Medicine in Microecology最新文献

Aims

To investigate the effects of Lactobacillus reuteri supplementation on the eradication rate of H. pylori and the treatment-related adverse effects caused by anti-H. pylori therapies.

Methods

The authors conducted independent searches of PubMed, Medline, Embase and Cochrane library from the inception of this study until May 2021 and extracted data from eligible randomised controlled trials published in English that compared Lactobacillus reuteri supplementation to placebo or no treatment during anti-H. pylori therapies. Review Manager 5.3 was used for all statistical analyses.

Results

Six randomized controlled trials involving 378 patients were included in the analysis. An intention-to-treat analysis via a fixed-effects model showed that the pooled relative risk (RR) for the eradication rate was higher for the Lactobacillus reuteri supplementation group than for the control group, but the difference was not significant [RR 1.12, 95% confidence interval (CI): 0.98–1.27, P ​= ​0.09). The incidence of total antibiotic-related side effects was lower in the Lactobacillus reuteri supplementation group than in the control group, with a pooled RR value of 0.55 (95% CI: 0.39–0.77, P ​= ​0.0006), which was determined using a fixed-effects model. Certain adverse events, such as diarrhoea (RR ​= ​0.31, 95% CI: 0.19–0.52, P ​< ​0.00001), abdominal pain (RR ​= ​0.71, 95% CI: 0.55–0.93, P ​= ​0.01) and constipation (RR ​= ​0.45, 95% CI: 0.25–0.83, P ​= ​0.01), were reported at lower rates in the Lactobacillus reuteri supplementation group than in the control group.

Conclusion

Lactobacillus reuteri supplementation during anti-Helicobacter pylori treatment may not be effective for improving H. pylori eradication rates. However, it can minimize the incidence of therapy-related adverse events and alleviate most disease-related symptoms. Our results should be interpreted with caution due to the lack of enough trials included in this analysis.

Appropriate sampling and storage processes are crucial for the accurate determination of the gut microbiome and metabolome. The present study evaluated the effect of the freeze-drying process on meconium and regular faecal samples of newborn babies. Triplicate samples were freeze-dried for 6 or 12 ​h and compared to samples that were only frozen. Microbiome analysis using 16 ​S rRNA sequencing showed that the microbial composition was similar between samples with freeze-drying and those without freeze-drying in general, while the determination efficiency of Bifidobacterium was significantly increased after freeze-drying for either time. A total of 300 commonly observed gut metabolites were quantified and classified into 13 categories, including amino acids, bile acids, carbohydrates, carnitines, fatty acids and so on. The compositions of most metabolites were consistently preserved before or after freeze-drying for the two time protocols. Moreover, the sensitivity of detection was significantly improved after freeze-drying, even for volatile compounds such as short-chain fatty acids. Accordingly, freeze-drying for 6 ​h is recommended for the pretreatment of bulk meconium and regular faecal samples for the determination of gut microbiota.

More than a decade of gut microbiome studies have a common goal of improving human health. However, while most of the disease studies have focused on the elderly or the middle-aged, a reference cohort for the gut microbiome in young individuals has been lacking. It is also not clear what other omics data need to be measured to better understand the gut microbiome. Here, we present a cohort including 2183 adults with high-depth metagenomic shotgun sequencing data for the fecal microbiome and other omics data. In this multiomic cohort, we observe a number of vitamins, hormones, amino acids, and trace elements that correlated with the gut microbiome. Many of the associations are validated in an additional cohort consisting of 1404 individuals. Our comprehensive data are poised to provide advice to future populations and mechanistic study designs to better understand and manage our gut microbiome.

Germ-free models and bacterial transplantation technology facilitate the mechanism study of the host-gut microbe interaction. Among them, zebrafish is an economical and practical model with its characteristics, such as transparent larva and efficient gene manipulation, differing from the mouse. Here we enumerate the similarities and differences of the genes, the digestive tract structure and the gut microbiota of zebrafish and humans. And the recent reports on colonizing human gut microbes to zebrafish are elaborated. We summarize the advantages and limitations of this model and revalidate those with some important discoveries on the utilization of zebrafish in modeling human gut microbe research. This review will make the readers clear the advances in the application of zebrafish in gut microbiota-related researches.

India carries approximately 34% of the global oral cancer burden. Along with tobacco chewing habit, there are other factors that are being studied globally like the involvement of bacteria in oral cancer. NGS studies have identified few bacterial species and the changes in their abundance in healthy and diseased populations based on 16S rRNA metagenomics. The present study shows a method for absolute bacterial quantification from oral cavity rinse samples. The method is a real-time qPCR assay and based on the fact that certain genes are present in one copy per cell (rpoB gene) and we can correlate the copy numbers of these genes with cell numbers in a sample. This method is more accurate than the NGS 16S rRNA gene-based approach which is multicopy gene. Linear correlation between qPCR assay and cell numbers of a model system was established. Consequently, the assay was performed on oral rinse samples of oral cancer/tobacco chewers and healthy subjects to quantitate significant oral bacterial species. The obtained bacterial quantification correlated well with the previous reports. The developed qPCR method is an efficient, faster and resource-friendly method and can be used to quantify bacterial population in cancer/diseased subjects, and can have application in determining the susceptibility of an individual towards a specific disease.

