Analysis of by high-throughput sequencing: Helicobacter pylori infection and salivary microbiome

Effects of bacterial extracellular vesicles derived from oral and gastrointestinal pathogens on systemic diseases

Oral microbiota and gastrointestinal microbiota, the two largest microbiomes in the human body, are closely correlated and frequently interact through the oral-gut axis. Recent research has focused on the roles of these microbiomes in human health and diseases. Under normal conditions, probiotics and commensal bacteria can positively impact health. However, altered physiological states may induce dysbiosis, increasing the risk of pathogen colonization. Studies suggest that oral and gastrointestinal pathogens contribute not only to localized diseases at their respective colonized sites but also to the progression of systemic diseases. However, the mechanisms by which bacteria at these local sites are involved in systemic diseases remain elusive. In response to this gap, the focus has shifted to bacterial extracellular vesicles (BEVs), which act as mediators of communication between the microbiota and the host. Numerous studies have reported the targeted delivery of bacterial pathogenic substances from the oral cavity and the gastrointestinal tract to distant organs via BEVs. These pathogenic components subsequently elicit specific cellular responses in target organs, thereby mediating the progression of systemic diseases. This review aims to elucidate the extensive microbial communication via the oral-gut axis, summarize the types and biogenesis mechanisms of BEVs, and highlight the translocation pathways of oral and gastrointestinal BEVs in vivo, as well as the impacts of pathogens-derived BEVs on systemic diseases.

The role of periodontitis in cancer development, with a focus on oral cancers

Periodontitis is a severe gum infection that begins as gingivitis and can lead to gum recession, bone loss, and tooth loss if left untreated. It is primarily caused by bacterial infection, which triggers inflammation and the formation of periodontal pockets. Notably, periodontitis is associated with systemic health issues and has been linked to heart disease, diabetes, respiratory diseases, adverse pregnancy outcomes, and cancers. Accordingly, the presence of chronic inflammation and immune system dysregulation in individuals with periodontitis significantly contributes to the initiation and progression of various cancers, particularly oral cancers. These processes promote genetic mutations, impair DNA repair mechanisms, and create a tumor-supportive environment. Moreover, the bacteria associated with periodontitis produce harmful byproducts and toxins that directly damage the DNA within oral cells, exacerbating cancer development. In addition, chronic inflammation not only stimulates cell proliferation but also inhibits apoptosis, causes DNA damage, and triggers the release of pro-inflammatory cytokines. Collectively, these factors play a crucial role in the progression of cancer in individuals affected by periodontitis. Further, specific viral and bacterial agents, such as hepatitis B and C viruses, human papillomavirus (HPV), Helicobacter pylori (H. pylori), and Porphyromonas gingivalis, contribute to cancer development through distinct mechanisms. Bacterial infections have systemic implications for cancer development, while viral infections provoke immune and inflammatory responses that can lead to genetic mutations. This review will elucidate the link between periodontitis and cancers, particularly oral cancers, exploring their underlying mechanisms to provide insights for future research and treatment advancements.

Characterization of the unique oral microbiome of children harboring Helicobacter pylori in the oral cavity

Objective

Helicobacter pylori infection is acquired in childhood via the oral cavity, although its relationship with the characteristics of the oral microbiome has not been elucidated. In this study, we performed comprehensive analysis of the oral microbiome in children and adults with or without H. pylori in the oral cavity.

Methods

Bacterial DNA was extracted from 41 adult and 21 child saliva specimens, and H. pylori was detected using PCR. 16S rRNA gene amplification was performed for next-generation sequencing. Bioinformatic analyses were conducted using Quantitative Insights into Microbial Ecology 2 (QIIME 2).

Results

Faith's phylogenetic diversity analysis showed a significant difference between H. pylori-negative adult and child specimens in terms of α-diversity (p < 0.05), while no significant difference was observed between H. pylori-positive adult and child specimens. There was also a significant difference in β-diversity between H. pylori-positive and negative child specimens (p < 0.05). Taxonomic analysis at the genus level revealed that Porphyromonas was the only bacterium that was significantly more abundant in both H. pylori-positive adults and children than in corresponding negative specimens (p < 0.01 and p < 0.05, respectively).

Conclusion

These results suggest unique oral microbiome characteristics in children with H. pylori infection in the oral cavity.

