Reduced calorie diet combined with NNMT inhibition establishes a distinct microbiome in DIO mice

Treatment with a nicotinamide N-methyltransferase inhibitor (NNMTi; 5-amino-1-methylquinolinium) combined with low-fat diet (LD) promoted dramatic whole-body adiposity and weight loss in diet-induced obese (DIO) mice, rapidly normalizing these measures to age-matched lean animals, while LD switch alone was unable to restore these measures to age-matched controls in the same time frame. Since mouse microbiome profiles often highly correlate with body weight and fat composition, this study was designed to test whether the cecal microbiomes of DIO mice treated with NNMTi and LD were comparable to the microbiomes of age-matched lean counterparts and distinct from microbiomes of DIO mice maintained on a high-fat Western diet (WD) or subjected to LD switch alone. There were minimal microbiome differences between lean and obese controls, suggesting that diet composition and adiposity had limited effects. However, DIO mice switched from an obesity-promoting WD to an LD (regardless of treatment status) displayed several genera and phyla differences compared to obese and lean controls. While alpha diversity measures did not significantly differ between groups, beta diversity principal coordinates analyses suggested that mice from the same treatment group were the most similar. K-means clustering analysis of amplicon sequence variants by animal demonstrated that NNMTi-treated DIO mice switched to LD had a distinct microbiome pattern that was highlighted by decreased Erysipelatoclostridium and increased Lactobacillus relative abundances compared to vehicle counterparts; these genera are tied to body weight and metabolic regulation. Additionally, Parasutterella relative abundance, which was increased in both the vehicle- and NNMTi-treated LD-switched groups relative to the controls, significantly correlated with several adipose tissue metabolites’ abundances. Collectively, these results provide a novel foundation for future investigations.

Changes in the gut bacterial communities in colon cancer surgery patients: an observational study

Background Colon surgery has been shown to modulate the intestinal microbiota. Our objective was to characterize these changes using state-of-the-art next generation sequencing techniques. Methods We performed a single-centre prospective observational cohort study to evaluate the changes in the gut microbiota, i.e., taxon distribution, before and after elective oncologic colon surgery in adult patients with different antimicrobial prophylaxis regimens (standard prophylaxis with cefuroxime/metronidazole versus carbapenems for extended-spectrum beta-lactamase-producing Enterobacterales [ESBL-E] carriers). We obtained rectal samples on the day of surgery, intraoperative luminal samples, and rectal or stoma samples 3 days after surgery. We performed metataxonomic analysis based on sequencing of the bacterial 16S rRNA gene marker. Similarities and differences between bacterial communities were assessed using Bray–Curtis similarity, visualised using principal coordinates analysis and statistically tested by PERMANOVA. Comparison of taxa relative abundance was performed using ANCOM. Results We included 27 patients between March 27, 2019 and September 17, 2019. The median age was 63.6 years (IQR 56.4–76.3) and 44% were females. Most (81%) patients received standard perioperative prophylaxis as they were not ESBL carriers. There was no significant association between ESBL carriage and differences in gut microbiome. We observed large and significant increases in the genus Enterococcus between the preoperative/intraoperative samples and the postoperative sample, mainly driven by Enterococcus faecalis. There were significant differences in the postoperative microbiome between patients who received standard prophylaxis and carbapenems, specifically in the family Erysipelotrichaceae. Conclusion This hypothesis-generating study showed rapid changes in the rectal microbiota following colon cancer surgery.

