Experimental Infection with Mycoplasma hyopneumoniae Strain 232 in Swine Influences the Lower Respiratory Microbiota

Mycoplasma (M.) hyopneumoniae, the etiological agent of swine enzootic pneumonia, has been reported to increase the susceptibility to secondary infections and modulate the respiratory microbiota in infected pigs. However, no studies have assessed the influence of M. hyopneumoniae on the respiratory microbiota diversity under experimental conditions. Therefore, this study evaluated the impact of M. hyopneumoniae infection on the respiratory microbiota of experimentally infected swine over time. To accomplish this, 12 weaned pigs from a M. hyopneumoniae-free farm were divided into two groups: M. hyopneumoniae strain 232 infected (n = 8) and non-infected (n = 4). The first group received 10 mL of Friis medium containing 10⁷ CCU/mL of M. hyopneumoniae while the control group received 10 mL of sterile Friis medium. Inoculation of both groups was performed intratracheally when the animals were 35 days old (d0). At 28 days post-inoculation (dpi) and 56 dpi, 4 infected animals plus 2 controls were humanely euthanized, and biopsy samples of nasal turbinates (NT) and bronchus-alveolar lavage fluid (BALF) samples were collected. The DNA was extracted from the individual samples, and each group had the samples pooled and submitted to next-generation sequencing. Taxonomic analysis, alpha and beta diversity indexes, weighted unifrac, and unweighted unifrac distances were calculated. A high relative frequency (99%) of M. hyopneumoniae in BALF samples from infected animals was observed with no significant variation between time points. The infection did not seem to alter the diversity and evenness of bacterial communities in NT, thus, M. hyopneumoniae relative frequency was low in NT pools from infected animals (28 dpi-0.83%; 56 dpi-0.89%). PCoA diagrams showed that BALF samples from infected pigs were grouped and far from the control samples, whereas NT from infected animals were not separated from the control. Under the present coditions, M. hyopneumoniae infection influenced the lower respiratory microbiota, which could contribute to the increased susceptibility of infected animals to respiratory infections.

Decreasing Species Richness with Increase in Elevation and Positive Rapoport Effects of Crambidae (Lepidoptera) on Mount Taibai

Rapoport's rule proposes that a species' range size increases with the increase in a gradient (such as latitude, altitude or water depth). However, altitudinal distributions and Rapoport's rule have rarely been tested for Asian Lepidoptera. Pyraustinae and Spilomelinae (Lepidoptera: Crambidae) are extremely diverse in temperate Asia, including on Mount Taibai, which is considered a hotspot area for studying the vertical distribution patterns of insect species. Based on the investigation of altitudinal distribution data with identification by using both DNA barcoding and the morphological classification of Pyraustinae and Spilomelinae, this paper determines the altitudinal gradient pattern for these two subfamilies on the north slope of Mount Taibai, and provides a test of the universality of Rapoport's rule in Lepidoptera by using four methods, including Stevens' method, Pagel's method, Rohde's method, and the cross-species method. Our results show that the alpha diversity of Pyraustinae and Spilomelinae both decrease with rising altitude. By contrast, the species' ranges increase with rising altitude. Three of the four methods used to test Rapoport's rule yielded positive results, while Rohde's results show a unimodal distribution model and do not support Rapoport's rule. Our findings fill the research gap on the elevational diversity of Lepidoptera in temperate Asia.

Associations between Changes in Fat-Free Mass, Fecal Microbe Diversity, and Mood Disturbance in Young Adults after 10-Weeks of Resistance Training

BACKGROUND

The gut microbiome contributes to numerous physiological processes in humans, and diet and exercise are known to alter both microbial composition and mood. We sought to explore the effect of a 10-week resistance training (RT) regimen with or without peanut protein supplementation (PPS) in untrained young adults on fecal microbiota and mood disturbance (MD).

METHODS

Participants were randomized into PPS (n = 25) and control (CTL [no supplement]; n = 24) groups and engaged in supervised, full-body RT twice a week. Measures included body composition, fecal microbe relative abundance, alpha- and beta-diversity from 16 s rRNA gene sequencing with QIIME2 processing, dietary intake at baseline and following the 10-week intervention, and post-intervention MD via the profile of mood states (POMS) questionnaire. Independent samples t-tests were used to determine differences between PPS and CTL groups. Paired samples t-tests investigated differences within groups.

RESULTS

Our sample was mostly female (69.4%), white (87.8%), normal weight (body mass index 24.6 ± 4.2 kg/m²), and 21 ± 2.0 years old. Shannon index significantly increased from baseline in all participants (p = 0.040), with no between-group differences or pre-post beta-diversity dissimilarities. Changes in Blautia abundance were associated with the positive POMS subscales, Vigor and self-esteem-related-affect (SERA) (rho = -0.451, p = 0.04; rho = -0.487, p = 0.025, respectively). Whole tree phylogeny changes were negatively correlated with SERA and Vigor (rho = -0.475, p = 0.046; rho = -0.582, p = 0.011, respectively) as well as change in bodyfat percentage (rho = -0.608, p = 0.007). Mediation analysis results indicate changes in PD Whole Tree Phylogeny was not a significant mediator of the relationship between change in fat-free mass and total MD.