The impact of Helicobacter pylori eradication with vonoprazan-amoxicillin dual therapy combined with probiotics on oral microbiota: a randomized double-blind placebo-controlled trial

Background

Helicobacter pylori infection and eradication have been reported to cause dysbiosis of the oral microbiota. Probiotics are increasingly being used to maintain the balance of the oral microbiota. We aimed to investigate the effects of H. pylori infection, H. pylori eradication with vonoprazan-amoxicillin dual therapy, and probiotics supplementation on the oral microbiota.

Methods

H. pylori positive patients were randomly assigned to a vonoprazan-amoxicillin regimen plus probiotics (BtT group) or the placebo (PT group) for 14 days. H. pylori negative population served as normal controls. Tongue coating samples were collected from 60 H. pylori positive patients at three time points (before H. pylori eradication, after H. pylori eradication, and at confirmation of H. pylori infection cure) and 20 H. pylori negative subjects. 16S rRNA gene sequencing was used to analyze the oral microbiota.

Results

H. pylori was detected in the oral cavity in positive (34/60), negative (7/20), and eradicated (1/60) subjects using high-throughput sequencing. Compared with normal controls, H. pylori positive patients exhibited higher richness (p = 0.012) and comparable diversity (p = 0.075) of oral microbiota. Beta diversity and KEGG analysis showed oral flora composition and function differences in H. pylori positive and negative subjects. Alpha diversity dramatically decreased after H. pylori eradication and modestly increased with confirmation of H. pylori eradication. Beta diversity and LEfSe analysis revealed distinct structures, and KEGG analysis showed distinct signaling pathways of tongue coating flora at three time points. There was a significant reduction of Firmicutes and Lactobacillus after H. pylori erdication. The PT group and BtT group had identical compositional and functional differences of oral microbiota at three time points.

Conclusion

No substantial link existed between oral and stomach H. pylori, while removing gastric H. pylori helped eliminate oral H. pylori. H. pylori infection and vonoprazan-amoxicillin dual therapy affected oral microbiota diversity, structure, and function. H. pylori eradication demonstrated a suppressive impact on the proliferation of oral pathogens, specifically Firmicutes and Lactobacillus. Nevertheless, probiotics supplementation did not reduce the oral microbial disturbance caused by H. pylori eradication.

Clinical trial registration

https://www.chictr.org.cn/, identifiers CHICTR2200060023.

Sample Collection Methods in Upper Gastrointestinal Research

In recent years, significant translational research advances have been made in the upper gastrointestinal (GI) research field. Endoscopic evaluation is a reasonable option for acquiring upper GI tissue for research purposes because it has minimal risk and can be applied to unresectable gastric cancer. The optimal number of biopsy samples and sample storage is crucial and might influence results. Furthermore, the methods for sample acquisition can be applied differently according to the research purpose; however, there have been few reports on methods for sample collection from endoscopic biopsies. In this review, we suggested a protocol for collecting study samples for upper GI research, including microbiome, DNA, RNA, protein, single-cell RNA sequencing, and organoid culture, through a comprehensive literature review. For microbiome analysis, one or two pieces of biopsied material obtained using standard endoscopic forceps may be sufficient. Additionally, 5 mL of gastric fluid and 3-4 mL of saliva is recommended for microbiome analyses. At least one gastric biopsy tissue is necessary for most DNA or RNA analyses, while proteomics analysis may require at least 2-3 biopsy tissues. Single cell-RNA sequencing requires at least 3-5 tissues and additional 1-2 tissues, if possible. For successful organoid culture, multiple sampling is necessary to improve the quality of specimens.

Biological functions of endophytic bacteria in Robinia pseudoacacia 'Hongsen'

Introduction

Endophytes and their host plants have co-evolved for a very long time. This relationship has led to the general recognition of endophytes as a particular class of microbial resources. R. pseudoacacia 'Hongsen' is drought- and barren-resistant species that can be grown in both the north and south of China, efficiently addresses the ecological issues caused by China's 'southern eucalyptus and northern poplar. Up to date, cultured-dependent studies are available for the R. pseudoacacia nitrogen-fixing and other endophytes. Therefore, the present research studied the R. pseudoacacia 'Hongsen,' microbiome in detail by high-throughput sequencing and culture dependant.

Methods

This study examined microbial species and functional diversity in Robinia pseudoacacia 'Hongsen' using culture-dependent (isolation) and culture-independent techniques.

