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Letters in Applied Microbiology Jul 2017Bacteriophages are an attractive alternative to faecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport, due to their closer... (Review)
Review
UNLABELLED
Bacteriophages are an attractive alternative to faecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport, due to their closer morphological and biological properties. Based on a review of published data, we summarize densities of coliphages (F+ and somatic), Bacteroides spp. and enterococci bacteriophages (phages) in individual human waste, raw wastewater, ambient fresh and marine waters and removal through wastewater treatment processes utilizing traditional treatments. We also provide comparisons with FIB and enteric viruses whenever possible. Lastly, we examine fate and transport characteristics in the aquatic environment and provide an overview of the environmental factors affecting their survival. In summary, concentrations of bacteriophages in various sources were consistently lower than FIB, but more reflective of infectious enteric virus levels. Overall, our investigation indicates that bacteriophages may be adequate viral surrogates, especially in built systems, such as wastewater treatment plants.
SIGNIFICANCE AND IMPACT OF THE STUDY
Bacteriophage are alternative fecal indicators that may be better surrogates for viral pathogens than fecal indicator bacteria (FIB). This report offers a summary of the existing literature concerning the utility of bacteriophage as indicators of viral presence (fecal sources and surface waters) and persistence (in built infrastructure and aquatic environments). Our findings indicate that bacteriophage levels in all matrices examined are consistently lower than FIB, but similar to viral pathogens. Furthermore, in built infrastructure (e.g. wastewater treatment systems) bacteriophage closely mimic viral pathogen persistence suggesting they may be adequate sentinels of enteric virus removal.
Topics: Bacteroides; Coliphages; Enterococcus; Enterovirus; Environmental Monitoring; Feces; Humans; Wastewater; Water Microbiology; Water Purification
PubMed: 28304098
DOI: 10.1111/lam.12736 -
Cell Host & Microbe Sep 2021Bacterial ADP-ribosyltransferases (ADPRTs) have been described as toxins involved in pathogenesis through the modification of host proteins. Here, we report that ADPRTs...
Bacterial ADP-ribosyltransferases (ADPRTs) have been described as toxins involved in pathogenesis through the modification of host proteins. Here, we report that ADPRTs are not pathogen restricted but widely prevalent in the human gut microbiome and often associated with phage elements. We validated their biochemical activity in a large clinical isolate collection and further examined Bxa, a highly abundant ADPRT in Bacteroides. Bxa is expressed, secreted, and enzymatically active in Bacteroides and can ADP-ribosylate non-muscle myosin II proteins. Addition of Bxa to epithelial cells remodeled the actin cytoskeleton and induced secretion of inosine. Bxa-encoding B. stercoris can use inosine as a carbon source and colonizes the gut to significantly greater numbers than a bxa-deleted strain in germ-free and altered Schaedler flora (ASF) mice. Colonization correlated with increased inosine concentrations in the feces and tissues. Altogether, our results show that ADPRTs are abundant in the microbiome and act as bacterial fitness factors.
Topics: ADP Ribose Transferases; Actin Cytoskeleton; Animals; Bacteriophages; Bacteroides; Bacteroides thetaiotaomicron; Caco-2 Cells; Cell Line, Tumor; Epithelial Cells; Feces; Female; Gastrointestinal Microbiome; Germ-Free Life; HT29 Cells; Humans; Inosine; Intestinal Mucosa; Male; Mice; Mice, Inbred C57BL; Myosin Heavy Chains
PubMed: 34403684
DOI: 10.1016/j.chom.2021.07.011 -
Polish Journal of Microbiology 2018The growing number of children with overweight and obesity constitutes a major health problem of the modern world and it has been suggested that intestinal microbiota...
The growing number of children with overweight and obesity constitutes a major health problem of the modern world and it has been suggested that intestinal microbiota may influence energy intake from food. The objectives of this study were to determine quantity and proportions of dominant genera of Bacteroides, Prevotella (phylum Bacteroidetes ); Clostridium , Lactobacillus (phylum Firmicutes ) and Bifidobacterium (phylum Actinobacteria ) in the intestines and to determine the content of short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) in the stool of 20 obese children and 20 children with normal body weight. Strains classified as Firmicutes ( Clostridium and Lactobacillus ) predominated in stool microbiota of obese children, while those of Bacteroidetes ( Prevotella and Bacteroides ) were in minority ( p < 0.001). Concentration of SCFAs in the stool of obese children was lower in comparison to the stool of normal weight children ( p = 0.04). However, these differences were significant only in obese children, not in overweight children in comparison with the lean ones. Therefore, in our study obesity was associated with intestinal dysbiosis and a predominance of phylum Firmicutes . Secondly, stool of obese children contained lower amounts of SCFAs.
