Estimating Alpha, Beta, and Gamma Diversity Through Deep Learning

Effects of different grazing intensities on plant species diversity at different spatial scales in a desert steppe in Inner Mongolia

The effect of grazing intensity on plant diversity has been widely studied. In this study, desert steppes with different grazing intensities (no grazing (CK), light grazing (LG), moderate grazing (MG), heavy grazing (HG), and extremely heavy grazing (EG)) in Inner Mongolia were selected to study the changes in species diversity at different spatial scales (α, β, and γ diversity) and the α diversity of different plant groups (dominant species, common species, and rare species).The results showed that the α, β, and γ diversity first decreased and then increased with increasing grazing intensity, and β diversity was observed to be the most sensitive index to the grazing intensity. Grazing had the greatest impact on the α diversity of rare species and the least impact on the α diversity of common species. Therefore, rare species are of great significance for the maintenance and assessment of biodiversity. We concluded that grazing leads to a sensitive response of β diversity, and this sensitive phenomenon is mainly affected by rare species. The results could provide scientific bases for the protection of plant diversity and sustainable grazing in desert steppes.

Biodiversity and Evaluation of Genetic Resources of Some Coffee Trees Grown in Al-Baha, Saudi Arabia

The biodiversity of 12 coffee (Coffea arabica L.) cultivars collected from the Al-Baha region in the southwest of Saudi Arabia was evaluated using 25 morphological variations and genetic diversity as demonstrated by molecular polymorphism generated by eight Inter Simple Sequence Repeats (ISSRs) and nine Start Codon Targeted (SCoT) primers. Substantial variations were scored in the morphological traits reflected in the clustering of the examined cultivars in PCA of the coffee cultivars. The examined cultivars were grouped in two groups, one included the cultivars coded Y5, Y6, R113, and Y7 and the other group comprised two clusters; one comprised cultivars coded R8 and R4 and the other comprised cultivars R112, R114, and Y2. In the meantime, the cultivars coded R9 and R111 were differentiated together from other cultivars, while the Y3 cultivar was confirmed by the analysis of ISSR data and SCoT data, which also support the grouping of R9 and R111 cultivars. Principle Component Analysis (PCA) of morphological, ISSR, and SCoT data as a combined set differentiated the examined species into four groups in a scatter plot in agreement with their separation in the cluster trees. The diversity profile among the examined C. arabica cultivars proved that R111 and R4 cultivars are highly diverse, while R8 and Y5 cultivars exhibit low diversity. Alpha diversity indices indicated that R9 and R111 cultivars are the most dominant and stable C. arabica cultivars among the examined samples in the study region.

Effect of different killing methods during curing on the phytochemical and bacterial composition of Vanilla planifolia using multi-omic approaches

Vanilla planifolia Jacks. ex Andrews, is cultivated for its aromatic pods, obtaining the primary source of vanillin, a molecule valued for its flavor and bioactivity. Mexico ranks among the top five global producers, and Papantla, Veracruz, contributes 70 % of national production. Developing vanilla's characteristic aroma involves a curing process composed of killing, sweating, drying, and conditioning, which enzymatic reactions and microbial activity play essential roles. This study assessed the impact of four killing treatments: microwave, hot water immersion, sonication, and freezing on the phenolic composition and bacterial communities in vanilla curing through metabolomic and 16S sequencing approaches. Freezing treatment resulted in the most substantial changes in phenolic profiles, including higher vanillin concentrations. Bacillus was the dominant bacterial genus, with hot water immersion and sonication showing the greatest α-diversity. These findings underscore the value of omic sciences in refining curing processes, enabling producers to achieve higher-quality vanilla through more efficient and technical methods.

Substituting animal protein with black soymilk reduces advanced glycation end product level and improves gut microbiota composition in obese prediabetic individuals: a randomized crossover intervention trial