Results

A total of 210 isolates were isolated from R. pseudoacacia 'Hongsen.' These isolates were clustered into 16 groups by the In Situ PCR (IS-PCR) fingerprinting patterns. 16S rRNA gene sequence analysis of the representative strain of each group revealed that these groups belonged to 16 species of 8 genera, demonstrating the diversity of endophytes in R. pseudoacacia 'Hongsen'. 'Bacillus is the most prevalent genus among all the endophytic bacteria. High-throughput sequencing of endophytic bacteria from R. pseudoacacia 'Hongsen' of the plant and the rhizosphere soil bacteria showed that the bacterial populations of soil near the root, leaf, and rhizosphere differed significantly. The microbial abundance decreased in the endophytes as compared to the rhizosphere. We observed a similar community structure of roots and leaves. With and without root nodules, Mesorhizobium sp. was significantly different in R. pseudoacacia 'Hongsen' plant.

Discussion

It was predicted that R. pseudoacacia 'Hongsen' plant endophytic bacteria would play a significant role in the metabolic process, such as carbohydrate metabolism, amino acid metabolism, membrane transport, and energy metabolism.

Role of salivary miRNAs in the diagnosis of gastrointestinal disorders: a mini-review of available evidence

MiRNAs are short, non-coding RNA molecules, which are involved in the regulation of gene expression and which play an important role in various biological processes, including inflammation and cell cycle regulation. The possibility of detecting their extracellular expression, within body fluids, represented the main background for their potential use as non-invasive biomarkers of various diseases. Salivary miRNAs particularly gained interest recently due to the facile collection of stimulated/unstimulated saliva and their stability among healthy subjects. Furthermore, miRNAs seem to represent biomarker candidates of gastrointestinal disorders, with miRNA-based therapeutics showing great potential in those conditions. This review aimed to highlight available evidence on the role of salivary miRNAs in different gastrointestinal conditions. Most salivary-based miRNA studies available in the literature that focused on pathologies of the gastrointestinal tract have so far been conducted on pancreatic cancer patients and delivered reliable results. A few studies also showed the diagnostic utility of salivary miRNAs in conditions such as esophagitis, esophageal cancer, colorectal cancer, or inflammatory bowel disease. Moreover, several authors showed that salivary miRNAs may confidently be used as biomarkers of gastric cancer, but the use of salivary miRNA candidates in gastric inflammation and pre-malignant lesions, essential stages of Correa's cascade, is still put into question. On the other hand, besides miRNAs, other salivary omics have shown biomarker potential in gastro-intestinal conditions. The limited available data suggest that salivary miRNAs may represent reliable biomarker candidates for gastrointestinal conditions. However, their diagnostic potential requires validation through future research, performed on larger cohorts.

The Eradication of Helicobacter pylori Was Significantly Associated with Compositional Patterns of Orointestinal Axis Microbiota

BACKGROUND

Helicobacter pylori (H. pylori) is significantly linked to various diseases that seriously impact human health, such as gastric ulcers, chronic gastritis and gastric adenocarcinoma.

METHODS

The compositional shifts in bacterial communities of the orointestinal axis were surveyed pre/post-eradication of H. pylori. In total, 60 samples, including stool and salivary specimens, were collected from 15 H. pylori-positive individuals (HPP) before beginning and 2 months after receiving the eradication therapy. The V3-V4 regions of the 16S rRNA gene were sequenced using MiSeq.

RESULTS

Overall, oral microbiomes were collectively more diverse than the gut microbiomes (Kruskal-Wallis; p = 3.69 × 10^-5). Notably, the eradication of H. pylori was associated with a significant reduction in the bacterial diversity along the orointestinal axis (Wilcoxon rank sum test; p = 6.38 × 10^-3). Interestingly, the oral microbiome of HPP showed a positive correlation between Proteobacteria and Fusobacteria, in addition to a significant predominance of Streptococcus, in addition to Eubacterium_eligens, Haemophilus, Ruminococcaceae, Actinomyces and Staphylococcus. On the other hand, Fusobacterium, Veillonella, Catenibacterium, Neisseria and Prevotella were significantly enriched upon eradication of H. pylori. Generally, Bacteroidetes and Fusobacteria positively coexisted during H. pylori infection along the orointestinal axis (r = 0.67; p = 0.0006). The eradication of H. pylori was positively linked to two distinctive orotypes (O3 and O4). Orotype O4 was characterized by a robust abundance of Veillonella and Fusobacteria. The gut microbiomes during H. pylori infection showed a remarkable predominance of Clostridium_sensu_stricto_1 and Escherichia_Shigella. Likewise, Bifidobacterium and Faecalibacterium were significantly enriched upon eradication of H. pylori.