CONCLUSIONS

Mood state subscales are associated with changes in microbial taxa and body composition. PD Whole Tree Phylogeny increased following the 10-week RT regimen; further research is warranted to explore how RT-induced changes in microbial diversity are related to changes in body composition and mood disturbance.

Searching for a Consensus Among Inflammatory Bowel Disease Studies: A Systematic Meta-Analysis

BACKGROUND

Numerous studies have examined the gut microbial ecology of patients with Crohn's disease (CD) and ulcerative colitis, but inflammatory bowel disease-associated taxa and ecological effect sizes are not consistent between studies.

METHODS

We systematically searched PubMed and Google Scholar and performed a meta-analysis of 13 studies to analyze how variables such as sample type (stool, biopsy, and lavage) affect results in inflammatory bowel disease gut microbiome studies, using uniform bioinformatic methods for all primary data.

RESULTS

Reduced alpha diversity was a consistent feature of both CD and ulcerative colitis but was more pronounced in CD. Disease contributed significantly variation in beta diversity in most studies, but effect size varied, and the effect of sample type was greater than the effect of disease. Fusobacterium was the genus most consistently associated with CD, but disease-associated genera were mostly inconsistent between studies. Stool studies had lower heterogeneity than biopsy studies, especially for CD.

CONCLUSIONS

Our results indicate that sample type variation is an important contributor to study variability that should be carefully considered during study design, and stool is likely superior to biopsy for CD studies due to its lower heterogeneity.

First Steps into Ruminal Microbiota Robustness

Despite its central role in ruminant nutrition, little is known about ruminal microbiota robustness, which is understood as the ability of the microbiota to cope with disturbances. The aim of the present review is to offer a comprehensive description of microbial robustness, as well as its potential drivers, with special focus on ruminal microbiota. First, we provide a briefing on the current knowledge about ruminal microbiota. Second, we define the concept of disturbance (any discrete event that disrupts the structure of a community and changes either the resource availability or the physical environment). Third, we discuss community resistance (the ability to remain unchanged in the face of a disturbance), resilience (the ability to return to the initial structure following a disturbance) and functional redundancy (the ability to maintain or recover initial function despite compositional changes), all of which are considered to be key properties of robust microbial communities. Then, we provide an overview of the currently available methodologies to assess community robustness, as well as its drivers (microbial diversity and network complexity) and its potential modulation through diet. Finally, we propose future lines of research on ruminal microbiota robustness.

Different contributions of plant diversity and soil properties to the community stability in the arid desert ecosystem

As a one of the focuses of ecological research, understanding the regulation of plant diversity on community stability is helpful to reveal the adaption of plant to environmental changes. However, the relationship between plant diversity and community stability is still controversial due to the scale effect of its influencing factors. In this study, we compared the changes in community stability and different plant diversity (i.e., species, functional, and phylogenetic diversities) between three communities (i.e., riparian forest, ecotone community, and desert shrubs), and across three spatial scales (i.e., 100, 400, and 2500 m²), and then quantified the contribution of soil properties and plant diversity to community stability by using structural equation model (SEM) in the Ebinur Lake Basin Nature Reserve of the Xinjiang Uygur Autonomous Region in the NW China. The results showed that: (1) community stability differed among three communities (ecotone community > desert shrubs > riparian forest). The stability of three communities all decreased with the increase of spatial scale (2) species diversity, phylogenetic richness and the mean pairwise phylogenetic distance were higher in ecotone community than that in desert shrubs and riparian forest, while the mean nearest taxa distance showed as riparian forest > ecotone community > desert shrubs. (3) Soil ammonium nitrogen and total phosphorus had the significant direct negative and positive effects on the community stability, respectively. Soil ammonium nitrogen and total phosphorus also indirectly affected community stability by adjusting plant diversity. The interaction among species, functional and phylogenetic diversities also regulated the variation of community stability across the spatial scales. Our results suggested that the effect of plant diversities on community stability were greater than that of soil factors. The asynchronous effect caused by the changes in species composition and functional traits among communities had a positive impact on the stability. Our study provided a theoretical support for the conservation and management of biodiversity and community functions in desert areas.

Host taxonomy determines the composition, structure, and diversity of the earthworm cast microbiome under homogenous feeding conditions

Host evolutionary history is a key factor shaping the earthworm cast microbiome, although its effect can be shadowed by the earthworm's diet. To untangle dietary from taxon effects, we raised nine earthworm species on a uniform diet of cow manure and compared cast microbiome across species while controlling for diet. Our results showed that, under controlled laboratory conditions, earthworm microbiomes are species-specific, more diverse than that of the controlled diet, and mainly comprised of native bacteria (i.e., not acquired from the diet). Furthermore, diet has a medium to large convergence effect on microbiome composition since earthworms shared 16 to 74% of their bacterial amplicon sequence variants (ASV). The inter-species core microbiome included 10 ASVs, while their intra-species core microbiomes were larger and varied in ASV richness (24-48%) and sequence abundance across earthworm species. This specificity in core microbiomes and variable degree of similarity in bacterial composition suggest that phylosymbiosis could determine earthworm microbiome assembly. However, lack of congruence between the earthworm phylogeny and the microbiome dendrogram suggests that a consistent diet fed over several generations may have weakened potential phylosymbiotic effects. Thus, cast microbiome assembly in earthworms seem to be the result of an interplay among host phylogeny and diet.

