Regulation of the intestinal dysbiosis of high – fat diet obese mice via gut microbia–TLR2 / 4 pathway by electroacupuncture

Objective: We design experimental study to explore the impacts of electroacupuncture (EA) treatment on the interaction between TLR2 / 4 pathway and gut flora in high – fat diet obese mice. Methods: Reverse transcriptase polymerase chain reaction, western blotting and 16S rRNA pyrosequencing were to study the association among groups (normal (N), model (M), electroacupuncture for 7 d (A7), 14 d (A14), 21 d (A21) and 28 d (A28) group). Results: EA reduced the relative expression of TLR2 / 4 gene and protein, and regulated the significant difference species flora in different levels, such as Firmicutes and Actinobacteria in Phylum, Coriobacteriia in Class, Coriobacteriales in Order, Atopobiaceae in Family, and Oscillibacter, Intestinimonas, Lachniclostridium and Acetatifactor in Genus. In all acupuncture groups, the analytical data of A21 group was similar to normal mice. Conclusion: These findings suggested the interaction between TLR2/ 4 pathway and gut flora could be a novel target of EA treatment against obesity.

Differential Microbial Pattern Description in Subjects with Autoimmune-Based Thyroid Diseases: A Pilot Study

The interaction between genetic susceptibility, epigenetic, endogenous, and environmental factors play a key role in the initiation and progression of autoimmune thyroid diseases (AITDs). Studies have shown that gut microbiota alterations take part in the development of autoimmune diseases. We have investigated the possible relationship between gut microbiota composition and the most frequent AITDs. A total of nine Hashimoto’s thyroiditis (HT), nine Graves–Basedow’s disease (GD), and 11 otherwise healthy donors (HDs) were evaluated. 16S rRNA pyrosequencing and bioinformatics analysis by Quantitative Insights into Microbial Ecology and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) were used to analyze the gut microbiota. Beta diversity analysis showed that gut microbiota from our groups was different. We observed an increase in bacterial richness in HT and a lower evenness in GD in comparison to the HDs. GD showed a significant increase of Fusobacteriaceae, Fusobacterium and Sutterella compared to HDs and the core microbiome features showed that Prevotellaceae and Prevotella characterized this group. Victivallaceae was increased in HT and was part of their core microbiome. Streptococcaceae, Streptococcus and Rikenellaceae were greater in HT compared to GD. Core microbiome features of HT were represented by Streptococcus, Alistipes, Anaerostipes, Dorea and Haemophilus. Faecalibacterium decreased in both AITDs compared to HDs. PICRUSt analysis demonstrated enrichment in the xenobiotics degradation, metabolism, and the metabolism of cofactors and vitamins in GD patients compared to HDs. Moreover, correlation studies showed that some bacteria were widely correlated with autoimmunity parameters. A prediction model evaluated a possible relationship between predominant concrete bacteria such as an unclassified genus of Ruminococcaceae, Sutterella and Faecalibacterium in AITDs. AITD patients present altered gut microbiota compared to HDs. These alterations could be related to the immune system development in AITD patients and the loss of tolerance to self-antigens.

The aquatic microbial community: a bibliometric analysis of global research trends (1991– 2018)

We performed a bibliometric analysis of relevant research trends, based on academic articles about the aquatic microbial community and recorded in the Web of Science during 1991–2018. The number of publications per annum is clearly rising and began to grow rapidly in 2005. Developed countries (e.g.the USA and some European countries) published the most articles, and led international cooperation. International cooperation benefitted from the implementation of the European Union (EU) Water Framework Directive and from the origination and development of molecular biological techniques. A strong correlation existed among such key words as "bacteria", "DGGE" (Denaturing Gradient Gel Electrophoresis), "16S rRNA", "pyrosequencing" and "sediment" as key research directions for many years. Sediment, biofilm and wetland were the main habitats studied; and high-throughput sequencing gradually replaced the traditional DGGE and other technologies, remaining the most popular research method at present. Studies still focus on basic research; interest in microbial community composition, structure, diversity and ecology remains high; and metagenomics and the microbiome have received considerable attention recently. Key words such as "organic matter", "nutrient", "enzyme activity", "nitrification", "denitrification" and "cyanobacteria" indicate current research hotspots, and we suggest this is because increasing attention is paid to environmental protection and management of the water environment by aquatic microorganisms. We predict that future research will promote the ultimate goals of warning about threats to the water environment and restoration by investigating the function of the aquatic microbial community.

