there was also a significant reduction in the production of microbial metabolites such as acetate, butyrate, isobutyrate and some amino acids (alanine, serine and hypoxanthine) observed in ME/CFS patients. This review provides a comprehensive analysis of recent advances in understanding the role of the intestinal microbiome in patients with ME/CFS. In addition, we also highlight the potential for using several microbiome-related interventions to alleviate ME/CFS symptoms.

Decoupled responses of above- and below-ground beta-diversity to nitrogen enrichment in a typical steppe.

Increased atmospheric nitrogen (N) deposition affects biodiversity in terrestrial ecosystems. However, we do not know whether the effects of N on above-ground plant β-diversity are coupled with changes occurring in the soil seed bank. We conducted a long-term N-addition experiment in a typical steppe and found that above-ground β-diversity increased and then decreased with increasing N addition, whereas below-ground β-diversity decreased linearly. This suggests decoupled dynamics of plant communities and their soil seed bank under N enrichment. Species substitution determined above- and below-ground β-diversity change via an increasing role of deterministic processes with N addition. These effects were mostly driven by differential responses of the above-ground vegetation and the soil seed bank β-diversities to N-induced changes in environmental heterogeneity, increased soil inorganic N concentrations and soil acidification. Our findings highlight the importance of considering above- and below-ground processes simultaneously for effectively conserving grassland ecosystems under N enrichment.

Altered Bile Acid and Pouch Microbiota Composition in Patients With Chronic Pouchitis.

Patients with ulcerative colitis and total abdominal proctocolectomy with ileal pouch-anal anastomosis have a 50% risk of pouchitis and a 5% to 10% risk of chronic pouchitis. The goal of the study was to compare pouch microbiota and stool bile acid composition in patients with chronic pouchitis, chronic pouchitis and primary sclerosing cholangitis, and normal pouch. Patients with ulcerative colitis and ileal pouch-anal anastomosis were recruited from March 20, 2014, to August 6, 2019, and categorized into normal pouch, chronic pouchitis, and chronic pouchitis/primary sclerosing cholangitis groups. Stool samples were subjected to bile acid quantification and 16S rRNA gene sequencing. Statistical comparisons of absolute bile acid abundance and pouch microbiota α-diversity, β-diversity, and taxa abundance were performed among the patient groups. A total of 51 samples were analyzed. Both α-diversity (P = .01, species richness) and β-diversity (P = .001) significantly differed among groups. Lithocholic acid was significantly lower in patients with chronic pouchitis/primary sclerosing cholangitis than in those with chronic pouchitis (P = .01) or normal pouch (P = .03). Decreased α-diversity was associated with an increased primary to secondary bile acid ratio (P = .002), which was also associated with changes in β-diversity (P = .006). Pouch microbiota α- and β-diversity differed among patients with normal pouch, chronic pouchitis, and chronic pouchitis/primary sclerosing cholangitis. Lithocholic acid level and primary to secondary bile acid ratio were highly associated with pouch microbiota richness, structure, and composition. These findings emphasize the associations between pouch microbiota and bile acid composition in dysbiosis and altered metabolism, suggesting that secondary bile acids are decreased in chronic pouchitis.

Fungal dysbiosis and decreased tear mucin at the conjunctiva in patients with conjunctival mucosa-associated lymphoid tissue lymphoma

ObjectiveThis study aimed to examine the differences in the fungal microbiome between patients with conjunctival mucosa-associated lymphoid tissue (MALT) and healthy controls using metagenomic analysis.Methods and analysisThis case-control study was...

Definition of a Dietary Pattern Expressing the Intake of Vegetables and Fruits and Its Association with Intestinal Microbiota

Daily dietary habits directly or indirectly influence the intestinal microbiota, and the resulting changes in its composition and metabolic activity alter the health conditions of the host. Although many studies have analyzed the association between individual nutrients/food items and intestinal microbiota, the assessment of the diet and intestinal microbiota from a macroscopic perspective has not yet been performed in Japan. Therefore, we focused on vegetables and fruits and aimed to identify dietary patterns of high intake of these foods and to examine their relationship with the intestinal microbiota. This cross-sectional study included 1019 healthy individuals aged ≥20 years in a rural area in northern Japan. Six dietary patterns were detected by factor analysis using the brief-type self-administered diet history questionnaire (BDHQ) data to identify the “vege pattern”, which was the dietary pattern rich in vegetables and fruits. Permutational multivariate analysis of variance revealed changes in β-diversity according to dietary patterns. In multivariable-adjusted models, the adherence to the vege pattern was positively correlated with α-diversity. This is the first study to reveal a correlation between intestinal microbiota and dietary habits rich in vegetables and fruits in a rural area of Japan.

