The development of gut microbiota in critically ill extremely low birth weight infants assessed with 16S rRNA gene based sequencing

Objective: An increasing number of studies that are using high-throughput molecular methods are rapidly extending our knowledge of gut microbial colonization in preterm infants whose immaturity and requirement for extensive treatment may result in altered colonization process. We aimed to describe the profile of gut microbiota in 50 extremely low birth weight (<1200 g) critically ill infants at three different time points during the first two months of life by using 16S rRNA gene specific sequencing.   Patients and Methods: Stool samples were collected at the age of one week, one month and two months. Bacterial community profiling was done using universal amplification of 16S rRNA gene and 454 pyrosequencing. Results: The diversity of gut microbiota in preterm neonates in the first week of life was low but increased significantly over two months. The gut microbiota was dominated by facultative anaerobic bacteria (Staphylococcus spp. and Enterobacteriaceae) and lacked colonization with bacteria known to provide resistance against pathogens (Bacteroides, Bifidobacterium, and Lactobacillus) throughout the study. Colonization of Escherichia coli and uncultured Veillionella was positively correlated with maturity. Infants born to mothers with chorioamnionitis had significantly higher bacterial diversity than those without. Conclusions: High prevalence and abundance of potentially pathogenic Enterobacteriaceae and Staphylococcaceae with low prevalence and abundance of colonization resistance providing taxa bifidobacteria, Bacteroides and lactobacilli may lead to high infection risk via microbial translocation from the gut. Additionally, our data suggest that maternal chorioamnionitis may have an effect on the diversity of infants’ gut microbiota; however, the mechanisms involved remain to be elucidated.     

Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin

Gut microbiota play a key role in the host''s health system. Broad antibiotic therapy is known to disrupt the microbial balance affecting pathogenic as well as host-associated microbes. The aim of the present study was to investigate the influence of antibiotic paromomycin on the luminal and mucosa-associated microbiota at the DNA (abundance) and RNA (potential activity) level as well as to identify possible differences. The influence of antibiotic treatment on intestinal microbiota was investigated in 5 healthy individuals (age range: 20–22 years). All participants received the antibiotic paromomycin for 3 d. Fecal samples as well as sigmoidal biopsies were collected before and immediately after cessation of antibiotic treatment as well as after a recovery phase of 42 d. Compartment- and treatment status-specific indicator operational taxonomic units (OTUs) as well as abundance- and activity-specific patterns were identified by 16S rRNA and 16S rRNA gene amplicon libraries and high-throughput pyrosequencing. Microbial composition of lumen and mucosa were significantly different at the DNA compared to the RNA level. Antibiotic treatment resulted in changes of the microbiota, affecting the luminal and mucosal bacteria in a similar way. Several OTUs were identified as compartment- and/or treatment status-specific. Abundance and activity patterns of some indicator OTUs differed considerably. The study shows fundamental changes in composition of gut microbiota under antibiotic therapy at both the potential activity and the abundance level at different treatment status. It may help to understand the complex processes of gut microbiota changes involved in resilience mechanisms and on development of antibiotic-associated clinical diseases.     

Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin

Gut microbiota play a key role in the host's health system. Broad antibiotic therapy is known to disrupt the microbial balance affecting pathogenic as well as host-associated microbes. The aim of the present study was to investigate the influence of antibiotic paromomycin on the luminal and mucosa-associated microbiota at the DNA (abundance) and RNA (potential activity) level as well as to identify possible differences. The influence of antibiotic treatment on intestinal microbiota was investigated in 5 healthy individuals (age range: 20–22 years). All participants received the antibiotic paromomycin for 3 d. Fecal samples as well as sigmoidal biopsies were collected before and immediately after cessation of antibiotic treatment as well as after a recovery phase of 42 d. Compartment- and treatment status-specific indicator operational taxonomic units (OTUs) as well as abundance- and activity-specific patterns were identified by 16S rRNA and 16S rRNA gene amplicon libraries and high-throughput pyrosequencing. Microbial composition of lumen and mucosa were significantly different at the DNA compared to the RNA level. Antibiotic treatment resulted in changes of the microbiota, affecting the luminal and mucosal bacteria in a similar way. Several OTUs were identified as compartment- and/or treatment status-specific. Abundance and activity patterns of some indicator OTUs differed considerably. The study shows fundamental changes in composition of gut microbiota under antibiotic therapy at both the potential activity and the abundance level at different treatment status. It may help to understand the complex processes of gut microbiota changes involved in resilience mechanisms and on development of antibiotic-associated clinical diseases.     