Prediabetes (PreDM) and obesity increase the risk of type 2 diabetes. Individuals with these conditions often consume diets higher in animal protein than in plant protein, which are associated with elevated levels of dietary advanced glycation end products (dAGEs). Increased dAGE intake has been linked to blood glucose abnormalities, oxidative stress, and dysbiosis of the microbiota, all of which exacerbate metabolic disorders. Black soybeans, as a plant-based protein source, contain substantially lower levels of dAGEs compared with pork. This study aimed to investigate the effects of substituting animal protein with black soybeans on advanced glycation end product (AGE) levels, oxidative stress, and the gut microbiota in individuals with both PreDM and obesity. This study was a randomized crossover intervention trial conducted over 16 weeks. We recruited men and women aged 20-64 years with both prediabetes and obesity. This study had four periods: 0-4 weeks for the run-in period, 4-8 weeks and 12-16 weeks for the pork or black soymilk intervention period, and 8-12 weeks for the wash-out period. During the intervention period, the participants consumed pork or black soymilk with similar protein content as their dietary protein source. The participants maintained 3 day dietary records, and we measured anthropometric items and collected blood and fecal samples for analysis. The results showed that partially substituting pork with black soymilk as a dietary protein source for 4 weeks significantly reduced dAGE intake. The black soymilk group also exhibited significantly lower blood AGE fluorescence intensity, oxidative stress, and levels of glycative stress markers. Furthermore, black soymilk consumption significantly increased the relative abundance of short-chain fatty acid-producing genera compared with pork consumption. In conclusion, partially substituting dietary pork with black soymilk may reduce serum AGE levels, reduce oxidative and glycation stress, and increase the abundance of short-chain fatty acid-producing microbiota in individuals with both PreDM and obesity. Registration number of Clinical Trial: NCT05290519 (ClinicalTrials.gov).

Microbiome and Communication Disorders: A Tutorial for Clinicians

PURPOSE

Emerging research in the field of microbiology has indicated that host-microbiota interactions play a significant role in regulating health and disease. Whereas the gut microbiome has received the most attention, distinct microbiota in other organs (mouth, larynx, and trachea) may undergo microbial shifts that impact disease states. A comprehensive understanding of microbial mechanisms and their role in communication and swallowing deficits may have downstream diagnostic and therapeutic implications.

METHOD

A literature review was completed to provide a broad overview of the microbiome, including differentiation of commensal versus pathogenic bacteria; cellular mechanisms by which bacteria interact with human cells; site-specific microbial compositional shifts in certain organs; and available reports of oral, laryngeal, and tracheal microbial dysbiosis in conditions that are associated with communication and swallowing deficits.

RESULTS/CONCLUSIONS

This review article is a valuable tutorial for clinicians, specifically introducing them to the concept of dysbiosis, with potential contributions to communication and swallowing deficits. Future research should delineate the role of specific pathogenic bacteria in disease pathogenesis to identify therapeutic targets.

The Oral Microbiome in Diabetes, Arterial Hypertension, and Obesity: A Scoping Review

BACKGROUND

Changes in the oral microbiome are expected in the presence of chronic conditions such as type 2 diabetes mellitus (T2D), arterial hypertension (AH), and obesity (OB).

OBJECTIVE

We aimed to map the literature regarding oral microbiome changes in people with T2D, AH, or OB compared to those without these conditions.

METHODS

This scoping review was guided by the JBI Manual for Evidence Synthesis and reported according to the PRISMA extension for scoping reviews (PRISMA-ScR). A search strategy was developed and adapted to five databases (Embase, LILACS, PubMed, Scopus, and Web of Science) and gray literature (Google Scholar and ProQuest Dissertation and Thesis). Two reviewers individually screened studies for inclusion. Data from the studies, including the molecular method to evaluate the microbiome and the type of sample, were extracted and analyzed. The focus was significant changes in phylum and genera.

RESULTS

A total of 1413 records were retrieved from databases, 86 from gray literature, and 7 from reference lists. After the screening process, 50 records were included, 28 on T2D, 8 on AH, and 12 on OB. Two studies addressed metabolic syndromes. Most studies identified the oral microbiome in saliva using 16S rRNA amplicon sequencing.

CONCLUSION

At the phylum level, Fusobacteria was enriched in ≥3 studies in people with T2D. Firmicutes enrichment was associated with T2D and OB. Genera enriched in T2D comprised Catonella, Leptotrichia, Prevotella, and Rothia. Aggregatibacter and Prevotella were enriched in OB. No phylum or genera were consistently enriched in AH.OSF protocol registration: DOI 10.17605/OSF.IO/XK72V (available at https://osf.io/z5fp4 ).