Genetic diversity of the Central European wild boar (Sus scrofa scrofa) population and domestic pig (Sus scrofa domesticus) breeds based on a microsatellite DNA locus

The results of studies of the genetic structure of the Central European wild boar (Sus scrofa scrofa) population and four breeds of domestic pigs (Duroc, Yorkshire, Large White and Landrace) bred in the Central Black Earth region of Russia are presented in this work. Based on 12 microsatellite loci, a significant ( p <0.05) decrease in the level of genetic variability in bred breeds was shown. The expected heterozygosity and Shannon index were as follows: in the wild boar, Ho = 0.763 ± 0.026, I = 1.717 ± 0.091; in the Duroc breed, Ho = 0.569 ± 0.068, I = 1.191 ± 0.157; in the Landrace, Ho = 0.618 ± 0.062, I = 1.201 ± 0.147; in the Large White, Ho = 0.680 ± 0.029, I = 1.362 ± 0.074; and in the Yorkshire, Ho = 0.642 ± 0.065, I = 1.287 ± 0.156. The results of checking genotypic Hardy–Weinberg equilibrium based on the G-test of maximum likelihood demonstrated that the overwhelming majority of loci in the wild boar population were in the state of said equilibrium. By contrast, in pig breed populations, some loci demonstrated a significant deviation from the indicated equilibrium. In addition, the Yorkshire, Large White, and Landrace populations had loci, for which the hypothesis of neutrality was reliably rejected based on the results of the Ewens–Watterson test. The revealed private alleles, characteristic of the wild boar and breeds, can later be used to identify them. The ordination of the centroids of different herds in the space of the first two principal coordinates based on the matrix of pairwise estimates of Nei’s genetic distances showed that the most distant populations are the Duroc and Boar breeds, and the most genetically close are the Yorkshire and Landrace breeds. The closest to the wild boar population was the Large White breed. The assessment of the effective size, carried out using the method based on the linkage disequilibrium and the molecular coancestry method, showed that in all studied groups, including the wild boar population, the effective size was less than 100 individuals. The low effective size of the wild boar population (Ne = 21.8, Neb = 4.0) is probably caused by the death and shooting of animals due to Pestis africana suum.

Phenolic substances and cyanogenesis in galled and non-galled tissue of the fern species Microgramma vacciniifolia

Galls, neo-formed plant structures that can occur in different organs, are generated by species-specific interaction with an inducing organism. Inducers manipulate the metabolism of its host. Microgramma vacciniifolia (Langsd. & Fisch.) Copel. is a Neotropical epiphytic fern that hosted two stem galls, one induced by a midge species (Diptera) and other by a micromoth species (Lepidoptera). The aim of this study was to evaluate the impact of these two gall-inducing insects on the biochemistry of phenolic acids and the cyanogenesis in galls, stems and leaves of M. vacciniifolia. High performance liquid chromatography (HPLC) indicated a total of 14 phenol derivatives, including caffeic and coumaric acid. Principal Coordinates Analysis (PCoA) of the phenolic substances indicated three groups consisting (1) non-galled stems and micromoth-induced galls; (2) midge-induced galls; (3) midge-induced galls with parasitoids. Regarding the frequency of cyanogenesis assessed by the picrate paper test, the chi-squared test showed significant difference between fertile leaves (8.3%), sterile leaves (27.7%), non-galled stems (0%) and galls. Among galls, only the midge-induced galls analyzed were cyanogenic (15%). Our results indicated that the different gall-inducers (midge and micromoth) promote species-specific alterations to the phenolic substance composition of the host fern.

Optimizing mangrove conservation efforts with improved understanding of phytosociology-ecology synergy in Sri Lanka

The study aimed to understand the forest structure and ecological factors influencing mangrove distribution in eight mangrove forests across three climatic zones in Sri Lanka. We studied mangrove diversity and vegetation structure with 10m wide belt transects laid of different lengths (n=96) across the land-water gradient. Mangroves along the transect were identified, enumerated, and measured diameter at breast height (DBH). Subsurface water samples were taken in the adjoining lagoon/estuary to assess the environmental parameters (n=144), and water quality parameters were measured. Site-dependent spatial changes in the community structure were depicted through cluster analysis (CA). The forest survey revealed a heterogeneous mixture of 20 true mangrove species across the sites dominated by Avicennia, Rhizophora, and Sonneratia spp. Among the several environmental parameters analyzed by the distance-based redundancy ordination analysis (dbRDA), salinity, dissolved oxygen, and precipitation were found to be controlling factors in mangrove community structure. In addition, discriminant analysis confirmed the presence of ecological-phytosociological influence on mangrove assemblages identified through CA. The significant structural parameters tree density, and taxonomic diversity when tested using the canonical analysis of principal coordinates (CAP), altered the species abundance across the sites surveyed. The results suggest that there is a strong linkage between phytosociology and ecology with the mangrove forest distribution and this relationship needs to be considered wisely to fortify successful restoration practices.