Microbial Risk Score for Capturing Microbial Characteristics, Integrating Multi-omics Data, and Predicting Disease Risk

Background

With the rapid accumulation of microbiome-wide association studies, a great amount of microbiome data are available to study the microbiome's role in human disease and advance the microbiome's potential use for disease prediction. However, the unique features of microbiome data hinder its utility for disease prediction.

Methods

Motivated from the polygenic risk score framework, we propose a microbial risk score (MRS) framework to aggregate the complicated microbial profile into a summarized risk score that can be used to measure and predict disease susceptibility. Specifically, the MRS algorithm involves two steps: 1) identifying a sub-community consisting of the signature microbial taxa associated with disease, and 2) integrating the identified microbial taxa into a continuous score. The first step is carried out using the existing sophisticated microbial association tests and pruning and thresholding method in the discovery samples. The second step constructs a community-based MRS by calculating alpha diversity on the identified sub-community in the validation samples. Moreover, we propose a multi-omics data integration method by jointly modeling the proposed MRS and other risk scores constructed from other omics data in disease prediction.

Results

Through three comprehensive real data analyses using the NYU Langone Health COVID-19 cohort, the gut microbiome health index (GMHI) multi-study cohort, and a large type 1 diabetes cohort separately, we exhibit and evaluate the utility of the proposed MRS framework for disease prediction and multi-omics data integration. In addition, the disease-specific MRSs for colorectal adenoma, colorectal cancer, Crohn's disease, and rheumatoid arthritis based on the relative abundances of 5, 6, 12, and 6 microbial taxa respectively are created and validated using the GMHI multi-study cohort. Especially, Crohn's disease MRS achieves AUCs of 0.88 ([0.85-0.91]) and 0.86 ([0.78-0.95]) in the discovery and validation cohorts, respectively.

Conclusions

The proposed MRS framework sheds light on the utility of the microbiome data for disease prediction and multi-omics integration, and provides great potential in understanding the microbiome's role in disease diagnosis and prognosis.

Composition, Structure and Diversity of Soil Bacterial Communities before, during and after Transit through the Gut of the Earthworm Aporrectodea caliginosa

Earthworms heavily modify the soil microbiome as it passes throughout their guts. However, there are no detailed studies describing changes in the composition, structure and diversity of soil microbiomes during gut transit and once they are released back to the soil as casts. To address this knowledge gap, we used 16S rRNA next-generation sequencing to characterize the microbiomes of soil, gut and casts from the earthworm Aporrectodea caliginosa. We also studied whether these three microbiomes are clearly distinct in composition or can be merged into metacommunities. A large proportion of bacteria was unique to each microbiome-soil (82%), gut (89%) and casts (75%), which indicates that the soil microbiome is greatly modified during gut transit. The three microbiomes also differed in alpha diversity, which peaked during gut transit and decreased in casts. Furthermore, gut transit also modified the structure of the soil microbiome, which clustered away from those of the earthworm gut and cast samples. However, this clustering pattern was not supported by metacommunity analysis, which indicated that soil and gut samples make up one metacommunity and cast samples another. These results have important implications for understanding the dynamics of soil microbial communities and nutrient cycles.

A 4-Week Diet Low or High in Advanced Glycation Endproducts Has Limited Impact on Gut Microbial Composition in Abdominally Obese Individuals: The deAGEing Trial

Dietary advanced glycation endproducts (AGEs), abundantly present in Westernized diets, are linked to negative health outcomes, but their impact on the gut microbiota has not yet been well investigated in humans. We investigated the effects of a 4-week isocaloric and macronutrient-matched diet low or high in AGEs on the gut microbial composition of 70 abdominally obese individuals in a double-blind parallel-design randomized controlled trial (NCT03866343). Additionally, we investigated the cross-sectional associations between the habitual intake of dietary dicarbonyls, reactive precursors to AGEs, and the gut microbial composition, as assessed by 16S rRNA amplicon-based sequencing. Despite a marked percentage difference in AGE intake, we observed no differences in microbial richness and the general community structure. Only the Anaerostipes spp. had a relative abundance >0.5% and showed differential abundance (0.5 versus 1.11%; p = 0.028, after low- or high-AGE diet, respectively). While the habitual intake of dicarbonyls was not associated with microbial richness or a general community structure, the intake of 3-deoxyglucosone was especially associated with an abundance of several genera. Thus, a 4-week diet low or high in AGEs has a limited impact on the gut microbial composition of abdominally obese humans, paralleling its previously observed limited biological consequences. The effects of dietary dicarbonyls on the gut microbiota composition deserve further investigation.