CONCLUSIONS

Finally, the impact of eradication therapy clearly existed on the representation of certain genera, especially in the oral microbiome, which requires particular concern in order to counteract and limit their subsequent threats.

Influence of Environmental Factors on Salivary Microbiota and Their Metabolic Pathway: Next-Generation Sequencing Approach

The current study aimed to investigate the effect of periodontitis and long-term heavy metal (HM) exposure on the salivary microbiome. The patients were divided into four groups as Wu Wei control (WWC) group involved healthy individuals, Wu Wei periodontitis (WWP) patients having periodontitis, Jing Chang with metal pollution periodontally healthy individuals (JCP), and Kuang periodontitis (KP). The most abundant bacteria identified at the phylum level in the WWC group were Bacteroides, Firmicutes, and Fusobacteria. Firmicutes were observed in a significantly higher proportion in the KP group than in the WWC, WWP, and JCP. At the genus level, the WWC has major dominating bacterial genera (such as Leptotrichia, Neisseria, and Fusobacterium) which were similar to WWP and KP group. The significant difference (p < 0.05) was found in alpha diversity while in beta diversity, the significant (p = 0.005) results were found among the four groups. The correlation of oral microbiota revealed that HMs present in the soil (Cr, Ni, and Cu) are associated with the growth of Capnocytophaga, Selenomonas, Aggregatibacter, and Campylobacter. The bacterial functions in the KP group were higher in translation and nucleotide metabolism than in the WWP group. This demonstrated that long-term exposure to HMs can influence the salivary microbiota which can alter the functioning, and diversity of bacteria.

A novel loop-mediated isothermal amplification-lateral flow dipstick method for Helicobacter pylori detection

Introduction

To eradicate Helicobacter pylori (H. pylori) and reduce the risk of gastric cancer, a sensitive, specific, convenient, and simple detection method is needed. This study aimed to establish a novel loop-mediated isothermal amplification-lateral flow dipstick (LAMP-LFD) method for H. pylori detection.

Methods

LAMP primer design software was used to design primers for the conserved sites of the H. pylori ureB gene. UreB-FIP-labeled biotin was used for LAMP amplification, and FAM-labeled probes were specifically hybridized with LAMP amplification products, which were then detected by LFD. In addition, a clinical study was conducted to assess LAMP-LFD in 20 fecal samples.

Results

The results of the optimization indicated that H. pylori could be specifically detected by LFD without cross-reaction with other non-H. pylori bacteria when the LAMP was performed at 65°C for 60 min. The lower limit of the detection method was 10² copies/μL, which was 100 times the sensitivity of polymerase chain reaction (PCR). H. pylori-positive fecal samples were detected by LAMP-LFD in 13/20 patients.

Discussion

In conclusion, a new LAMP-LFD assay has been fully established and confirmed for H. pylori detection. The entire process can be completed in approximately 1.5 h, with the advantages of strong specificity, high sensitivity, and simple operation. This study provides a novel potential method for the detection of H. pylori in the clinical settings of primary hospitals and low-resource countries.

Probiotics modulate gastrointestinal microbiota after Helicobacter pylori eradication: A multicenter randomized double-blind placebo-controlled trial

BACKGROUND

Helicobacter pylori (H. pylori) eradication has been reported to cause short-term disruption of gut microbiota. It is acknowledged that probiotics supplementation mitigates side effects induced by H. pylori eradication, yet its role on alleviating dysbiosis of microbiota is obscure.

OBJECTIVES

To evaluate the impact of probiotics on gastrointestinal microbiota after eradication therapy.

METHODS

This was a multicenter, double-blinded, randomized trial done at seven centers in China. A total of 276 treatment-naïve H. pylori-positive patients were randomly assigned to receive 14-day bismuth-containing quadruple therapy (esomeprazole, bismuth, amoxicillin, furazolidone) combined with probiotics (Bifidobacterium Tetragenous viable Bacteria Tablets) (n=140) or placebo (n=136) for 28 days. Saliva, gastric mucosa and fecal samples were collected before and after therapy for 16S rRNA gene sequencing.