Consumption of Wild Rice (Zizania latifolia) Prevents Metabolic Associated Fatty Liver Disease through the Modulation of the Gut Microbiota in Mice Model

Metabolic associated fatty liver disease (MAFLD) due to excess weight and obesity threatens public health worldwide. Gut microbiota dysbiosis contributes to obesity and related diseases. The cholesterol-lowering, anti-inflammatory, and antioxidant effects of wild rice have been reported in several studies; however, whether it has beneficial effects on the gut microbiota is unknown. Here, we show that wild rice reduces body weight, liver steatosis, and low-grade inflammation, and improves insulin resistance in high-fat diet (HFD)-fed mice. High-throughput 16S rRNA pyrosequencing demonstrated that wild rice treatment significantly changed the gut microbiota composition in mice fed an HFD. The richness and diversity of the gut microbiota were notably decreased upon wild rice consumption. Compared with a normal chow diet (NCD), HFD feeding altered 117 operational taxonomic units (OTUs), and wild rice supplementation reversed 90 OTUs to the configuration in the NCD group. Overall, our results suggest that wild rice may be used as a probiotic agent to reverse HFD-induced MAFLD through the modulation of the gut microbiota.

Effects of an Eco-Friendly Sanitizing Wash on Spinach Leaf Bacterial Community Structure and Diversity

Ready-to-eat (RTE) spinach is considered a high-risk food, susceptible to colonization by foodborne pathogens; however, other microbial populations present on the vegetable surface may interact with foodborne pathogens by inhibiting/inactivating their growth. In addition, sanitizers applied to minimally processed salad leaves should not disrupt this autochthonous barrier and should be maintained throughout the shelf life of the product. This investigation aimed at comparing the effects of a pH neutral electrochemically activated solution (ECAS), a peroxyacetic acid (PAA)-based commercial sanitizer (Ecolab Tsunami® 100), and tap water wash on the minimally processed spinach leaf microbiome profile for 10 days after washing. The bacterial microbiota composition on spinach samples was assessed by 16S rRNA pyrosequencing and downstream analyses. Predominant phyla observed in decreasing order of abundance were Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes corresponding with the dominant families Micrococcaceae, Clostridiales Family XII, Flavobacteriaceae, Pseudomonadaceae, and Burkholderiaceae. Bacterial species richness and evenness (alpha diversity) and bacterial community composition among all wash types were not significantly different. However, a significant difference was apparent between sampling days, corresponding to a loss of overall heterogeneity over time. Analysis of composition of microbiome (ANCOM) did not identify any amplicon sequence variants (ASVs) or families having significantly different abundance in wash types; however, differences (17 ASVs and five families) were found depending on sampling day. This was the first bacterial microbiome composition study focused on ECAS and PAA-based wash solutions. These wash alternatives do not significantly alter microbial community composition of RTE spinach leaves; however, storage at refrigerated temperature reduces bacterial species heterogeneity.