The composition and richness of the gut microbiota differentiate the top Polish endurance athletes from sedentary controls

ABSTRACT

Background

Little data are available on the subject of gut microbiota composition in endurance athletes as well as connections between diet and specific bacteria abundance. However, most studies suggest that athletes’ microbiota undergoes major alterations, which may contribute to increased physical performance. Therefore, we decided to investigate differences in gut microbiota between healthy controls and endurance athletes.     

Comparative analysis of the gut microbiota of wild adult rats from nine district areas in Hainan,China

BACKGROUND Wild rats have the potential to hold zoonotic infectious agents that can spread to humans and cause disease.AIM To better understand the composition of gut bacterial communities in rats is essential for preventing and treating such diseases. As a tropical island located in the south of China, Hainan province has abundant rat species. Here, we examined the gut bacterial composition in wild adult rats from Hainan province.METHODS Fresh fecal samples were collected from 162 wild adult ra...     

COPD and the microbiome

Traditional culture techniques confirm that bacteria have an important role in Chronic Obstructive Pulmonary Disease (COPD). In individuals with COPD, acquisition of novel bacterial strains is associated with onset of acute exacerbation of COPD, which leads to further lung dysfunction and enormous health‐care costs. Recent study of the human microbiome, the total composite of the bacteria on the human body, posited the microbiome as the last human organ studied, as the microbiome performs a multitude of metabolic functions absent in the human genome. The largest project to study the human microbiome was the National Institutes of Health (NIH) human microbiome project (HMP) started in 2007 to understand the ‘normal’ microbiome. However due to the presumption that the healthy human lung was sterile, the respiratory tract was not included in that study. The advent of next‐generation sequencing technologies has allowed the investigation of the human respiratory microbiome, which revealed that the healthy lung does have a robust microbiome. Subsequent studies in individuals with COPD revealed that the microbiome composition fluctuates with severity of COPD, composition of the individual aero‐digestive tract microbiomes, age, during an acute exacerbation of COPD and with the use of steroids and/or antibiotics. Understanding the impact of the microbiome on COPD progression and risk of exacerbation will lead to directed therapies for prevention of COPD progression and exacerbation.     

Moxibustion treatment modulates the gut microbiota and immune function in a dextran sulphate sodium-induced colitis rat model

AIM To investigate the effect and mechanism of moxibustion in rats with ulcerative colitis.METHODS A rat colitis model was established by administering 4% dextran sulphate sodium solution. Seventy male rats were randomly divided into seven groups: Healthy controls(HC), ulcerative colitis model group(UC), UC with 7 d of moxibustion(UC-7), UC with 14 d of moxibustion(UC-14), UC with mesalazine gavage(UC-W), HC with 7 d of moxibustion(HC-7), HC with 14 d of moxibustion(HC-14). Moxibustion was applied to the bilateral Tianshu(ST25). Gut microbiome profiling was conducted by 16 S r RNA amplicon sequencing, and PCR and ELISA determined the expression of inflammatory cytokines in colon mucosa and serum, respectively. RESULTS Moxibustion treatment restored the colonic mucosa and decreased submucosal inflammatory cell infiltration in colitis rats. Rats treated with moxibustion and mesalazine had significantly lower levels of the dominant phyla Proteobacteria and the genera Saccharibacteria, Sphingomonas and Barnesiella than colitis rats, and they could restore the microbiome to levels similar to those observed in healthy rats. UC rats had reduced alpha diversity, which could be alleviated by moxibustion therapy, and UC-7 had a higher alpha diversity than UC-14. This finding suggests that short-term(7 d) but no longer term(14 d) moxibustion treatment may significantly affect the gut microbiome. The potential bacterial functions affected by moxibustion may be ascorbate and aldarate metabolism, and amino acid metabolism. Compared with HC group, the levels of the cytokines interleukin-12(IL-12)(P 0.05) and IL-6, IL-17, IL-23, interferon-γ, lipopolysaccharide, Ig A, tumour necrosis factor-α and its receptors 1(TNFR1) and TNFR2(P 0.01) were all increased, whereas anti-inflammatory cytokine IL-2 and IL-10(P 0.01) and transforming growth factor-β(P 0.05) were decreased in UC rats. These changes were reversed by moxibustion.CONCLUSION Our findings suggest that moxibustion exerts its therapeutic effect by repairing mucosal tissue damage and modulating the gut microbiome and intestinal mucosal immunity.     