Multivariate analysis and characterization of low impact crime in Mexico City

Background: Multivariate analysis is fast becoming a key instrument that can be used to address crimes or incidents. It may be helpful to assess government policies on crime prevention. Methods: To distinguish between the 25 official crime categories reported in Mexico City (Jan 2019 - Jun 2019), principal coordinates analysis was used to determine the quality of a characteristic in this context. This study used cluster analysis via K-means and Biplot based on time and location in terms of crime occurrence. Results: The results obtained from this preliminary analysis indicates that around 70% of crime occurrence is shown in the following boroughs: Cuauhtémoc, Iztapalapa, Gustavo A. Madero, Benito Juárez, Álvaro Obregón, Coyoacán, and Miguel Hidalgo. Conclusion: There are two factors that contribute to the difficulties in crime analysis in Mexico City, namely, the lack of people’s trust in authorities and the insufficiency of tools for data analysis. The latter is an integral part in achieving justice for the victims of crimes because it impedes the process of observing patterns and predicting the perpetrators’ next actions, which may help in solving a number of types of crimes. It is then imperative for law enforcement to utilize data analysis tools that aid in identifying crime patterns and trends, such that the occurrences of crime show a downward trend and consequentially increase the people’s trust in law enforcement agencies.

Phenotyping and Genotyping Analyses Reveal the Spread of Puccinia striiformis f. sp. tritici Aeciospores From Susceptible Barberry to Wheat in Qinghai of China

Puccinia striiformis f. sp. tritici Eriks., the cause of wheat yellow or stripe rust on wheat, undergoes sexual reproduction on barberry, but it is unclear if barberry plays any role in stripe rust epidemics under natural conditions. P. striiformis f. sp. tritici was isolated from its alternate host barberry (Berberis spp.) and primary host wheat in the vicinity of barberry by inoculation of aeciospores and urediniospores on Mingxian 169 cultivar in Qinghai province of China in 2018. The P. striiformis f. sp. tritici isolates from barberry and wheat were characterized to virulence patterns by inoculation on 24 differentials bearing Yr gene under control conditions and analyzed using 12 polymorphic simple sequence repeat (SSR) markers. The occurrence frequency of P. striiformis f. sp. tritici on barberry was 1.87% by inoculation aecia, collected from barberry on Mingxian 169 of wheat. A close virulence relationship was presented between P. striiformis f. sp. tritici isolates from both barberry and wheat based on virulence simple matching coefficient and principal coordinates analysis (PCoA). Additionally, the same genetic ancestry, based on structure analysis by STRUCTURE program and genetic relationship analyses using discriminant analysis of principal components and PCoA, was shared between P. striiformis f. sp. tritici isolates from barberry and those from wheat. Together, all the results indicated that the role of barberry in providing aeciospores as an inoculum source causing wheat stripe rust epidemic in Qinghai in spring is of considerable importance.