A Guide to Dietary Pattern-Microbiome Data Integration

The human gut microbiome is linked to metabolic and cardiovascular disease risk. Dietary modulation of the human gut microbiome offers an attractive pathway to manipulate the microbiome to prevent microbiome-related disease. However, this promise has not been realized. The complex system of diet and microbiome interactions is poorly understood. Integrating observational human diet and microbiome data can help researchers and clinicians untangle the complex systems of interactions that predict how the microbiome will change in response to foods. The use of dietary patterns to assess diet-microbiome relations holds promise to identify interesting associations and result in findings that can directly translate into actionable dietary intake recommendations and eating plans. In this article, we first highlight the complexity inherent in both dietary and microbiome data and introduce the approaches generally used to explore diet and microbiome simultaneously in observational studies. Second, we review the food group and dietary pattern-microbiome literature focusing on dietary complexity-moving beyond nutrients. Our review identified a substantial and growing body of literature that explores links between the microbiome and dietary patterns. However, there was very little standardization of dietary collection and assessment methods across studies. The 54 studies identified in this review used ≥7 different methods to assess diet. Coupled with the variation in final dietary parameters calculated from dietary data (e.g., dietary indices, dietary patterns, food groups, etc.), few studies with shared methods and assessment techniques were available for comparison. Third, we highlight the similarities between dietary and microbiome data structures and present the possibility that multivariate and compositional methods, developed initially for microbiome data, could have utility when applied to dietary data. Finally, we summarize the current state of the art for diet-microbiome data integration and highlight ways dietary data could be paired with microbiome data in future studies to improve the detection of diet-microbiome signals.

Ulcerative Colitis Seems to Imply Oral Microbiome Dysbiosis

Ulcerative colitis (UC) is a recurrent pathology of complex etiology that has been occasionally associated with oral lesions, but the overall composition of the oral microbiome in UC patients and its role in the pathogenesis of the disease are still poorly understood. In this study, the oral microbiome of UC patients and healthy individuals was compared to ascertain the possible changes in the oral microbial communities associated with UC. For this, the salivary microbiota of 10 patients diagnosed with an active phase of UC and 11 healthy controls was analyzed by 16S rRNA gene sequencing (trial ref. ISRCTN39987). Metataxonomic analysis revealed a decrease in the alpha diversity and an imbalance in the relative proportions of some key members of the oral core microbiome in UC patients. Additionally, Staphylococcus members and four differential species or phylotypes were only present in UC patients, not being detected in healthy subjects. This study provides a global snapshot of the existence of oral dysbiosis associated with UC, and the possible presence of potential oral biomarkers.

Parasite communities in English Sole (Parophrys vetulus) have changed in composition but not richness in the Salish Sea, Washington, USA since 1930

Earth is rapidly losing free-living species. Is the same true for parasitic species? To reveal temporal trends in biodiversity, historical data are needed, but often such data do not exist for parasites. Here, parasite communities of the past were reconstructed by identifying parasites in fluid-preserved specimens held in natural history collections. Approximately 2500 macroparasites were counted from 109 English Sole (Parophrys vetulus ) collected between 1930 and 2019 in the Salish Sea, Washington, USA. Alpha and beta diversity were measured to determine if and how diversity changed over time. Species richness of parasite infracommunities and community dispersion did not vary over time, but community composition of decadal component communities varied significantly over the study period. Community dissimilarity also varied: prior to the mid-20th century, parasites shifted in abundance in a seemingly stochastic manner and, after this time period, a canalization of community change was observed, where species' abundances began to shift in consistent directions. Further work is needed to elucidate potential drivers of these changes and to determine if these patterns are present in the parasite communities of other fishes of the Salish Sea.

Discriminating ecological processes affecting different dimensions of α- and β-diversity in desert plant communities

Understanding the spatial distribution of plant diversity and its drivers are major challenges in biogeography and conservation biology. Integrating multiple facets of biodiversity (e.g., taxonomic, phylogenetic, and functional biodiversity) may advance our understanding on how community assembly processes drive the distribution of biodiversity. In this study, plant communities in 60 sampling plots in desert ecosystems were investigated. The effects of local environment and spatial factors on the species, functional, and phylogenetic α- and β-diversity (including turnover and nestedness components) of desert plant communities were investigated. The results showed that functional and phylogenetic α-diversity were negatively correlated with species richness, and were significantly positively correlated with each other. Environmental filtering mainly influenced species richness and Rao quadratic entropy; phylogenetic α-diversity was mainly influenced by dispersal limitation. Species and phylogenetic β-diversity were mainly consisted of turnover component. The functional β-diversity and its turnover component were mainly influenced by environmental factors, while dispersal limitation dominantly effected species and phylogenetic β-diversity and their turnover component of species and phylogenetic β-diversity. Soil organic carbon and soil pH significantly influenced different dimensions of α-diversity, and soil moisture, salinity, organic carbon, and total nitrogen significantly influenced different dimensions of α- and β-diversity and their components. Overall, it appeared that the relative influence of environmental and spatial factors on taxonomic, functional, and phylogenetic diversity differed at the α and β scales. Quantifying α- and β-diversity at different biodiversity dimensions can help researchers to more accurately assess patterns of diversity and community assembly.