Covariation of taxonomic and functional facets of β-diversity in Chilean freshwater fish assemblages: Implications for current and future processes of biotic homogenization.

The biodiversity of assemblages that experience the introduction and extinction of species may lead to responses in two important facets: The taxonomic and functional diversity. The way in which these facets are associated may reveal important implications and consequences for the conservation of those assemblages. Considering the critical situation of freshwater fishes in continental Chile (30° - 56° S), we analyzed how the taxonomic (TDβ) and functional (FDβ) facets of β-diversity, and their components of turnover and nestedness, are associated. We evaluated changes in β-diversity (ΔTDβ and ΔFDβ), turnover (ΔTDtur and ΔFDtur), and nestedness (ΔTDnes and ΔFDnes) in 20 fish assemblages from their historical (pre-European) to current composition. We also simulated future trends of these changes, assuming that native species with conservation issues would become extinct. Our results show that the fish assemblages studied are in a process of loss of β-diversity, both in taxonomic and functional facets (ΔTDβ = -3.9%; ΔFDβ = -30.4%); also, that these facets are positively correlated in the assemblages studied (r = 0.617; P < 0.05). Both components showed by loss in nestedness (ΔTDnes = -36.9%; ΔFDnes = -60.9%) but gain in turnover (ΔTDtur = 9.2%; ΔFDtur = 12.3%). The functional β-diversity decreased more than the taxonomic (ΔFDβ > ΔTDβ), which was caused chiefly by six exotic species of Salmonidae, whose geographical spread was wider and that at the same time shared several morpho-functional traits. Our forecasts, assuming an intensification in the extinction of Endangered and Vulnerable native species, indicate that the process of homogenization will continue, though at a lower rate. Our study shows that the freshwater ichthyofauna of continental Chile is undergoing biotic homogenization, and that this process involves the facets of taxonomic and functional β-diversity, which are show high correlation between historical and current compositions. Both facets show that process is influenced by nestedness, and while turnover contributes to differentiation (both taxonomic and functional), its importance is overshadowed by nestedness.

The intervention effects of konjac glucomannan with different molecular weights on high-fat and high-fructose diet-fed obese mice based on the regulation of gut microbiota

Konjac is a high-quality dietary fiber rich in β-glucomannan, which has been reported to possess anti-obesity effects. To explore the effective components and the structure–activity relationships of konjac glucomannan (KGM), three different molecular weight components (KGM-1 (90 kDa), KGM-2 (5 kDa), KGM-3 (1 kDa)) were obtained, and systematical comparisons of their effects on high-fat and high-fructose diet (HFFD)-induced obese mice were investigated in the present study. Our results indicated that KGM-1, with its larger molecular weight, reduced mouse body weight and improved their insulin resistance status. KGM-1 markedly inhibited lipid accumulation in mouse livers induced by HFFD by downregulating Pparg expression and upregulating Hsl and Cpt1 expressions. Further investigation revealed that dietary supplementation with konjac glucomannan at different molecular weights caused β-diversity changes in gut microbes. The potential weight loss effect of KGM-1 maybe attributed to the abundance of changes in Coprobacter, Streptococcus, Clostridium IV, and Parasutterella. The results provide a scientific basis for the in-depth development and utilization of konjac resources.

The Effects of Enteral Nutrition on the Intestinal Environment in Patients in a Persistent Vegetative State.