RESULTS

The incidence of gastrointestinal adverse events was lower in probiotics group compared to placebo group (23.6% vs 37.7%, p=0.016), while there was no significant difference in eradication rate. We found dramatic perturbations of gut microbiota immediately following eradication, with the predominance of Proteobacteria in replacement of commensal Firmicutes and Bacteroidetes, and gradually restored after two weeks. The reduction of gut Bacteroidetes caused by eradication drugs was neutralized with probiotics supplementation. The gastric microbiota was completely reconstituted with H. pylori depleted and other taxa flourished. Of note, patients treated with probiotics showed smaller fluctuations of gastric microbiota compared to those with placebo. We also observed changes of saliva microbiota after H. pylori eradication, illustrated by the overgrowth of Neisseria and depletion of Streptococcus. The expansion of some pathogenic genera, including Porphyromonas, Leptotrichia, in the mouth was suppressed by probiotics.

CONCLUSION

This study not only demonstrated the beneficial effect of probiotics implementation on side events during H. pylori eradication but also provided a comprehensive profile of microbiome alterations along gastrointestinal tract that modulated by probiotics.

Helicobacter pylori in the Oral Cavity: Current Evidence and Potential Survival Strategies

Helicobacter pylori (H. pylori) is transmitted primarily through the oral–oral route and fecal–oral route. The oral cavity had therefore been hypothesized as an extragastric reservoir of H. pylori, owing to the presence of H. pylori DNA and particular antigens in distinct niches of the oral cavity. This bacterium in the oral cavity may contribute to the progression of periodontitis and is associated with a variety of oral diseases, gastric eradication failure, and reinfection. However, the conditions in the oral cavity do not appear to be ideal for H. pylori survival, and little is known about its biological function in the oral cavity. It is critical to clarify the survival strategies of H. pylori to better comprehend the role and function of this bacterium in the oral cavity. In this review, we attempt to analyze the evidence indicating the existence of living oral H. pylori, as well as potential survival strategies, including the formation of a favorable microenvironment, the interaction between H. pylori and oral microorganisms, and the transition to a non-growing state. Further research on oral H. pylori is necessary to develop improved therapies for the prevention and treatment of H. pylori infection.

Analysis of oral microbiota alterations induced by Helicobacter pylori infection and vonoprazan-amoxicillin dual therapy for Helicobacter pylori eradication

BACKGROUND

The oral cavity is considered a potential reservoir of Helicobacter pylori (H. pylori), and the imbalance of oral microbiota directly reflects the health of the host. We aimed to explore the relationship among oral microbiota, H. pylori infection, and vonoprazan-amoxicillin (VA) dual therapy for H. pylori eradication.

METHODS

Helicobacter pylori-positive patients were randomized into low- or high-dose VA dual therapy (i.e., amoxicillin 1 g b.i.d. or t.i.d. and vonoprazan 20 mg b.i.d) for 7 or 10 days. H. pylori-negative patients served as normal controls. Saliva samples were collected from 41 H. pylori-positive patients and 13 H. pylori-negative patients. The oral microbiota was analyzed by 16S rRNA gene sequencing, followed by bioinformatics analysis.

RESULTS

Helicobacter pylori-positive patients had higher richness and diversity and better evenness of oral microbiota than normal controls. Beta diversity analysis estimated by Bray-Curtis or weighted UniFrac showed distinct clustering between H. pylori-positive patients and normal controls. The number of bacterial interactions was reduced in H. pylori-positive patients compared with that in negative patients. Forty-one patients evaluated before and after successful H. pylori eradication were divided into low (L-VA) and high dose (H-VA) amoxicillin dose groups. The alpha and beta diversity of the oral microbiota between L-VA and H-VA patients exhibited no differences at the three time points (before eradication, after eradication, and at confirmation of H. pylori infection cure).

CONCLUSION

Helicobacter pylori infection could alter the diversity, composition, and bacterial interactions of the oral microbiota. Both L-VA and H-VA dual therapy showed minimal influence on the oral microbiota.