Antidepressant treatment with fluoxetine during pregnancy and lactation modulates the gut microbiome and metabolome in a rat model relevant to depression

ABSTRACT

Up to 10% of women use selective serotonin reuptake inhibitor (SSRI) antidepressants during pregnancy and postpartum. Recent evidence suggests that SSRIs are capable of altering the gut microbiota. However, the interaction between maternal depression and SSRI use on bacterial community composition and the availability of microbiota-derived metabolites during pregnancy and lactation is not clear.

We studied this using a rat model relevant to depression, where adult females with a genetic vulnerability and stressed as pups show depressive-like behaviors. Throughout pregnancy and lactation, females received the SSRI fluoxetine or vehicle. High-resolution 16S ribosomal RNA marker gene sequencing and targeted metabolomic analysis were used to assess the fecal microbiome and metabolite availability, respectively.

Not surprisingly, we found that pregnancy and lactation segregate in terms of fecal microbiome diversity and composition, accompanied by changes in metabolite availability. However, we also showed that fluoxetine treatment altered important features of this transition from pregnancy to lactation most clearly in previously stressed dams, with lower fecal amino acid concentrations. Amino acid concentrations, in turn, correlated negatively with the relative abundance of bacterial taxa such as Prevotella and Bacteroides.

Our study demonstrates an important relationship between antidepressant use during the perinatal period and maternal fecal metabolite availability in a rat model relevant to depression, possibly through parallel changes in the gut microbiome. Since microbial metabolites contribute to homeostasis and development, insults to the maternal microbiome by SSRIs might have health consequences for mother and offspring.     

Association between SARS-CoV-2 infections during pregnancy and preterm live birth

We examined associations between mild or asymptomatic prenatal SARS-CoV-2 infection and preterm live birth in a prospective cohort study. During August 2020–October 2021, pregnant persons were followed with systematic surveillance for RT-PCR or serologically confirmed SARS-CoV-2 infection until pregnancy end. The association between prenatal SARS-CoV-2 infection and preterm birth was assessed using Cox proportional-hazards regression. Among 954 pregnant persons with a live birth, 185 (19%) had prenatal SARS-CoV-2 infection and 123 (13%) had preterm birth. The adjusted hazard ratio for the association between SARS-CoV-2 infection and preterm birth was 1.28 (95% confidence interval 0.82–1.99, p = 0.28), although results did not reach statistical significance.     