Enteral nutrition (EN) is a rational approach to providing nutritional intake via the intestines in patients who are unable to tolerate parenteral nutrition. We conducted a preliminary study to investigate the effects of EN on the intestinal environment in 10 patients in a persistent vegetative state (PVS) (n = 5 each in the EN and EN with probiotics; Clostridium butyricum MIYAIRI 588) groups compared with 10 healthy controls. The results of 16S amplicon sequencing of the intestinal microbiota showed that EN led to dysbiosis with a decrease in α-diversity and an obvious change in β-diversity. A particularly significant decrease was seen in useful intestinal bacteria such as Bifidobacterium and butyrate-producing bacteria. Analysis of intestinal metabolites also supported these results, showing significant decreases in butyric and pyruvic acid after EN. Although C. butyricum MIYAIRI 588 improved some intestinal metabolites that were decreased after EN, it did not improve the dysbiosis of the intestinal microbiota. These findings indicate that EN causes dysbiosis of the intestinal microbiota and an imbalance in some intestinal metabolites in patients in a PVS. Moreover, although C. butyricum MIYAIRI 588 improved the imbalance of some intestinal metabolites after EN, it did not prevent dysbiosis of the intestinal microbiota.

Homogenization of terrestrial mammals in fragmented rainforests: the loss of species turnover and its landscape drivers

Understanding the factors and mechanisms shaping differences in species composition across space and time (β-diversity) in human-modified landscapes has key ecological and applied implications. This topic is, however, challenging because landscape disturbance can promote either decreases (biotic homogenization) or increases (biotic differentiation) in β-diversity. We assessed temporal differences in intersite β-diversity of medium-bodied and large-bodied mammals in the fragmented Lacandona rainforest, Mexico. We hypothesized that, given the relatively short history of land-use changes in the region, and the gain and loss of some species caused by landscape spatial changes, β-diversity would increase through time, especially its nestedness component. We estimated β-diversity between 24 forest sites (22 forest patches and two continuous forest sites) in 2011 and 2017 to assess whether β-diversity is decreasing or increasing in the region, and calculated its turnover and nestedness components to understand the mechanisms responsible for changes in β-diversity, separately assessing mammal groups with different body mass, feeding guild, and habitat specialization. We then related such temporal changes in β-diversity to temporal changes in five landscape variables (forest cover, matrix openness, number of patches, edge density and interpatch distance) to identify the landscape drivers of β-diversity. In contrast with our expectations, β-diversity decreased over time, suggesting an ongoing biotic homogenization process. This pattern was mostly driven by a decrease in species turnover in all mammal groups, especially in landscapes with decreasing forest cover and increasing forested matrices. Although the nestedness component showed a three-fold increase through time, species turnover was 22 and six times higher than nestedness in 2011 and 2017, respectively. The decreased turnover appears to be driven by an increase in dispersal (i.e., spillover) of native species among patches. The prevalence of species turnover over nestedness indicates that different forest sites have a fairly distinct subset of species (i.e., high complementarity in species composition). Therefore, conserving all remaining forest patches and increasing forest cover is of utmost importance to effectively maintain β-diversity and conserve the total diversity (γ) of mammal assemblages in this Mesoamerican biodiversity hotspot.

Systematic review of gut microbiota changes in patients with chronic heart failure

Objective: To analyze the changes on gut microbiota and metabolic products in patients with chronic heart failure. Methods: By searching the Pubmed, EMBASE, Cochrane Library, and CNKI, Wanfang, and CMB databases from the day of built up to December 2019, we screened related literature exploring the intestinal flora of chronic heart failure patients, and systematic review was performed to study changes in intestinal flora composition, function, and metabolites among chronic heart failure patients. Results: A total of 10 articles were included to study the gut microbiota of patients with chronic heart failure in this analysis. The systematic review showed significant changes in β-diversity in patients with heart failure. The abundance of faecalibacterium, blautia, bacteroides, prevotella and anaerostipes was decreased, while the abundance of streptococcus, escherichia/shigella, veillonella, and enterobacte was increased. The increased microbial gene function in patients with heart failure included tryptophan metabolism, lipid metabolism, LPS synthesis,and so on, especially, bacterial genes related to trimethylamine oxide production increased significantly, while genes related to key enzymes producing the beneficial metabolite butyrate decreased significantly, and harmful metabolite trimethylamine oxide levels increased in chronic heart failure patients. Conclusion: There are significant changes in the structure, function and metabolites of intestinal flora in patients with chronic heart failure.