The interactions between oral-gut axis microbiota and Helicobacter pylori

In the human body, each microbial habitat exhibits a different microbial population pattern, and these distinctive microflorae are highly related to the development of diseases. The microbial interactions from host different niches are becoming crucial regulators to shape the microbiota and their physiological or pathological functions. The oral cavity and gut are the most complex and interdependent microbial habitats. Helicobacter pylori is one of the most important pathogens from digestive tract, especially the stomach, due to its direct relationships with many gastric diseases including gastric cancer. H. pylori infections can destroy the normal gastric environment and make the stomach a livable channel to enhance the microbial interactions between oral cavity and gut, thus reshaping the oral and gut microbiomes. H. pylori can be also detected in the oral and gut, while the interaction between the oral-gut axis microbiota and H. pylori plays a major role in H. pylori’s colonization, infection, and pathogenicity. Both the infection and eradication of H. pylori and its interaction with oral-gut axis microbiota can alter the balance of the microecology of the oral-gut axis, which can affect the occurrence and progress of related diseases. The shift of oral-gut axis microbiota and their interactions with H. pylori maybe potential targets for H. pylori infectious diagnosis and treatment.

Differential Signature of the Microbiome and Neutrophils in the Oral Cavity of HIV-Infected Individuals

HIV infection is associated with a wide range of changes in microbial communities and immune cell components of the oral cavity. The purpose of this study was to evaluate the oral microbiome in relationship to oral neutrophils in HIV-infected compared to healthy individuals. We evaluated oral washes and saliva samples from HIV-infected individuals (n=52) and healthy controls (n=43). Using 16S-rRNA gene sequencing, we found differential β-diversity using Principal Coordinate Analysis (PCoA) with Bray-Curtis distances. The α-diversity analysis by Faith’s, Shannon, and observed OTUs indexes indicated that the saliva samples from HIV-infected individuals harbored significantly richer bacterial communities compared to the saliva samples from healthy individuals. Notably, we observed that five species of Spirochaeta including Spirochaetaceae, Spirochaeta, Treponema, Treponema amylovorum, and Treponema azotonutricum were significantly abundant. In contrast, Helicobacter species were significantly reduced in the saliva of HIV-infected individuals. Moreover, we found a significant reduction in the frequency of oral neutrophils in the oral cavity of HIV-infected individuals, which was positively related to their CD4⁺ T cell count. In particular, we noted a significant decline in CD44 expressing neutrophils and the intensity of CD44 expression on oral neutrophils of HIV-infected individuals. This observation was supported by the elevation of soluble CD44 in the saliva of HIV-infected individuals. Overall, the core oral microbiome was distinguishable between HIV-infected individuals on antiretroviral therapy compared to the HIV-negative group. The observed reduction in oral neutrophils might likely be related to the low surface expression of CD44, resulting in a higher bacterial diversity and richness in HIV-infected individuals.

The impact of Helicobacter pylori infection, eradication therapy, and probiotics intervention on gastric microbiota in young adults

BACKGROUND

The impact of probiotics on non-Helicobacter pylori gastric microbiota and its role in microbial restoration after eradication were relatively unknown. We aimed to explore the effect of H. pylori eradication and probiotic intervention on gastric microbiota in young adults.

METHODS

Fifty-six H. pylori-negative and 95 H. pylori-positive subjects aged 19-30 were included in this study. H. pylori-infected individuals were randomly assigned to quadruple therapy, probiotics supplemented quadruple therapy, or probiotics monotherapy group. Gastric mucosa and gastric juice samples were collected before and 2 months after treatment for 16SrRNA gene sequencing.

RESULTS

The gastric microbial community structure and composition differed from H. pylori-negative subjects 2 months after successful H. pylori eradication. The α diversity of gastric mucosal microbiota significantly increased and was higher than H. pylori-negative subjects, while the α diversity of gastric juice microbiota decreased and was lower than the H. pylori-negative. After probiotics supplemented eradication treatment, Bifidobacterium was enriched in gastric mucosa, Lactobacillus was enriched in gastric juice, potentially pathogenic bacteria such as Fusobacterium and Campylobacter decreased, and the microbial diversity was closer to that of H. pylori-negative subjects compared to quadruple therapy group. Probiotics monotherapy significantly altered the diversity, community structure, and composition of gastric microbiota but showed no advantage in H. pylori inhibition and upregulating beneficial bacteria such as Bifidobacterium and Lactobacillus and related metabolism pathways. Certain potentially pathogenic bacteria such as Fusobacterium increased after probiotic monotherapy.