Human gut microbiome, diet, and mental disorders

Diet is one of the most important external factor shaping the composition and metabolic activities of the gut microbiome. The gut microbiome plays a crucial role in host health, including immune system development, nutrients metabolism, and the synthesis of bioactive molecules. In addition, the gut microbiome has been described as critical for the development of several mental disorders. Nutritional psychiatry is an emerging field of research that may provide a link between diet, microbial function, and brain health. In this study, we have reviewed the influence of different diet types, such as Western, Mediterranean, vegetarian, and ketogenic, on the gut microbiota composition and function, and their implication in various neuropsychiatric and psychological disorders.

DNA metabarcoding reveals diet diversity and niche partitioning by two sympatric herbivores in summer

Background

Food provides essential nutrients and energy necessary for animals to sustain life activities. Accordingly, dietary niche analysis facilitates the exploration of foraging strategies and interspecific relationships among wildlife. The vegetation succession has reduced understory forage resources (i.e., shrubs and herbs) available to sika deer (Cervus nippon kopschi). Little is known about the summer foraging strategies or the interspecific relationship between sika deer and Reeves' muntjac (Muntiacus reevesi).

Methods

The present study used high-throughput sequencing and DNA metabarcoding techniques to investigate the feeding habits and interspecific relationships between sika deer and Reeves' muntjac in our study.

Results

A total of 458 amplicon sequence variants (ASVs) were identified from fecal samples, with 88 ASVs (~19.21%) unique to sika deer and 52 ASVs (~11.35%) unique to Reeves' muntjac, suggesting the consumption and utilization of specific food items for the two species. The family Rosaceae was the most abundant for both species, especially Rubus spp. and Smilax china. Alpha diversity (local species richness) indicated that the dietary species richness of sika deer was higher than that of Reeves' muntjac, but the difference was not statistically significant. Sika deer also exhibited a higher evenness index (J' = 0.514) than Reeves' muntjac (J' = 0.442). Linear discriminant effect size analysis revealed significant differences in forage plants between the two herbivores. The niche breadths of sika deer and Reeves' muntjac were 11.36 and 14.06, respectively, and the dietary niche overlap index was 0.44. Our findings indicate the diet partitioning primarily manifested in the differentiation of food items and the proportion, which ultimately reduces the overlap of nutritional niches and helps avoid conflicts resulting from resource utilization. This study provides a deeper insight into the diversity of foraging strategies and the interspecific relationship of herbivores from the food dimension.

"Gut" to grips with the science of the microbiome - a symposium report

The latest Yakult Science Study Day was held virtually on 2 November 2023. Aimed at healthcare professionals, researchers, and students, a variety of experts explored the latest gut microbiome research and what it means in practice. The morning sessions discussed the role of the microbiome in health and disease, the rapid advancements in DNA sequencing and implications for personalised nutrition, the current state of evidence on health benefits associated with fermented foods, prebiotics and probiotics and the challenges involved in interpreting research in this area. The afternoon session considered the emerging research on the microbiota-gut-brain axis in mediating effects of food on mood, the bidirectional impact of menopause on the gut microbiota, and the interplay between the gut and skin with implications for the treatment of rare and common skin disorders. The session ended with an update on the use of faecal microbiota transplant in both research and clinical practice. Undoubtedly, the gut microbiome is emerging as a key conductor of human health, both in relation to gastrointestinal and non-gastrointestinal outcomes. As research continues to elucidate mechanisms of action and confirm their effects in human trials, the gut microbiome should be a key consideration within a holistic approach to health moving forward.

Salvianolic acids modulate lifespan and gut microbiota composition in amyloid-β-expressing Drosophila melanogaster