Expansion of Rare and Harmful Lineages is Associated with Established Rheumatoid Arthritis

Objectives: To characterize the gut microbiota profile in rheumatoid arthritis (RA) patients and investigate its association with certain characteristics of RA. Patients and methods: A nested case–control cohort of 40 patients with RA and 40 sex-age matched controls was studied. Subjects with diabetes, with any other inflammatory disease, practicing extreme diets, taking antibiotics, probiotics or under any new treatment for at least three months prior to sampling were excluded. The microbiota composition was determined by 16S rRNA pyrosequencing and bioinformatics analysis by Quantitative Insights Into Microbial Ecology (QIIME). Other variables included clinical-laboratory variables and average Disease Activity Score 28 points during the follow-up period. Multiple linear regression models were constructed to investigate the possible risk factors for the microbiota. Results: β-diversity data showed that patients tend to differ from healthy subjects according to their microbiota (p = 0.07). The analysis showed an increase in Collinsella aerofaciens, Sedimentibacter and Enterococcus genera in patients compared to controls, as well as a decrease in Dorea formicigenerans. Likewise, an increase in the activity of arginine deiminase was observed, which was found in approximately 90% of the RA genes of the genus Collinsela. The sequence number of Collinsella aerofaciens was independently associated with age (B (95%CI), −0.347 (−21.6, −2.1)), high ACPA (0.323 (27.4–390.0)) and smoking (0.300 (8.8–256.4)) in RA patients. In addition, we observed decreases in Sarcina, 02d06 and Porphyromonas bacterial lineages. Conclusion: Patients with RA present dysbiosis, resulting from an abundance of certain bacterial lineages and a decrease in others. These alterations could influence the maintenance of autoimmunity to this disease.

Microbial dysbiosis and polyamine metabolism as predictive markers for early detection of pancreatic cancer

The lack of tools for early detection of pancreatic ductal adenocarcinoma (PDAC) is directly correlated with the abysmal survival rates in patients. In addition to several potential detection tools under active investigation, we tested the gut microbiome and its metabolic complement as one of the earliest detection tools that could be useful in patients at high risk for PDAC. We used a combination of 16s rRNA pyrosequencing and whole-genome sequencing of gut fecal microbiota in a genetically engineered PDAC murine model (KRASG12DTP53R172HPdxCre or KPC). Metabolic reconstruction of microbiome was done using the HUMAnN2 pipeline. Serum polyamine levels were measured from murine and patient samples using chromogenic assay. Our results showed a Proteobacterial and Firmicutes dominance in gut microbiota in early stages of PDAC development. Upon in silico reconstruction of active metabolic pathways within the altered microbial flora, polyamine and nucleotide biosynthetic pathways were significantly elevated. These metabolic products are known to be actively assimilated by the host and eventually utilized by rapidly dividing cells for proliferation validating their importance in the context of tumorigenesis. In KPC mice, as well as PDAC patients, we show significantly elevated serum polyamine concentrations. Therefore, at the early stages of tumorigenesis, there is a strong correlation between microbial changes and release of metabolites that foster host tumorigenesis, thereby fulfilling the ‘vicious cycle hypothesis’ of the role of microbiome in health and disease states. Our results provide a potential, precise, noninvasive tool for early detection of PDAC, which may result in improved outcomes.

Gut microbiota in obstructive sleep apnea–hypopnea syndrome: disease-related dysbiosis and metabolic comorbidities

Gut microbiota alterations manifest as intermittent hypoxia and fragmented sleep, thereby mimicking obstructive sleep apnea–hypopnea syndrome (OSAHS). Here, we sought to perform the first direct survey of gut microbial dysbiosis over a range of apnea–hypopnea indices (AHI) among patients with OSAHS. We obtained fecal samples from 93 patients with OSAHS [5 < AHI ≤ 15 (n=40), 15 < AHI ≤ 30 (n=23), and AHI ≥ 30 (n=30)] and 20 controls (AHI ≤ 5) and determined the microbiome composition via 16S rRNA pyrosequencing and bioinformatics analysis of variable regions 3–4. We measured fasting levels of homocysteine (HCY), interleukin-6 (IL-6), and tumor necrosis factor α (TNF-α). Results revealed gut microbial dysbiosis in several patients with varying severities of OSAHS, reliably separating them from controls with a receiver operating characteristic-area under the curve (ROC-AUC) of 0.789. Functional analysis in the microbiomes of patients revealed alterations; additionally, decreased in short-chain fatty acid (SCFA)-producing bacteria and increased pathogens, accompanied by elevated levels of IL-6. Lactobacillus levels correlated with HCY levels. Stratification analysis revealed that the Ruminococcus enterotype posed the highest risk for patients with OSAHS. Our results show that the presence of an altered microbiome is associated with HCY among OSAHS patients. These changes in the levels of SCFA affect the levels of pathogens that play a pathophysiological role in OSAHS and related metabolic comorbidities.