CONCLUSION

H. pylori eradication significantly disrupted gastric microbiota in young adults and could not be restored in a short time. Probiotics supplementation partially helped restore the gastric dysbiosis caused by eradication therapy, but it might be unnecessary for H. pylori-infected young adults to take probiotics alone.

Helicobacter pylori and the intestinal microbiome among healthy school-age children

BACKGROUND

Helicobacter pylori (H. pylori) infection is acquired during childhood and causes chronic gastritis that remains asymptomatic in most infected people. H. pylori alters the gastric microbiota and causes peptic ulcer disease. Evidence on the relationship between asymptomatic H. pylori infection and children's gut microbiota remains elusive.

AIM

We characterized the relationship between H. pylori infection and the intestinal microbiome of healthy children, adjusting for known inter-personal and environmental exposures.

MATERIALS AND METHODS

This cross-sectional study included stool samples obtained from 163 Israeli Arab children aged 6-9 years from different socioeconomic strata. Sociodemographic information was collected through maternal interviews. H. pylori infection was determined using monoclonal antigen detection stool enzyme immunoassay. The gut microbiome was characterized by implementing 16S rRNA gene sequencing of the V4 region and a multivariate downstream analysis.

RESULTS

Overall, 57% of the participants were positive for H. pylori infection and it was significantly associated with low socioeconomic status. There was no significant association between H. pylori infection and bacterial richness of fecal microbiome. H. pylori infection was significantly associated with intestinal bacterial composition, including a strong association with Prevotella copri and Eubacterium biforme. Moreover, socioeconomic status was strongly associated with bacterial composition.

DISCUSSION AND CONCLUSIONS

H. pylori infection in healthy children was significantly associated with altered intestinal microbiome structure. Socioeconomic determinants exhibit a strong effect, related to both H. pylori infection and intestinal diversity and composition in childhood. These findings are clinically important to the understanding of the role of H. pylori infection and other intestinal microbes in health and disease.

Characteristics of the lung microbiota in lower respiratory tract infections with and without history of pneumonia

Lung microbiota plays an important role in many diseases including lower respiratory tract infections (LRTI) and pneumonia. This study aimed to explore the effects of community-acquired pneumonia (CAP) on microbial diversity and identify potential biomarkers of respiratory tract in CAP LRTI patients. In the current study, a comprehensive bioinformatics analysis was performed based on metagenomic next generation sequencing technology, followed by alpha and beta diversity, LEfSe, and co-occurrence network analysis, and random forest model construction. Our results showed that CAP dramatically influenced taxon abundance, and the significant differences in microbiota including Proteobacteria, Bacteroidetes, Euryarchaeota, Firmicutes and Spirochaetes were observed at the phylum level. Co-occurrence network selected out novel modules involved in microbial proliferation-associated pathways. A random forest model screened Klebsiella pneumoniae and Bacillus cereus as potential diagnostic biomarkers with high AUC values. The microbial composition was different between CAP LRTI patients and non-CAP LRTI patients. Klebsiella pneumoniae and Bacillus cereus were strongly associated with increased severity of LRTI with a pneumonia history. Our findings provided an insight for a better understanding of community and structure of lung microbiota for future diagnosis and treatment in LRTI patients with a history of pneumonia. Moreover, these microbes were considered as potential biomarkers for predicting the risks for the treatment strategies of LRTI.

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.

Interactions between H. pylori and the Gastric Microbiome: Impact on Gastric Homeostasis and Disease

Like many seemingly inhospitable environments on our planet, the highly acidic human stomach harbors a diverse bacterial microflora. The best-known member of the human gastric flora, Helicobacter pylori, causes a number of gastric diseases, including peptic ulcer disease and gastric adenocarcinoma. In the absence of Helicobacter pylori infection, the gastric microbiota displays some features similar to the oral cavity with Firmicutes the most common phylum, followed by Proteobacteria and Bacteroidetes. When present, H. pylori dominates the gastric microbiome and reduces diversity and composition of other taxa. The composition of the gastric microbiome also is altered in the setting of proton pump inhibitor therapy and gastric neoplasia. This review summarizes foundational and recent studies that have investigated the composition of the human gastric microbiome in a variety of patient groups, with a focus on potential mechanisms involved in regulation of gastric microbial community structure.