Alzheimer's disease (AD), a form of neurodegenerative disorder characterized by the accumulation of amyloid-β (Aβ), hyperphosphorylated Tau, and neuroinflammation. The increasing population affected by AD urges for the development of effective treatments. The correlation between AD and gut microbiome remains underexplored, potentially providing a better understanding of the disease. Salvianolic acid A (Sal A) and salvianolic acid B (Sal B) are the active components extracted from Salvia miltiorrhiza (Danshen), and their antioxidant, anti-inflammation and Aβ inhibition activities were shown previously. In this study, these compounds were used to investigate their effects on Aβ toxicity, using Drosophila melanogaster expressing human Aβ42 as the model organism, by examining their lifespan and changes in gut bacterial communities. The study used two batches of flies, reared on food with or without methylparaben (MP) supplementation to evaluate the influence of MP on this animal model during pharmacological studies. MP is a common antimicrobial agent used in flies' food. The treatment of Sal A prolonged the lifespan of Aβ-expressing flies reared on MP-supplemented food significantly (P < 0.001), but not those without MP. The lifespan of Sal B-treated flies did not show a significant difference compared to untreated flies for both groups reared on food with and without MP. Sal A-treated flies in the presence of MP exhibited a lower abundance of Corynebacterium and Enterococcus than the untreated flies, while Lactiplantibacillus was the most dominant taxa. Urea cycle was predicted to be predominant in this group compared to the untreated group. The control group, Aβ-expressing flies treated with Sal A and Sal B on MP-supplemented food had improved lifespan compared to their respective groups reared on food without MP, while untreated Aβ-expressing flies was the exception. The gut microbiota composition of flies reared on MP-supplemented food was also significantly different from those without MP (P < 0.001).

Targeting Gut Microbiota with Probiotics and Phenolic Compounds in the Treatment of Atherosclerosis: A Comprehensive Review

Atherosclerosis (AS) is a chronic inflammatory vascular disease. Dysregulated lipid metabolism, oxidative stress, and inflammation are the major mechanisms implicated in the development of AS. In addition, evidence suggests that gut dysbiosis plays an important role in atherogenesis, and modulation of the gut microbiota with probiotics and phenolic compounds has emerged as a promising strategy for preventing and treating AS. It has been shown that probiotics and phenolic compounds can improve atherosclerosis-related parameters by improving lipid profile, oxidative stress, and inflammation. In addition, these compounds may modulate the diversity and composition of the gut microbiota and improve atherosclerosis. The studies evaluated in the present review showed that probiotics and phenolic compounds, when consumed individually, improved atherosclerosis by modulating the gut microbiota in various ways, such as decreasing gut permeability, decreasing TMAO and LPS levels, altering alpha and beta diversity, and increasing fecal bile acid loss. However, no study was found that evaluated the combined use of probiotics and phenolic compounds to improve atherosclerosis. The available literature highlights the synergistic potential between phenolic compounds and probiotics to improve their health-promoting properties and functionalities. This review aims to summarize the available evidence on the individual effects of probiotics and phenolic compounds on AS, while providing insights into the potential benefits of nutraceutical approaches using probiotic strains, quercetin, and resveratrol as potential adjuvant therapies for AS treatment through modulation of the gut microbiota.

Predicting the responses of European grassland communities to climate and land cover change

European grasslands are among the most species-rich ecosystems on small spatial scales. However, human-induced activities like land use and climate change pose significant threats to this diversity. To explore how climate and land cover change will affect biodiversity and community composition in grassland ecosystems, we conducted joint species distribution models (SDMs) on the extensive vegetation-plot database sPlotOpen to project distributions of 1178 grassland species across Europe under current conditions and three future scenarios. We further compared model accuracy and computational efficiency between joint SDMs (JSDMs) and stacked SDMs, especially for rare species. Our results show that: (i) grassland communities in the mountain ranges are expected to suffer high rates of species loss, while those in western, northern and eastern Europe will experience substantial turnover; (ii) scaling anomalies were observed in the predicted species richness, reflecting regional differences in the dominant drivers of assembly processes; (iii) JSDMs did not outperform stacked SDMs in predictive power but demonstrated superior efficiency in model fitting and predicting; and (iv) incorporating co-occurrence datasets improved the model performance in predicting the distribution of rare species. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Bifidobacterium pseudocatenulatum In Vitro In Vivo

The genus Bifidobacterium has been widely used in functional foods for health promotion due to its beneficial effects on human health, especially in the gastrointestinal tract (GIT). In this study, we characterize the anti-inflammatory potential of the probiotic strain Bifidobacterium pseudocatenulatum G7, isolated from a healthy male adult. G7 secretion inhibited inflammatory response in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages. Moreover, oral administration of bacteria G7 alleviated the severity of colonic inflammation in dextran sulfate sodium (DSS)-treated colitis mice, which was evidenced by a decreased disease activity index (DAI) and enhanced structural integrity of the colon. The 16S rRNA gene sequencing result illustrated that the G7 alleviated DSS-induced gut microbiota dysbiosis, accompanied by the modulated bile acids and short-chain fatty acid (SCFA) levels. Overall, our results demonstrated the potential anti-inflammatory effects of Bifidobacterium pseudocatenulatum G7 on both in vitro and in vivo models, which provided a solid foundation for further development of a novel anti-inflammatory probiotic.