Contrasting Community Assembly Mechanisms Underlie Similar Biogeographic Patterns of Surface Microbiota in the Tropical North Pacific Ocean

Marine microbiota are critical components of global biogeochemical cycles. However, the biogeographic patterns and ecological processes that structure them remain poorly understood, especially in the oligotrophic ocean. In this study, we used high-throughput sequencing of 16S and 18S rRNA genes to investigate the distribution patterns of bacterial and microeukaryotic communities and their assembly mechanisms in the surface waters of the tropical North Pacific Ocean. The fact that both the bacterial and the microeukaryotic communities showed similar distribution patterns (i.e., similar distance-decay patterns) and were clustered according to their geographic origin (i.e., the western tropical North Pacific and central tropical North Pacific) suggested that there was a significant biogeographic pattern of microbiota in the North Pacific Ocean. Indices of alpha diversity such as species richness, phylogenetic diversity, and the Shannon diversity index also differed significantly between regions. The correlations were generally similar between spatial and environmental variables and the alpha and beta diversities of bacteria and microeukaryotes across the entire region. The relative importance of ecological processes differed between bacteria and microeukaryotes: ecological drift was the principal mechanism that accounted for the structure of bacterial communities; heterogeneous selection, dispersal limitation, and ecological drift collectively explained much of the turnover of the microeukaryote communities.

IMPORTANCE Bacteria and microeukaryotes are extremely diverse groups in the ocean, where they regulate elemental cycling and energy flow. Studies of marine microbial ecology have benefited greatly from the rapid progress that has been made in genomic sequencing and theoretical microbial ecology. However, the spatial distribution of marine bacteria and microeukaryotes and the nature of the assembly mechanisms that determine their distribution patterns in oligotrophic marine waters are poorly understood. In this study, we used high-throughput sequencing methods to identify the distribution patterns and ecological processes of bacteria and microeukaryotes in an oligotrophic, tropical ocean. Our study showed that contrasting community assembly mechanisms underlaid similar biogeographic patterns of surface bacterial and microeukaryotic communities in the tropical North Pacific Ocean.

Gut Microbiota in Heart Failure Patients With Preserved Ejection Fraction (GUMPTION Study)

Introduction: Heart failure with preserved ejection fraction (HFpEF) is associated with disrupted intestinal epithelial function, resulting from intestinal congestion. Intestinal congestion changes the morphology and permeability of the intestinal wall, and it becomes easy for the gut microbiota to change and transfer. Intervention on gut microbiota may become a new target for HFpEF treatment. However, the characteristics of gut microbiota in patients with HFpEF remain unknown. This preliminary report aims to detect the structure of gut microbiota in HFpEF patients so as to explore their characteristic changes, thereby providing a theoretical basis for future research. Methods: This research recruited 30 patients diagnosed with HFpEF and 30 healthy individuals. Stool specimens of research subjects were collected separately, and the microarray analyses of gut microbiota were conducted by Illumina high-throughput DNA sequencing. The differences in gut microbiota composition, alpha diversity, and beta diversity between the two groups were finally obtained. Results: The composition of gut microbiota was significantly different between the two groups. At the phylum classification level, the abundance of Synergistetes tended to be higher in the HFpEF group (P = 0.012). At genus classification level, the abundance of Butyricicoccus (P < 0.001), Sutterella (P = 0.004), Lachnospira (P = 0.003), and Ruminiclostridium (P = 0.009) in the HFpEF group were lower, while the abundance of Enterococcus (P < 0.001) and Lactobacillus (P = 0.005) were higher. According to the Chao index of alpha diversity analysis, HFpEF patients showed a nominally significant lower species richness when compared with controls (P = 0.046). However, there was no statistical difference in the Shannon index (P = 0.159) and Simpson index (P = 0.495), indicating that there was no difference in species diversity between the two groups. Beta diversity analysis revealed a highly significant separation of HFpEF patients and controls. Conclusions: An imbalance in the gut microbiota of HFpEF patients was observed. Patients with HFpEF have an increased abundance of microbiota associated with inflammation and a decreased abundance of microbiota associated with anti-inflammatory effects in the gut environment. In line with that, the species richness of gut microbiota in HFpEF patients tended to be lower.

Multigene Phylogeny, Diversity and Antimicrobial Potential of Endophytic Sordariomycetes From Rosa roxburghii

