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.

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.

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.

Effects of Dietary Tributyrin on Growth Performance, Biochemical Indices, and Intestinal Microbiota of Yellow-Feathered Broilers

This study aimed to evaluate the effects of tributyrin on growth performance, biochemical indices and intestinal microbiota of yellow-feathered broilers. 360 one-day-old chicks were randomly allocated to three treatments with six replicates of 20 chicks each, including a normal control group (NC), an antibiotic group (PC), and a tributyrin (250 mg/kg) group (TB) for 63 days. The results showed that compared with the control, the feed conversion ratio (FCR) in the TB group decreased during the d22 to d42 (p < 0.05) and overall, the final weight and FCR of broilers tended to increase and decrease, respectively. Moreover, the TB group showed the highest creatine concentrations at the entire period (p < 0.05). TB treatment increased the Bacteroidetes relative abundance and decreased Firmicutes. Principal coordinates analysis yielded clear clustering of the three groups. Linear discriminant analysis effect size analysis found seven differentially abundant taxa in the TB group, including several members of Bacteroidedetes. The relative abundance of Eisenbergiella, Phascolarctobacterium, Megasphaera and Intestinimonas increased in tributyrin-treated broilers. Spearman correlation analysis identified a correlation between Eisenbergiella abundance and overall feed efficiency. These results demonstrated that tributyrin could improve the growth performance by modulating blood biochemical indices and the cecal microflora composition of broilers.

Changes in the gut microbiota after hepatitis C virus eradication

The gut microbiota interacts with infectious diseases and affects host immunity. Liver disease is also reportedly associated with changes in the gut microbiota. To elucidate the changes in the gut microbiota before and after hepatitis C virus (HCV) eradication through direct-acting antiviral (DAA) treatment in patients with chronic hepatitis C (CHC), we investigated 42 samples from 14 patients who received DAA therapy for HCV. Fecal samples were obtained before treatment (Pre), when treatment ended (EOT), and 24 weeks after treatment ended (Post24). The target V3–4 region of the 16S rRNA gene from fecal samples was amplified using the Illumina Miseq sequencing platform. The diversity of the gut microbiota did not significantly differ between Pre, EOT, and Post24. Principal coordinates analysis showed that for each patient, the values at Pre, EOT, and Post24 were concentrated within a small area. The linear discriminant analysis of effect size showed that the relative abundances of Faecalibacterium and Bacillus increased at EOT, further increased at Post24, and were significantly increased at Post24 compared to Pre. These suggest that changes in the gut microbiota should be considered as among the various effects observed on living organisms after HCV eradication.

A Predictive Model Based on the Gut Microbiota Improves the Diagnostic Effect in Patients With Cholangiocarcinoma

Cholangiocarcinoma (CCA) is a malignant hepatic tumor with a poor prognosis, which needs early diagnosis urgently. The gut microbiota has been shown to play a crucial role in the progression of liver cancer. Here, we explored a gut microbiota model covering genera Burkholderia-Caballeronia-Paraburkholderia, Faecalibacterium, and Ruminococcus_1 (B-F-R) for CCA early diagnosis. A case-control study was conducted to enroll 53 CCA patients, 47 cholelithiasis patients, and 40 healthy controls. The feces samples and clinical information of participants were collected in the same period. The gut microbiota and its diversity of individuals were accessed with 16S rDNA sequencing, and the gut microbiota profile was evaluated according to microbiota diversity. Finally, four enriched genera in the CCA group (genera Bacteroides, Muribaculaceae_unclassified, Muribaculum, and Alistipes) and eight enriched genera in the cholelithiasis group (genera Bifidobacterium, Streptococcus, Agathobacter, Ruminococcus_gnavus_group, Faecalibacterium, Subdoligranulum, Collinsella, Escherichia-Shigella) constitute an overall different microbial community composition (P = 0.001). The B-F-R genera model with better diagnostic value than carbohydrate antigen 19-9 (CA19-9) was identified by random forest and Statistical Analysis of Metagenomic Profiles (STAMP) to distinguish CCA patients from healthy controls [area under the curve (AUC) = 0.973, 95% CI = 0.932–1.0]. Moreover, the correlative analysis found that genera Burkholderia-Caballeronia-Paraburkholderia were positively correlated with body mass index (BMI). The significantly different microbiomes between cholelithiasis and CCA were found via principal coordinates analysis (PCoA) and linear discriminant analysis effect size (LEfSe), and Venn diagram and LEfSe were utilized to identify four genera by comparing microbial compositions among patients with malignant obstructive jaundice (MOJ-Y) or not (MOJ-N). In brief, our findings suggest that gut microbiota vary from benign and malignant hepatobiliary diseases to healthy people and provide evidence supporting gut microbiota to be a non-invasive biomarker for the early diagnosis of CCA.

Elderly Patients with Mild Cognitive Impairment Exhibit Altered Gut Microbiota Profiles

Background. As a transitional state between normal aging and Alzheimer’s disease (AD), mild cognitive impairment (MCI) is characterized by a worse cognitive decline than that of natural aging. The association between AD and gut microbiota has been reported in a number of studies; however, microbial research regarding MCI remains limited. Methods. This study examined 48 participants, of whom 22 were MCI cases and 26 were normal control cases. Fecal samples were collected for 16S ribosomal RNA (rRNA) quantitative arrays and bioinformatics analysis. Results. A principal coordinates analysis (PCoA) and nonmetric multidimensional scaling (NMDS) both demonstrated that the microbial composition of participants with MCI deviated from that of healthy control participants. Multiple bacterial species were significantly increased (e.g., Staphylococcus intermedius) or decreased (e.g., Bacteroides salyersiae) in samples from the MCI group. Conclusion. The composition of gut microbiota differed between normal control and MCI cases. This is the first study to identify a signature series of species in the gut microbiota of individuals with MCI. The results provide a new direction for the future development of an early diagnosis and probiotic regimen.

Estimating genetic diversity in Sorghum bicolor using molecular markers

Aim: The present study aimed at measuring the genetic diversity of a set of 219 sorghum accessions differing in their grain colour. Methodology: About 219 diverse sorghum lines differing in their grain colour were obtained from National Bureau of Plant Genetics Resources (NBPGR), New Delhi and genotyped using 17 SSR markers. Polymorphism information content (PIC) and allele frequency were determined using PowerMarker V3.25. Clustering and factorial analysis were performed using DARwin 6.0. GenAlex version 6.5 was used to perform Principal Coordinates Analysis (PCoA) and AMOVA. Diversity analysis was performed by using Darwin. Results: Genotyping of 219 sorghum accessions using 17 SSR markers produced a total of 399 alleles with an average PIC value of 0.85 and gene diversity of 0.87. Highest allele frequency was observed for the marker, Xtxp 265 whereas highest major allele frequency was observed in 196 accessions for the marker, Xtxp 278. Diversity analysis divided the 219 accessions into three clusters (1, 2 and 3) and genotypes belonging to same geographical origin were found to be clustered together. Interpretation: SSR marker based genetic diversity analysis grouped 219 sorghum accessions into three clusters. Grouping and clustering of accessions was mostly based on the geographical origins with some exceptions which may be due to cross hybridisation of accessions between countries paving a way for cross gene flow.