Prostate Tissue Microbiome in Patients with Prostate Cancer: A Systematic Review

Some researchers have speculated that the prostatic microbiome is involved in the development of prostate cancer (PCa) but there is no consensus on certain microbiota in the prostatic tissue of PCa vs. healthy controls. This systematic review aims to investigate and compare the microbiome of PCa and healthy tissue to determine the microbial association with the pathogenesis of PCa. We searched MEDLINE, Embase, and Scopus databases. Articles were screened by two independent and blinded reviewers. Literature that compared the prostatic tissue microbiome of patients with PCa with benign controls was included. We found that PCa may be associated with increased Propionibacterium acnes, the herpesviridae and papillomaviridae families, and Mycoplasma genitalium, but definitive conclusions cannot be drawn from the existing data. Challenges include the difficulty of obtaining uncontaminated tissue samples and securing tissue from healthy controls. As a result, methods are varied with many studies using cancerous and "healthy" tissue from the same prostate. The organisms chosen for each study were also highly variable, making it difficult to compare studies. These issues have led to lower confidence in our results. Overall, further work is warranted to better understand the implications of the prostatic microbiome in the pathogenesis of PCa.

Characterizing Gut Microbiota in Older Chinese Adults with Cognitive Impairment: A Cross-Sectional Study

Background

Cognitive impairment is a clinical manifestation that occurs in the course of dementia like Alzheimer's disease. The association between cognitive impairment and gut microbiota is unclear.

Objective

We aimed to identify gut microbiota characteristics and key gut microbiota biomarkers associated with cognitive impairment in a relatively large cohort of older adults in China.

Methods

A total of 229 adults aged ≥60 years from Shenzhen, China were recruited into this cross-sectional study. Participants were divided into cognitive impairment (CI) and no cognitive impairment (NCI) groups according to the results of the Mini-Mental State Examination. Diversity analysis and network analysis were used to characterize the gut microbiota between the two groups. The linear discriminant analysis effect size method and machine learning approaches were sequentially performed to identify gut microbiota biomarkers. The relationship between biomarkers and lifestyle factors was explored using Transformation-based redundancy analysis (tb-RDA).

Results

A total of 74 CI participants and 131 NCI participants were included in the analysis. The CI group demonstrated lower α-diversity compared to the NCI group (Shannon: 2.798 versus 3.152, p < 0.001). The density of the gut microbiota interaction network was lower in the CI group (0.074) compared to the NCI group (0.081). Megamonas, Blautia, Pseudomonas, Stenotrophomonas, and Veillonella were key biomarkers for CI. The tb-RDA revealed that increased fruit intake and exercise contribute to a higher abundance of Megamonas, Blautia, and Veillonella.

Conclusions

We identified a significantly reduced abundance of certain beneficial gut microbiota in older Chinese adults with cognitive impairment.

The Role of Gut Microbiota and Circadian Rhythm Oscillation of Hepatic Ischemia-Reperfusion Injury in Diabetic Mice

Circadian rhythm oscillation and the gut microbiota play important roles in several physiological functions and pathology regulations. In this study, we aimed to elucidate the characteristics of diabetic hepatic ischemia-reperfusion injury (HIRI) and the role of the intestinal microbiota in diabetic mice with HIRI. Hepatic ischemia-reperfusion injury surgery was performed at ZT0 or ZT12. The liver pathological score and the serum levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were analyzed to evaluate liver injury. We conducted an FMT experiment to examine the role of intestinal microbiota in diabetic mice with HIRI. The 16S rRNA gene sequencing of fecal samples was performed for microbial analysis. Our results showed that hyperglycemia aggravated HIRI in diabetic mice, but there was no diurnal variation seen in diabetic HIRI. We also demonstrated that there were significant alterations in the gut microbiota composition between the diabetic and control mice and that gut microbiota transplantation from diabetic mice had obvious harmful effects on HIRI. These findings provide some useful information for the future research of diabetic mice with HIRI.