Rosa roxburghii Tratt. is widely applied in food, cosmetics, and traditional medicine, and has been demonstrated to possess diverse bioactivities. Plant endophytic fungi are important microbial resources with great potential for application in many fields. They not only establish mutualistic symbiosis with host plants but also produce a variety of bioactive compounds. Therefore, in the present study, endophytic fungi were isolated from R. roxburghii, the diversity and antimicrobial activities were evaluated. As a result, 242 strains of endophytic Sordariomycetes were successfully isolated. Multigene phylogenetic analyses showed that these isolates included eight orders, 19 families, 33 genera. The dominant genera were Diaporthe (31.4%), Fusarium (14.4%), Chaetomium (7.9%), Dactylonectria (7.0%), Graphium (4.5%), Colletotrichum (4.1%), and Clonostachys (4.1%). For different tissues of R. roxburghii, alpha diversity analysis revealed that the diversity of fungal communities decreased in the order of root, fruit, stem, flower, leaf, and seed, and Clonostachys and Dactylonectria exhibited obvious tissue specificity. Meanwhile, functional annotation of 33 genera indicated that some fungi have multitrophic lifestyles combining endophytic, pathogenic, and saprophytic behavior. Additionally, antimicrobial activities of endophytic Sordariomycetes against Lasiodiplodia theobromae, Botryosphaeria dothidea, Colletotrichum capsici, Pyricularia oryzae, Rhizoctonia solani, Fusarium oxysporum, Pseudomonas syringae, Pantoea agglomerans, Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Pseudomonas aeruginosa were screened. Dual culture test assays showed that there were 40 different endophytic species with strong inhibition of at least one or moderate inhibition of two or more against the 12 tested strains. The results from the filter paper diffusion method suggested that extracellular metabolites may be more advantageous than intracellular metabolites in the development of antimicrobial agents. Eleven isolates with good activities were screened. In particular, Hypomontagnella monticulosa HGUP194009 and Nigrospora sphaerica HGUP191020 have shown promise in both broad-spectrum and intensity. Finally, some fungi that commonly cause disease have been observed to have beneficial biological activities as endophytic fungi. In conclusion, this study showed the species composition, alpha diversity, and lifestyle diversity of endophytic Sordariomycetes from R. roxburghii and demonstrated these isolates are potential sources for exploring antimicrobial agents.

Application of Clustering Method to Explore the Correlation Between Dominant Flora and the Autism Spectrum Disorder Clinical Phenotype in Chinese Children

Autism spectrum disorder (ASD) is characterized by deficits in social interactions and repetitive, stereotypic behaviors. Evidence shows that bidirectional communication of the gut-brain axis plays an important role. Here, we recruited 62 patients with ASD in southern China, and performed a cross-sectional study to test the relationship between repeated behavior, gut microbiome composition, and alpha diversity. We divided all participants into two groups based on the clustering results of their microbial compositions and found Veillonella and Ruminococcus as the seed genera in each group. Repetitive behavior differed between clusters, and cluster 2 had milder repetitive symptoms than Cluster 1. Alpha diversity between clusters was significantly different, indicating that cluster 1 had lower alpha diversity and more severe repetitive, stereotypic behaviors. Repetitive behavior had a negative correlation with alpha diversity. We demonstrated that the difference in intestinal microbiome composition and altered alpha diversity can be associated with repetitive, stereotypic behavior in autism. The role of Ruminococcus and Veillonella in ASD is not yet understood.

Advanced Dental Cleaning is Associated with Reduced Risk of COPD Exacerbations - A Randomized Controlled Trial

Purpose

Infections from the oral microbiome may lead to exacerbations of chronic obstructive pulmonary disease (COPD). We investigated whether advanced dental cleaning could reduce exacerbation frequency. Secondary outcomes were disease-specific health status, lung function, and whether the bacterial load and composition of plaque microbiome at baseline were associated with a difference in outcomes.

Patients and Methods

One-hundred-one primary and secondary care patients with COPD were randomized to intervention with advanced dental cleaning or to dental examination only, repeated after six months. At baseline and at 12 months, data of exacerbations, lung function, COPD Assessment Test (CAT) score, and periodontal status were collected from questionnaires, record review, and periodontal examination. Student’s t-test and Mann–Whitney-U (MWU) test compared changes in outcomes. The primary outcome variable was also assessed using multivariable linear regression with adjustment for potential confounders. Microbiome analyses of plaque samples taken at baseline were performed using Wilcoxon signed ranks tests for calculation of alpha diversity, per mutational multivariate analysis of variance for beta diversity, and receiver operating characteristic curves for prediction of outcomes based on machine learning models.

Results

In the MWU test, the annual exacerbation frequency was significantly reduced in patients previously experiencing frequent exacerbations (p = 0.020) and in those with repeated advanced dental cleaning (p = 0.039) compared with the non-treated control group, but not in the total population including both patients with a single and repeated visits (p = 0.207). The result was confirmed in multivariable linear regression, where the risk of new exacerbations was significantly lower in patients both in the intention to treat analysis (regression coefficient 0.36 (95% CI 0.25–0.52), p < 0.0001) and in the population with repeated dental cleaning (0.16 (0.10–0.27), p < 0.0001). The composition of microbiome at baseline was moderately predictive of an increased risk of worsened health status at 12 months (AUC = 0.723).

Conclusion

Advanced dental cleaning is associated with a reduced frequency of COPD exacerbations. Regular periodontal examination and dental cleaning may be of clinical importance to prevent COPD exacerbations.

Wildfire and topography drive woody plant diversity in a Sky Island mountain range in the Southwest USA

AIM

Drastic changes in fire regimes are altering plant communities, inspiring ecologists to better understand the relationship between fire and plant species diversity. We examined the impact of a 90,000-ha wildfire on woody plant species diversity in an arid mountain range in southern Arizona, USA. We tested recent fire-diversity hypotheses by addressing the impacts on diversity of fire severity, fire variability, historical fire regimes, and topography.