Alterations of gut microbiota and cytokines in elevated serum diamine oxidase disorder

The present study aimed to explore gut microbiota alterations and host cytokine responses in a population with elevated serum diamine oxidase (DAO) disorder. A total of 53 study participants were included in this study, segregated into 2 groups: subjects with high-level DAO (DAO-H, n = 22) subjects with normal DAO level (DAO-N, n = 31). We investigated the clinical and demographic parameters of study participants. The fecal bacterial communities and serum cytokines in 2 groups were assessed by 16S ribosomal RNA gene sequencing and immunoassay. High-pressure liquid chromatography was used to determine hemoglobin Alc. Flow cytometry was used to find the cytokine level in the blood serum. There is no difference in age, total cholesterol (TCHO), triglyceride (TG), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), hemoglobin Alc, fasting plasma glucose (FPG) and homocysteine between the 2 groups. No significant difference were found in α-diversity between the 2 groups, however, the gut microbiota of subjects in DAO-H were characterized by marked interindividual differences, decreased abundance of Phocaeicola, Lachnospira, Bacteroides, Alistipes, Agathobacter, Lachnospira and Bactetoides and increased abundances of Mediterraneibacter, Blautia, Faecallibacterium, Agathobacter, and Parasutterella. Furthermore, the cytokines were no related to the DAO level in both groups and exhibited no significant differences between DAO-H and DAO-N. This study adds a new dimension to our understanding of the DAO and gut microbiota, and revealed that an increase in the DAO level in the intestinal mucosa could alter the gut microbiota composition, which can cause gut-related complications. Research is needed to extensively evaluate downstream pathways and provide possible protective or treatment measures pertaining to relevant disorders.     

Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota

Recent work using culture-independent methods suggests that the lungs of cystic fibrosis (CF) patients harbor a vast array of bacteria not conventionally implicated in CF lung disease. However, sampling lung secretions in living subjects requires that expectorated specimens or collection devices pass through the oropharynx. Thus, contamination could confound results. Here, we compared culture-independent analyses of throat and sputum specimens to samples directly obtained from the lungs at the time of transplantation. We found that CF lungs with advanced disease contained relatively homogenous populations of typical CF pathogens. In contrast, upper-airway specimens from the same subjects contained higher levels of microbial diversity and organisms not typically considered CF pathogens. Furthermore, sputum exhibited day-to-day variation in the abundance of nontypical organisms, even in the absence of clinical changes. These findings suggest that oropharyngeal contamination could limit the accuracy of DNA-based measurements on upper-airway specimens. This work highlights the importance of sampling procedures for microbiome studies and suggests that methods that account for contamination are needed when DNA-based methods are used on clinical specimens.     

Altered diversity and composition of gut microbiota in Chinese patients with chronic pancreatitis

Background/ObjectivesGut microbiota alterations in chronic pancreatitis (CP) are seldomly described systematically. It is unknown whether pancreatic exocrine insufficiency (PEI) and different etiologies in patients with CP are associated with gut microbiota dysbiosis.MethodsThe fecal microbiota of 69 healthy controls (HCs) and 71 patients with CP were compared to investigate gut microbiome alterations in CP and the relationship among gut microbiome dysbiosis, PEI and different etiologies. Fecal microbiomes were analyzed through 16S ribosomal RNA gene profiling, based on next-generation sequencing. Pancreatic exocrine function was evaluated by determining fecal elastase 1 activity.ResultsPatients with CP showed gut microbiota dysbiosis with decreased diversity and richness, and taxa-composition changes. On the phylum level, the gut microbiome of the CP group showed lower Firmicutes and Actinobacteria abundances than the HC group and higher Proteobacteria abundances. The abundances of Escherichia-Shigella and other genera were high in gut microbiomes in the CP group, whereas that of Faecalibacterium was low. Kyoto Encyclopedia of Genes and Genomes pathways (lipopolysaccharide biosynthesis and bacterial invasion of epithelial cells) were predicted to be enriched in the CP group. Among the top 5 phyla and 8 genera (in terms of abundance), only Fusobacteria and Eubacterium rectale group showed significant differences between CP patients, with or without PEI. Correlation analysis showed that Bifidobacterium and Lachnoclostridium correlated positively with fecal elastase 1 (r = 0.2616 and 0.2486, respectively, P < 0.05).ConclusionsThe current findings indicate that patients with CP have gut microbiota dysbiosis that is partly affected by pancreatic exocrine function.