Improved description of terrestrial habitat types by including microbial communities as indicators

Soils host diverse communities of microorganisms essential for ecosystem functions and soil health. Despite their importance, microorganisms are not covered by legislation protecting biodiversity or habitats, such as the Habitats Directive. Advances in molecular methods have caused breakthroughs in microbial community analysis, and recent studies have shown that parts of the communities are habitat-specific. If distinct microbial communities are present in the habitat types defined in the Habitats Directive, the Directive may be improved by including these communities. Thus, monitoring and reporting of biodiversity and conservation status of habitat types could be based not only on plant communities but also on microbial communities. In the present study, bacterial and plant communities were examined in six habitat types defined in the Habitats Directive by conducting botanical surveys and collecting soil samples for amplicon sequencing across 19 sites in Denmark. Furthermore, selected physico-chemical properties expected to differ between habitat types and explain variations in community composition of bacteria and vegetation were analysed (pH, electrical conductivity (EC), soil texture, soil water repellency, soil organic carbon content (OC), inorganic nitrogen, and in-situ water content (SWC)). Despite some variations within the same habitat type and overlaps between habitat types, habitat-specific communities were observed for both bacterial and plant communities, but no correlation was observed between the alpha diversity of vegetation and bacteria. PERMANOVA analysis was used to evaluate the variables best able to explain variation in the community composition of vegetation and bacteria. Habitat type alone could explain 46% and 47% of the variation in bacterial and plant communities, respectively. Excluding habitat type as a variable, the best model (pH, SWC, OC, fine silt, and Shannon's diversity index for vegetation) could explain 37% of the variation for bacteria. For vegetation, the best model (pH, EC, ammonium content and Shannon's diversity index for bacteria) could explain 25% of the variation. Based on these results, bacterial communities could be included in the Habitats Directive to improve the monitoring, as microorganisms are more sensitive to changes in the environment compared to vegetation, which the current monitoring is based on.

The phytomicrobiome: solving plant stress tolerance under climate change

With extraordinary global climate changes, increased episodes of extreme conditions result in continuous but complex interaction of environmental variables with plant life. Exploring natural phytomicrobiome species can provide a crucial resource of beneficial microbes that can improve plant growth and productivity through nutrient uptake, secondary metabolite production, and resistance against pathogenicity and abiotic stresses. The phytomicrobiome composition, diversity, and function strongly depend on the plant's genotype and climatic conditions. Currently, most studies have focused on elucidating microbial community abundance and diversity in the phytomicrobiome, covering bacterial communities. However, least is known about understanding the holistic phytomicrobiome composition and how they interact and function in stress conditions. This review identifies several gaps and essential questions that could enhance understanding of the complex interaction of microbiome, plant, and climate change. Utilizing eco-friendly approaches of naturally occurring synthetic microbial communities that enhance plant stress tolerance and leave fewer carbon-foot prints has been emphasized. However, understanding the mechanisms involved in stress signaling and responses by phytomicrobiome species under spatial and temporal climate changes is extremely important. Furthermore, the bacterial and fungal biome have been studied extensively, but the holistic interactome with archaea, viruses, oomycetes, protozoa, algae, and nematodes has seldom been studied. The inter-kingdom diversity, function, and potential role in improving environmental stress responses of plants are considerably important. In addition, much remains to be understood across organismal and ecosystem-level responses under dynamic and complex climate change conditions.

Microbiota present in combined endodontic-periodontal diseases and its risks for endocarditis

INTRODUCTION

Infective endocarditis (IE) is an inflammatory disease usually caused by bacteria that enter the bloodstream and establish infections in the inner linings or valves of the heart, including blood vessels. Despite the availability of modern antimicrobial and surgical treatments, IE continues to cause substantial morbidity and mortality. Oral microbiota is considered one of the most significant risk factors for IE. The objective of this study was to evaluate the microbiota present in root canal (RC) and periodontal pocket (PP) clinical samples in cases with combined endo-periodontal lesions (EPL) to detect species related to IE using NGS.

METHODS

Microbial samples were collected from 15 RCs and their associated PPs, also from 05 RCs with vital pulp tissues (negative control, NC). Genomic studies associated with bioinformatics, combined with structuring of a database (genetic sequences of bacteria reported for infective endocarditis), allowed for the assessment of the microbial community at both sites. Functional prediction was conducted using PICRUSt2.