LOCATION

Chiricahua National Monument, Chiricahua Mountains, Arizona, USA, part of the Sky Islands of the US-Mexico borderlands.

TAXON

Woody plant species.

METHODS

We sampled woody plant diversity in 138 plots before (2002-2003) and after (2017-2018) the 2011 Horseshoe Two Fire in three vegetation types and across fire severity and topographic gradients. We calculated gamma, alpha, and beta diversity and examined changes over time in burned versus unburned plots and the shapes of the relationships of diversity with fire severity and topography.

RESULTS

Alpha species richness declined, and beta and gamma diversity increased in burned but not unburned plots. Fire-induced enhancement of gamma diversity was confined to low fire severity plots. Alpha diversity did not exhibit a clear continuous relationship with fire severity. Beta diversity was enhanced by variation in fire severity among plots and increased with fire severity up to very high severity, where it declined slightly.

MAIN CONCLUSIONS

The results reject the intermediate disturbance hypothesis for alpha diversity but weakly support it for gamma diversity. Spatial variation in fire severity promoted variation among plant assemblages, supporting the pyrodiversity hypothesis. Long-term drought probably amplified fire-driven diversity changes. Despite the apparent benign impact of the fire on diversity, the replacement of two large conifer species with a suite of drought-tolerant shrubs signals the potential loss of functional diversity, a pattern that may warrant restoration efforts to retain these important compositional elements.

Revisiting the effect of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding

Environmental DNA (eDNA) metabarcoding is an increasingly popular tool for measuring and cataloguing biodiversity. Because the environments and substrates in which DNA is preserved differ considerably, eDNA research often requires bespoke approaches to generating eDNA data. Here, we explore how two experimental choices in eDNA study design-the number of PCR replicates and the depth of sequencing of PCR replicates-influence the composition and consistency of taxa recovered from eDNA extracts. We perform 24 PCR replicates from each of six soil samples using two of the most common metabarcodes for Fungi and Viridiplantae (ITS1 and ITS2), and sequence each replicate to an average depth of ~84,000 reads. We find that PCR replicates are broadly consistent in composition and relative abundance of dominant taxa, but that low abundance taxa are often unique to one or a few PCR replicates. Taxa observed in one out of 24 PCR replicates make up 21-29% of the total taxa detected. We also observe that sequencing depth or rarefaction influences alpha diversity and beta diversity estimates. Read sampling depth influences local contribution to beta diversity, placement in ordinations, and beta dispersion in ordinations. Our results suggest that, because common taxa drive some alpha diversity estimates, few PCR replicates and low read sampling depths may be sufficient for many biological applications of eDNA metabarcoding. However, because rare taxa are recovered stochastically, eDNA metabarcoding may never fully recover the true amplifiable alpha diversity in an eDNA extract. Rare taxa drive PCR replicate outliers of alpha and beta diversity and lead to dispersion differences at different read sampling depths. We conclude that researchers should consider the complexity and unevenness of a community when choosing analytical approaches, read sampling depths, and filtering thresholds to arrive at stable estimates.

Altered Plasma Fatty Acids Associate with Gut Microbial Composition in Common Variable Immunodeficiency

PURPOSE

Fatty acid (FA) abnormalities are found in various inflammatory disorders and have been related to disturbed gut microbiota. Patients with common variable immunodeficiency (CVID) have inflammatory complications associated with altered gut microbial composition. We hypothesized that there is an altered FA profile in CVID patients, related to gut microbial dysbiosis.

METHODS

Plasma FAs were measured in 39 CVID patients and 30 healthy controls. Gut microbial profile, a food frequency questionnaire, and the effect of the oral antibiotic rifaximin were investigated in CVID patients.

RESULTS

The n-3 polyunsaturated fatty acids (PUFAs), eicosapentaenoic acid (EPA) (1.4 [1.0-1.8] vs. 1.9 [1.2-2.5], median (IQR), P < 0.05), and docosahexaenoic acid (DHA) (3.2 [2.4-3.9] vs. 3.5 [2.9-4.3], P < 0.05), all values expressed as weight percent of total plasma FAs, were reduced in CVID compared to controls. Also, n-6 PUFAs (34.3 ± 3.4 vs. 37.1 ± 2.8, mean ± SD, P < 0.001) and linoleic acid (LA) (24.5 ± 3.3 vs. 28.1 ± 2.7, P < 0.0001) and the FA anti-inflammatory index (98.9 [82.1-119.4] vs. 117.0 [88.7-153.1], median (IQR), P < 0.05) were reduced in CVID. The microbial alpha diversity was positively associated with plasma n-6 PUFAs (r = 0.41, P < 0.001) and LA (r = 0.51, P < 0.001), but not n-3 PUFAs (P = 0.78). Moreover, a 2-week course of rifaximin significantly reduced the proportion of n-6 PUFAs (P = 0.04, UNIANOVA). Serum immunoglobulin G (IgG) levels correlated with plasma n-3 PUFAs (rho = 0.36, P = 0.03) and DHA (rho = 0.41, P = 0.009).