A Soybean Resistant Protein-Containing Diet Increased the Production of Reg3γ Through the Regulation of the Gut Microbiota and Enhanced the Intestinal Barrier Function in Mice.

The maintenance of intestinal homeostasis is necessary for a good quality of life, and strengthening of the intestinal barrier function is thus an important issue. Therefore, we focused on soybean resistant protein (SRP) derived from kori-tofu (freeze-dried tofu), which is a traditional Japanese food, as a functional food component. In this study, to investigate the effect of SRP on the intestinal barrier function and intestinal microbiota, we conducted an SRP free intake experiment in mice. Results showed that ingestion of SRP decreased the serum level of lipopolysaccharide-binding protein and induced the expression of Reg3γ, thereby improving the intestinal barrier function. In addition, SRP intake induced changes in the cecal microbiota, as observed by changes in β-diversity. In particular, in the microbiota, the up-regulation of functional gene pathways related to the bacterial invasion of epithelial cells (ko05100) was observed, suggesting that Reg3γ expression was induced by the direct stimulation of epithelial cells. The results of this study suggest that SRP is a functional food component that may contribute to the maintenance of intestinal homeostasis.

Exotic species modify the functional diversity patterns of freshwater fish assemblages in continental Chile: Examining historical and geographical patterns

The Neotropical region is an important reservoir of functional diversity of freshwater fish in the world. Recent studies have shown that functional and taxonomic diversity in this region has increased as a consequence of the introduction of exotic species. However, little is known about how this phenomenon has modified functional diversity at the watershed level. In the present study, we analyze the spatio-temporal changes of functional diversity in 22 watersheds of continental Chile, hypothesizing that the introduction of exotic species could have contributed to increasing and homogenizing the functional diversity within and among watersheds. Toward this purpose, we implemented measures of functional diversity (FRic), β-diversity (FDiv), turnover (Ftur), and nestedness (Fnes) in two compositional stages, which we call “historical” and “current”. The former considered the most probable composition of native species prior to European colonization, while the latter considered the current distribution of native and exotic species. For these two stages, we determined the changes in (FRic, FDiv, Ftur, and Fnes between pairs of watersheds, as well as the effect of geographic distance. Our results showed that, on average, FRic has increased its historical value by 156%; on the other hand, ΔFDiv and ΔFtur decreased significantly from its historical composition to current one (ΔFDiv = −7.4%; ΔFtur = −13.2%; both P < 0.05), while nestedness showed no significant changes (ΔFnes = −3.6%; P > 0.05). Finally, geographic distance between watersheds was negatively and significantly correlated with change in β-diversity and spatial turnover (r = −0.267; r = −0.410, respectively; both P < 0.05), while ΔFnes did not show a significant correlation with distance (r = 0.178; P > 0.05). These results indicate that exotic species (a) have increased functional diversity in local assemblages, because they display historically absent functional features; and (b) have promoted functional homogenization between assemblages, which is more intense between geographically more distant ones. These findings suggest that, due to their functional features, the presence of exotic species poses a probable risk for the functional stability of watersheds in continental Chile, and that it is necessary to implement conservation measures to protect this unique fish fauna.

Functional differentiation accompanies taxonomic homogenization in freshwater fish communities.

The addition of nonnative species and loss of native species has modified the composition of communities globally. Although changes in β-diversity have been well documented, there is a need for studies incorporating multiple time periods, more than one dimension of biodiversity, and inclusion of nestedness and turnover components to understand the underlying mechanisms structuring community composition and assembly. Here, we examined temporal changes in functional dissimilarity of fish communities of the Laurentian Great Lakes and compared these changes to those of taxonomic dissimilarity by decade from 1870 to 2010. Jaccard-derived functional dissimilarity index was used to quantify changes in functional β-diversity within communities, between all possible pairs of communities, and using a multiple-site index among all communities. β-diversity was partitioned into components of nestedness and turnover, and changes were examined over time. Similar to patterns in taxonomic dissimilarity, each community functionally differentiated from the historical community of 1870, with Lake Superior changing the most (~24%) and Lake Ontario the least (~14%). Although communities have become taxonomically homogenized, functional β-diversity among all communities has increased over time, indicating functional differentiation. This is likely due to functional similarity between the communities being historically high (i.e., ~88% similar in 1870). The higher taxonomic relative to functional turnover indicates that the species being replaced between communities are functionally redundant, which could occur given the harsh environmental conditions of the region and/or as a result of the recent glacial history of the region. High functional nestedness across communities reflects dispersal limitations, with smaller communities being functional subsets of large communities closer to source populations. The functional differentiation observed is likely due to nonnative species with functional traits unique to the region establishing or the loss of functionally redundant native species; however, it is important to note that patterns of homogenization were periodically observed through time. Our study demonstrates the possible factors regulating diversity in the Laurentian Great Lakes fish communities, that patterns of taxonomic and functional β-diversity are dynamic over time and vary in the magnitude and direction of change, and that taxonomic diversity should not be used to predict changes in functional diversity.