RESULTS

Parvimonas, Streptococcus, and Enterococcus were the major genera detected in the RCs and PPs. A total of 79, 96, and 11 species were identified in the RCs, PPs, and NCs, respectively. From them, a total of 34 species from RCs, 53 from PPs, and 2 from NCs were related to IE. Functional inference demonstrated that CR and PP microbiological profiles may not be the only risk factors for IE but may also be associated with systemic diseases, including myocarditis, human cytomegalovirus infection, bacterial invasion of epithelial cells, Huntington's disease, amyotrophic lateral sclerosis, and hypertrophic cardiomyopathy. Additionally, it was possible to predict antimicrobial resistance variants for broad-spectrum drugs, including ampicillin, tetracycline, and macrolides.

CONCLUSION

Microorganisms present in the combined EPL may not be the only risk factor for IE but also for systemic diseases. Antimicrobial resistance variants for broad-spectrum drugs were inferred based on PICRUSt-2. State-of-the-art sequencing combined with bioinformatics has proven to be a powerful tool for conducting studies on microbial communities and could considerably assist in the diagnosis of serious infections.

CLINICAL RELEVANCE

Few studies have investigated the microbiota in teeth compromised by combined endo-periodontal lesions (EPL), but none have correlated the microbiological findings to any systemic condition, particularly IE, using NGS techniques. In such cases, the presence of apical periodontitis and periodontal disease can increase IE risk in susceptible patients.

Probiotic supplementation during antibiotic treatment is unjustified in maintaining the gut microbiome diversity: a systematic review and meta-analysis

BACKGROUND

Probiotics are often used to prevent antibiotic-induced low-diversity dysbiosis, however their effect is not yet sufficiently summarized in this regard. We aimed to investigate the effects of concurrent probiotic supplementation on gut microbiome composition during antibiotic therapy.

METHODS

We performed a systematic review and meta-analysis of randomized controlled trials reporting the differences in gut microbiome diversity between patients on antibiotic therapy with and without concomitant probiotic supplementation. The systematic search was performed in three databases (MEDLINE (via PubMed), Embase, and Cochrane Central Register of Controlled Trials (CENTRAL)) without filters on 15 October 2021. A random-effects model was used to estimate pooled mean differences (MD) with 95% confidence intervals (CI). This review was registered on PROSPERO (CRD42021282983).

RESULTS

Of 11,769 identified articles, 15 were eligible in the systematic review and 5 in the meta-analyses. Quantitative data synthesis for Shannon (MD = 0.23, 95% CI: [(-)0.06-0.51]), Chao1 (MD = 11.59 [(-)18.42-41.60]) and observed OTUs (operational taxonomic unit) (MD = 17.15 [(-)9.43-43.73]) diversity indices revealed no significant difference between probiotic supplemented and control groups. Lacking data prevented meta-analyzing other diversity indices; however, most of the included studies reported no difference in the other reported α- and ß-diversity indices between the groups. Changes in the taxonomic composition varied across the eligible studies but tended to be similar in both groups. However, they showed a potential tendency to restore baseline levels in both groups after 3-8 weeks. This is the first meta-analysis and the most comprehensive review of the topic to date using high quality methods. The limited number of studies and low sample sizes are the main limitations of our study. Moreover, there was high variability across the studies regarding the indication of antibiotic therapy and the type, dose, and duration of antimicrobials and probiotics.

CONCLUSIONS

Our results showed that probiotic supplementation during antibiotic therapy was not found to be influential on gut microbiome diversity indices. Defining appropriate microbiome diversity indices, their standard ranges, and their clinical relevance would be crucial.

Global patterns of vascular plant alpha diversity

Global patterns of regional (gamma) plant diversity are relatively well known, but whether these patterns hold for local communities, and the dependence on spatial grain, remain controversial. Using data on 170,272 georeferenced local plant assemblages, we created global maps of alpha diversity (local species richness) for vascular plants at three different spatial grains, for forests and non-forests. We show that alpha diversity is consistently high across grains in some regions (for example, Andean-Amazonian foothills), but regional 'scaling anomalies' (deviations from the positive correlation) exist elsewhere, particularly in Eurasian temperate forests with disproportionally higher fine-grained richness and many African tropical forests with disproportionally higher coarse-grained richness. The influence of different climatic, topographic and biogeographical variables on alpha diversity also varies across grains. Our multi-grain maps return a nuanced understanding of vascular plant biodiversity patterns that complements classic maps of biodiversity hotspots and will improve predictions of global change effects on biodiversity.