CONCLUSION

We found a potentially unfavorable FA profile in CVID, related to low IgG levels. High plasma n-6 PUFAs were related to increased gut microbial diversity and altered by rifaximin therapy.

Moderate-Intensity Physical Exercise Affects the Exercise Performance and Gut Microbiota of Mice

The gut microbiota is closely associated with the health of the host and is affected by many factors, including exercise. In this study, we compared the gut microbial changes and exercise performance over a 14-week period in mice that performed exercise (NE; n = 15) and mice that did not perform exercise (NC; n = 15). Mice were subjected to stool collection and exercise tests one week prior to adaptive training and after 2, 6, 10, and 14 weeks of exercise. Bacteria associated with the stool samples were assessed via Illumina-based 16S rRNA gene sequencing. While there was no significant difference in body weight between the groups (p > 0.05), the NE group had a significantly higher exercise performance from weeks 2-14 (p < 0.01) and lower fat coefficient (p < 0.01) compared with the NC group. The Shannon index of the gut microbiota in the NC group was higher than that in the NE group at weeks 6 and 10, and the Chao1 index was higher than that in the NE group at week 14. Exercise performance positively correlated with the relative abundance of Phascolarctobacterium. Grouped time series data analysis demonstrated that Bifidobacteria, Coprococcus, and one unnamed genus in the Clostridiales order were significantly increased in the NE group, which correlated with increased glucose, flavonoid, arginine, and proline metabolism. In conclusion, moderate-intensity treadmill exercise significantly increased the exercise performance of mice and changed the core bacteria and bacterial metabolic activity. These results provide a reference for studying the effects of exercise intervention and exercise performance on the gut microbiota of mice.

A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project

BACKGROUND

Individual diet components and specific dietary regimens have been shown to impact the gut microbiome.

OBJECTIVES

Here, we explored the contribution of long-term diet by searching for dietary patterns that would best associate with the gut microbiome in a population-based cohort.

METHODS

Using a priori and a posteriori approaches, we constructed dietary patterns from an FFQ completed by 1800 adults in the American Gut Project. Dietary patterns were defined as groups of participants or combinations of food variables (factors) driven by criteria ranging from individual nutrients to overall diet. We associated these patterns with 16S ribosomal RNA-based gut microbiome data for a subset of 744 participants.

RESULTS

Compared to individual features (e.g., fiber and protein), or to factors representing a reduced number of dietary features, 5 a posteriori dietary patterns based on food groups were best associated with gut microbiome beta diversity (P ≤ 0.0002). Two patterns followed Prudent-like diets-Plant-Based and Flexitarian-and exhibited the highest Healthy Eating Index 2010 (HEI-2010) scores. Two other patterns presented Western-like diets with a gradient in HEI-2010 scores. A fifth pattern consisted mostly of participants following an Exclusion diet (e.g., low carbohydrate). Notably, gut microbiome alpha diversity was significantly lower in the most Western pattern compared to the Flexitarian pattern (P ≤ 0.009), and the Exclusion diet pattern was associated with low relative abundance of Bifidobacterium (P ≤ 1.2 × 10-7), which was better explained by diet than health status.

CONCLUSIONS

We demonstrated that global-diet a posteriori patterns were more associated with gut microbiome variations than individual dietary features among adults in the United States. These results confirm that evaluating diet as a whole is important when studying the gut microbiome. It will also facilitate the design of more personalized dietary strategies in general populations.

Effects of Helicobacter pylori Infection on the Oral Microbiota of Reflux Esophagitis Patients

The human oral microbiota plays a vital role in maintaining metabolic homeostasis. To explore the relationship between Helicobacter pylori (Hp) and reflux esophagitis, we collected 86 saliva samples from reflux esophagitis patients (RE group) and 106 saliva samples from healthy people (C group) for a high-throughput sequencing comparison. No difference in alpha diversity was detected between the RE and the C groups, but beta diversity of the RE group was higher than the C group. Bacteroidetes was more abundant in the RE group, whereas Firmicutes was more abundant in the C group. The linear discriminant analysis effect size analysis demonstrated that the biomarkers of the RE group were Prevotella, Veillonella, Leptotrichia, and Actinomyces, and the biomarkers of the C group were Lautropia, Gemella, Rothia, and Streptococcus. The oral microbial network structure of the C group was more complex than that of the RE group. Second, to explore the effect of Hp on the oral microbiota of RE patients, we performed the ¹⁴C-urea breath test on 45 of the 86 RE patients. We compared the oral microbiota of 33 Hp-infected reflux esophagitis patients (REHpp group) and 12 non-Hp-infected reflux esophagitis patients (REHpn group). No difference in alpha diversity was observed between the REHpn and REHpp groups, and beta diversity of the REHpp group was significantly lower than that of the REHpn group. The biomarkers in the REHpp group were Veillonella, Haemophilus, Selenomonas, Megasphaera, Oribacterium, Butyrivibrio, and Campylobacter; and the biomarker in the REHpn group was Stomatobaculum. Megasphaera was positively correlated with Veillonella in the microbial network of the REHpp group. The main finding of this study is that RE disturbs the human oral microbiota, such as increased beta diversity. Hp infection may inhibit this disorderly trend.