Temporal Patterns of Bacterial and Viral Communities during Algae Blooms of a Reservoir in Macau

Compositions of microbial communities associated with blooms of algae in a storage reservoir in Macau, China were investigated between 2013 and 2016. Algae were enumerated by visible light microscopy. Profiles of organisms in water were examined by 16S rRNA sequences and viral metagenomics, based on next generation sequencing. Results of 16S rRNA sequencing indicated that majority of the identified organisms were bacteria closely related to Proteobacteria, Cyanobacteria, Verrucomicrobia, Bacteroidetes, and Actinobacteria. Metagenomics sequences demonstrated that the dominant virus was Phycodnavirus, accounting for 70% of the total population. Patterns of relative numbers of bacteria in the microbial community and their temporal changes were determined through alpha diversity indices, principal coordinates analysis (PCoA), relative abundance, and visualized by Venn diagrams. Ways in which the bacterial and viral communities are influenced by various water-related variables were elucidated based on redundancy analysis (RDA). Relationships of the relative numbers of bacteria with trophic status in a reservoir used for drinking water in Macau, provided insight into associations of Phycodnavirus and Proteobacteria with changes in blooms of algae.

Characteristics of Microbial Community and Function With the Succession of Mangroves

In this study, 16S high-throughput and metagenomic sequencing analyses were employed to explore the changes in microbial community and function with the succession of mangroves (Sonneratia alba, Rhizophora apiculata, and Bruguiera parviflora) along the Merbok river estuary in Malaysia. The sediments of the three mangroves harbored their own unique dominant microbial taxa, whereas R. apiculata exhibited the highest microbial diversity. In general, Gammaproteobacteria, Actinobacteria, Alphaproteobacteria, Deltaproteobacteria, and Anaerolineae were the dominant microbial classes, but their abundances varied significantly among the three mangroves. Principal coordinates and redundancy analyses revealed that the specificity of the microbial community was highly correlated with mangrove populations and environmental factors. The results further showed that R. apiculata exhibited the highest carbon-related metabolism, coinciding with the highest organic carbon and microbial diversity. In addition, specific microbial taxa, such as Desulfobacterales and Rhizobiales, contributed the highest functional activities related to carbon metabolism, prokaryote carbon fixation, and methane metabolism. The present results provide a comprehensive understanding of the adaptations and functions of microbes in relation to environmental transition and mangrove succession in intertidal regions. High microbial diversity and carbon metabolism in R. apiculata might in turn facilitate and maintain the formation of climax mangroves in the middle region of the Merbok river estuary.

Macrobenthic community responses to multiple environmental stressors in a subtropical estuary

We assessed how multi- and univariate models reflect marine environmental health based on macrobenthic community responses to three environmental stressor categories: hydrodynamics, organic enrichment and metal contamination. We then compared the models with the benthic index AMBI (AZTI Marine Biotic Index). Macrobenthic community and physicochemical variables were sampled at 35 sites along Babitonga Bay, a subtropical estuary in Southern Brazil. Distance-based linear modelling identified depth, grain size and organic matter as well as Cu and Zn as key stressors affecting the macrobenthos. Using canonical analysis of principal coordinates (CAP), we developed three multivariate models based on the variability in community composition, creating stress gradients. The metal gradient showed better correlation with the benthic community. Sediment quality indices (Geoaccumulation Index and Contamination Factor) showed a low to moderate contamination status, with higher concentrations for Cr, Ni and Zn at the inner areas of the bay. According to AMBI, Babitonga Bay has a “good” environmental health status, and the AMBI values show stronger correlations with the hydrodynamic and organic enrichment gradients (r = 0.50 and r = 0.47) rather than the metal gradient (r = 0.29). Lumbrineridae polychaetes (not included in the AMBI list) and Scoloplos sp. were negatively related to the metal contamination gradient and were considered sensitive, while Sigambra sp., Magelona papillicornis, the gastropod Heleobia australis and species of the crustacean order Mysida were positively related to the gradient and considered tolerant to higher concentrations of metals in the sediment. Despite the inconsistency in the ecological classification provided by AMBI and its relationship with the metal gradient, our results suggest that the environmental quality was satisfactory for the studied gradients. The metal gradient showed the weakest correlation to AMBI. In such cases, the ecological classification of taxa by the index should be evaluated under the perspective of the action of inorganic genotoxic contaminants represented by metals.