Partitioning β-diversity reveals that invasions and extinctions promote the biotic homogenization of Chilean freshwater fish fauna.

AimExotic species’ introductions together with extinction of native species represent the main mechanisms driving biotic homogenization of freshwater fish assemblages around the world. While generally ichtyofaunistic realms transit towards biotic homogenization, for conservation purposes it is essential to understand what specific mechanisms are promoting it on particular areas or regions. Here, we report the occurrence of biotic homogenization in 29 Chilean watersheds, analyzing its β-diversity (including turnover and nestedness) and predicting future trends.LocationContinental Chile (18o–56o S).MethodsWe determined fish composition per basin for historical and current assemblages; extant native, exotic, and extinct species were recorded as 1 (presence) or 0 (absence) in two matrices basins × species. For each matrix, we calculated the turnover (βsim), nestedness (βnes), and β-diversity (βsor); then, we obtained Δβsim, Δβnes, and Δβsor, as the arithmetical difference between basin pairs over time. In addition, we search for explanatory variables correlating Δβsim, Δβnes, and Δβsor with geographical and land use variables. Finally, simulating events of species introduction (i.e., invasion) and extinction, we generated 15 hypothetical assemblages, looking to establish future trends towards biotic change in Chilean basins.ResultsSpecies turnover and β-diversity significantly decreased from historical to current assemblages (Δβsim = -0.084; Δβsor = -0.061, respectively), while the species nestedness did not show significant changes (Δβnes = 0.08). Biotic changes have been driven mainly by the introduction of 28 exotic species, with a minor role of extinctions (one species) and translocations (0 species) of native species. Changes in β-diversity were negatively correlated with area, elevation, and geographical distance between basins but not with land-use nor human population. Finally, the analysis of 15 future assemblages predicts a significant decrease of β-diversity and turnover, and an increase for species nestedness, this time promoted by an increase in the extinction of native species.Main conclusionChilean basins show a significant decrease of the distributional β-diversity and species turnover of the freshwater fish fauna, evidencing a trend towards biotic homogenization. This trend is shared with other Neotropical basins; however, specific mechanisms driving it show different magnitude. Changes in the β-diversity components do not show correlation with variables associated to land use, thus suggesting that casual introductions of freshwater fishes in Chile follow an opportunistic mode related to commercial use. According to future scenarios simulated, biotic homogenization should increase further, mainly as consequence of increased native extinctions.

The Effect of Probiotics Supplementation on the Gut Microbiome of Healthy Dogs Assessed Using Metagenomic Sequencing: A Randomized Control Trial