Little is known about airway mycobiome, and its relationship with bacterial microbiome in chronic obstructive pulmonary disease (COPD). Here we report the first simultaneous characterization of sputum bacterial and fungal microbiome in 84 stable COPD and 29 healthy subjects, using 16S ribosomal DNA and fungal internal transcribed spacer DNA sequencing. Ascomycota predominated over Basidiomycota in fungal microbiome both in COPD patients and healthy controls. Meyerozyma, Candida, Aspergillus and Schizophyllum were most abundant at the genus level. There was a significant inverse correlation between bacterial and fungal microbial diversity, both of which altered in opposite directions in COPD patients versus controls, and in frequent versus non-frequent exacerbators. An enhanced bacterial-fungal ecological interaction was observed in COPD patients, which was characterized by higher proportion of co-occurrence intrakingdom interactions and co-exclusive interkingdom interactions. In COPD, four mutually co-occurring fungal operational taxonomic units (OTUs) in Candida palmioleophila, Aspergillus and Sordariomycetes exhibited co-exclusive relationships with other fungal OTUs, which was specifically present in frequent exacerbators but not in non-frequent exacerbators. The perturbed bacterial-fungal interactions in COPD were associated with increased airway inflammatory mediators such as IL-6 and IL-8. The disruption of airway bacterial-fungal community balance, characterized by the loss of commensal bacterial taxa and enriched pathogenic fungal taxa, is implicated in COPD. The emergence of pathogenic fungi such as Candida and Aspergillus could be a marker for the frequent exacerbator phenotype. The airway mycobiome is an important cofactor mediating pathogenic infection and host inflammation in COPD.

Human gut microbiota (GM) is a unique ecosystem harboring trillions of microbes, is arguably the largest endocrine and paracrine organ in the body. Microbes residing in human intestine produce several bioactive signaling molecules (BSM), which are transported in the systemic circulation to various organs. Development of heart disease or its acceleration is seen in individuals who have coexisting gastrointestinal disorders. Dysbiosed GM (altered gut microbial composition) produce high levels of harmful BSM such as trimethylamine (TMA)/trimethylamine-N-oxide (TMAO), bile acids (BAs), uremic toxins, lipopolysaccharide (LPS), low concentrations of short chain fatty acids (SCFAs). Intestinal epithelial cells (IECs) in dysbiosed gut synthesize reduced levels of proprotein convertase subtilisin/kexin type 9 (PCSK9), the key regulator of LDL-C clearance. The expression of PCSK9 in IECs depends on the host metabolic status and dietary habits. Decreased production of PCSK9 in the gut may promote imbalance in cholesterol metabolism leading to atherosclerotic cardiovascular disease (ASCVD). In contrast, in the normal gut the optimum production of PCSK9 show a protective effect on the cardiovascular system by regulating low-density lipoprotein receptor (LDLR) expression and apolipoprotein-B-lipoprotein cholesterol biosynthesis. However, a definitive link between the intestine-derived PCSK9 in cholesterol homeostasis and cardiovascular risk remains poorly understood. The objective of this review is to present the current knowledge and discuss the heart-gut-PCSK9 interaction, for a better understanding of the role GM in the regulation of cholesterol metabolism. We have presented the available evidences implicating a bidirectional cross-talk between heart and gut in reducing LDL-C through PCSK9, and also highlighted the prospects of GM-targeted treatment strategies for ASCVD prevention.

Staphylococcus aureus is an important opportunistic pathogen which can localize in human nares and skin. The bacteria carriage was deemed as a risk factor because it can cause endogenous S. aureus infection. However, epidemiological characteristics of these colonized strains have not yet been identified. Here, we isolated and analyzed all culturable bacteria from nasal and skin swabs of 526 healthy individuals with three different age groups. Obvious differences in culturable microbiomes either from different sites (the nares and skin) or from different age groups (children, young adults, and seniors) were observed. Remarkably, Staphylococcus was the predominant genus in both nares and skin, and coagulase-negative Staphylococci were the most abundant species in all groups. In addition, S. aureus can also be isolated from both nares or skin. Among them, we observed 52 co-localized S. aureus in both nares and skin simultaneously in 7 individuals. Further analyses of these S. aureus isolates revealed that the genotypes of S. aureus varied when isolated from a different or even from same organ per individual, while significantly different phenotypes including biofilm formation and hemolytic activity were also noted. Interestingly, we observed that human skin isolates were prone to adhere to skin epithelial cells as shown by both cell adhesion and mouse model. This suggests that bacteria evolved to adapt environments during colonization. In conclusion, S. aureus localized in different organs of the human body were not completely homogenous. The origin of S. aureus spread or endogenous infection was diverse.

Depression is a common mental health disorder that affects more than 260 million individuals worldwide. The aetiology of depression is likely multifactorial with biological, psychological and environmental factors. Subsequently, depression can present as a number of different subtypes with varying chronicity and severity. Recently, the gut microbiome has been implicated in many gastrointestinal and extra-gastrointestinal conditions including depression. Neurological systemic effects on host biology via the gut microbiome can occur through the bidirectional link known as the gut-brain axis. Dysbiosis is the imbalance of gut flora which may instigate a dysregulated immune response and lead to disorders such as irritable bowel syndrome. In this case series, depression and irritable bowel syndrome may have a shared pathogenesis. Our study aimed to explore the effects of faecal microbiota transplantation, a procedure in which a healthy donor’s microbiota is transplanted into an unwell recipient, in three cases of concomitant depression and irritable bowel syndrome. A single centre, retrospective medical records review assessed demographics, diagnosis, medications, symptoms and medical history of the cases to determine the outcome of a faecal microbiota transplantation. Despite varying symptom onsets, types and levels of neurological and gastrointestinal symptoms there was an objective improvement in mood, medication and/or symptoms reported by the patient and/or attending physician. These results demonstrate a modest improvement in both depression and irritable bowel syndrome which would benefit from further investigation by randomised controlled trials. Faecal microbiota transplantation may be a potential adjunct therapy for treating depression and irritable bowel syndrome through the gut-brain axis.