Basin-scale variability of microbial methanol uptake in the Atlantic Ocean

Methanol is a climate-active gas and the most abundant oxygenated volatile organic compound (OVOC) in the atmosphere and seawater. Marine methylotrophs are aerobic bacteria that utilise methanol from seawater as a source of carbon (assimilation) and/or energy (dissimilation). A few spatially limited studies have previously reported methanol oxidation rates in seawater; however, the basin-wide ubiquity of marine microbial methanol utilisation remains unknown. This study uniquely combines seawater 14C labelled methanol tracer studies with 16S rRNA pyrosequencing to investigate variability in microbial methanol dissimilation and known methanol-utilising bacteria throughout a meridional transect of the Atlantic Ocean between 47° N to 39° S. Microbial methanol dissimilation varied between 0.05 and 1.68 nmol L−1 h−1 in the top 200 m of the Atlantic Ocean and showed significant variability between biogeochemical provinces. The highest rates of methanol dissimilation were found in the northern subtropical gyre (average 0.99±0.41 nmol L−1 h−1), which were up to 8 times greater than other Atlantic regions. Microbial methanol dissimilation rates displayed a significant inverse correlation with heterotrophic bacterial production (determined using 3H-leucine). Despite significant depth stratification of bacterial communities, methanol dissimilation rates showed much greater variability between oceanic provinces compared to depth. There were no significant differences in rates between samples collected under light and dark environmental conditions. The variability in the numbers of SAR11 (16S rRNA gene sequences) were estimated to explain approximately 50 % of the changes in microbial methanol dissimilation rates. We estimate that SAR11 cells in the Atlantic Ocean account for between 0.3 % and 59 % of the rates of methanol dissimilation in Atlantic waters, compared to < 0.01 %–2.3 % for temperate coastal waters. These results make a substantial contribution to our current knowledge and understanding of the utilisation of methanol by marine microbial communities, but highlight the lack of understanding of in situ methanol production mechanisms.

Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis

Bacterial infection of the uterus is a normal event after parturition. While the healthy cow achieves uterine clearance early postpartum, cows unable to control the infection within 21 days after calving develop postpartum endometritis. Studies on the Microbial Ecology of the bovine reproductive tract have focused on either vaginal or uterine microbiomes. This is the first study that compares both microbiomes in the same animals. Terminal Restriction Fragment Length Polymorphism of the 16S rRNA gene showed that despite large differences associated to individuals, a shared community exist in vagina and uterus during the postpartum period. The largest changes associated with development of endometritis were observed at 7 days postpartum, a time when vaginal and uterine microbiomes were most similar. 16S rRNA Pyrosequencing of the vaginal microbiome at 7 days postpartum showed at least three different microbiome types that were associated with postpartum endometritis. All three microbiome types featured reduced bacterial diversity. Taken together, the above findings support a scenario where disruption of the compartmentalization of the reproductive tract during parturition results in the dispersal and mixing of the vaginal and uterine microbiomes, which subsequently are subject to differentiation. This microbial succession is likely associated to early clearance in the healthy cow. In contrast, loss of bacterial diversity and dominance of the microbiome by few bacterial taxa were related to a delayed succession in cows developing endometritis at 7 DPP.