Abstract Objectives Dogs share similar gut microbiome (GM) with humans, making them a great model for investigating the effects of probiotics (PR) on GM and health. This randomized control trial examined changes in MB and health outcomes in household dogs after PR supplementation. Methods All dogs recruited were fed human grade cooked food ≥ 1 mo, not fed any cultured food, PR, prebiotics, or on antibiotics ≥ 3 mo, and absent of major diseases. Dogs were randomized to receive a daily dose of PR (20 billion CFU of L. reuteri, P. acidilactici, E. faecium, L. acidophilus, B. animalis, L. fermentum, L. rhamnosus) or placebo (PL) for 4 weeks. Owners completed a health survey and collected stool samples at baseline and 4 weeks after the intervention in both groups. Additional stool samples were collected 2 weeks after stopping the PR in the PR group. GM profiling was performed with metagenomic sequencing. Results Twenty three dogs in the PR and 19 dogs in the PL group completed the trial (5.6 ± 3.0 y, 69% male). PR had no effect on α-diversity. As compared to baseline, changes in β-diversity at the species level in 4.3% of GM were significantly affected by PR at week 4 (P &amp;lt; 0.001) but not at week 6. A significant increase (adj P &amp;lt; 0.01) for ≥ 2-fold in abundance was observed at week 4 as compared to baseline for 41 bacterial taxa, 29 (71%) of which belong in the Lactobacillus genus. The abundance of E. coli also decreased at week 4 in the PR group (2.8 folds, adj P &amp;lt; 0.01). The abundance of these taxa returned to baseline at week 6. Such changes in diversity or abundance were not observed with PL. Dogs fed PR tended to be at a lower risk of diarrhea during the trial (0% vs 16%, P = 0.08). No change in other health outcomes was observed. Conclusions Oral PR supplementation has a small but significant effect on GM in healthy dogs. Findings warrant further investigation with longer duration in populations at a higher risk of gastrointestinal diseases. Funding Sources NomNomNow Inc.

Attributes of Physical Activity and Gut Microbiome in Adults: A Systematic Review.

Growing evidence shows the contribution of physical activity interventions to the gut microbiome. However, specific physical activity characteristics that can modify the gut microbiome are unknown. This review's aim was to explore the contribution of physical activity intervention characteristics on human gut microbiome composition, in terms of diversity, specific bacterial groups, and associated gut microbiome metabolites. A literature search in PubMed; Cochrane Library; CINAHL-EBSCO; SCOPUS; Web of Science; ClinicalTrials.gov; PROSPERO; and ProQuest. Five studies met the inclusion criteria of a physical activity intervention duration of at least five weeks, with any description of the type or dose used. All included studies reported an endurance training; two studies used endurance and an additional muscle-strengthening training regimen. All studies reported using a dietary intervention control. Reported gut microbiome α-diversity changes were non-significant, β-diversity changes were mixed (three studies reported an increase, two reported non-significant changes). All studies reported significant changes in the abundances of specific bacterial/archaea groups and bacteria-related metabolites following interventions. In conclusion, physical activity (regardless of specific characteristics) has significant contribution to gut microbiome composition and associated metabolites. There are no current recommendations for physical activity to promote gut microbiome composition. Future studies should focus on the contribution of current recommended physical activity dose to gut microbiome composition.

On the importance of spatial scales on beta diversity of coral assemblages: a study from Venezuelan coral reefs.

Estimating variability across spatial scales has been a major issue in ecology because the description of patterns in space is extremely valuable to propose specific hypotheses to unveil key processes behind these patterns. This paper aims to estimate the variability of the coral assemblage structure at different spatial scales in order to determine which scales explain the largest variability on β-diversity. For this, a fully-nested design including a series of hierarchical-random factors encompassing three spatial scales: (1) regions, (2) localities and (3) reefs sites across the Venezuelan territory. The variability among spatial scales was tested with a permutation-based analysis of variance (Permanova) based on Bray-Curtis index. Dispersion in species presence/absence across scales (i.e., β-diversity) was tested with a PermDisp analysis based on Jaccard’s index. We found the highest variability in the coral assemblage structure between sites within localities (Pseudo-F = 5.34; p-value = 0.001, CV = 35.10%). We also found that longitude (Canonical corr = 0.867, p = 0.001) is a better predictor of the coral assemblage structure in Venezuela, than latitude (Canonical corr = 0.552, p = 0.021). Largest changes in β-diversity of corals occurred within sites (F = 2.764, df1= 35, df2 = 107, p = 0.045) and within localities (F = 4.438, df1= 6, df2 = 29, p = 0.026). Our results suggest that processes operating at spatial scales of hundreds of meters and hundreds of kilometers might both be critical to shape coral assemblage structure in Venezuela, whereas smaller scales (i.e., hundreds of meters) showed to be highly- important for the species turnover component of β-diversity. This result highlights the importance of creating scale-adapted management actions in Venezuela and likely across the Caribbean region.