Topics: Adolescent; Bacteria; Bacteroidetes; Bifidobacterium; Child; Dysbiosis; Fatty Acids, Volatile; Feces; Female; Firmicutes; Gastrointestinal Microbiome; Humans; Male; Obesity; Overweight; RNA, Ribosomal, 16S
PubMed: 30451451
DOI: 10.21307/pjm-2018-041 -
Scientific Reports Jun 2023The inconsolable crying of a child for no apparent reason at an early age is a source of excitement and anxiety for parents. Previous studies have reported that crying... (Observational Study)
Observational Study
The inconsolable crying of a child for no apparent reason at an early age is a source of excitement and anxiety for parents. Previous studies have reported that crying may be caused by discomfort associated with the occupation of the intestines of the newborn by microbiota and its vital activity. We conducted a prospective observational study in which 62 newborns and their mothers were recruited. The study comprised two groups, each consisting of 15 infants with colic and 21 controls. Colic and control groups were vaginally born and exclusively breastfed. Fecal samples from children were collected over time from day 1 to 12 months. Full metagenomic sequencing of fecal samples from children and their mothers was carried out. It was determined that the trajectory of the development of the intestinal microbiome of children with colic was different from the group without colic. In the colic group, a depleted relative abundance of Bifidobacterium and enrichment of Bacteroides Clostridiales was found, while the microbial biodiversity in this group was enriched. Metabolic pathway profiling showed that the non-colic group was enriched by amino acid biosynthetic pathways, while the feces microbiome of the colic group was enriched by glycolysis metabolic pathways that correlated with the Bacteroides taxon. This study shows that infantile colic has a definite relationship with the microbiome structure of infants.
Topics: Infant, Newborn; Infant; Humans; Child; Gastrointestinal Microbiome; Colic; Microbiota; Amino Acids; Anxiety; Bacteroides
PubMed: 37308527
DOI: 10.1038/s41598-023-36641-z -
Scientific Reports Mar 2021The intestinal microbiome changes dynamically in early infancy. Colonisation by Bifidobacterium and Bacteroides and development of intestinal immunity is interconnected.... (Observational Study)
Observational Study
The intestinal microbiome changes dynamically in early infancy. Colonisation by Bifidobacterium and Bacteroides and development of intestinal immunity is interconnected. We performed a prospective observational cohort study to determine the influence of antibiotics taken by the mother immediately before delivery on the intestinal microbiome of 130 healthy Japanese infants. Faecal samples (383) were collected at 1, 3, and 6 months and analysed using next-generation sequencing. Cefazolin was administered before caesarean sections, whereas ampicillin was administered in cases with premature rupture of the membranes and in Group B Streptococcus-positive cases. Bifidobacterium and Bacteroides were dominant (60-70% mean combined occupancy) at all ages. A low abundance of Bifidobacterium was observed in infants exposed to antibiotics at delivery and at 1 and 3 months, with no difference between delivery methods. A lower abundance of Bacteroides was observed after caesarean section than vaginal delivery, irrespective of antibiotic exposure. Additionally, occupancy by Bifidobacterium at 1 and 3 months and by Bacteroides at 3 months differed between infants with and without siblings. All these differences disappeared at 6 months. Infants exposed to intrapartum antibiotics displayed altered Bifidobacterium abundance, whereas abundance of Bacteroides was largely associated with the delivery method. Existence of siblings also significantly influenced the microbiota composition of infants.
Topics: Ampicillin; Anti-Bacterial Agents; Bacteroides; Bifidobacterium; Cefazolin; Cesarean Section; Delivery, Obstetric; Feces; Female; Gastrointestinal Microbiome; Humans; Infant; Infant, Newborn; Intestines; Japan; Pregnancy; Pregnancy Complications, Infectious; Prospective Studies; Siblings; Streptococcal Infections
PubMed: 33737648
DOI: 10.1038/s41598-021-85670-z -
Lipids in Health and Disease Feb 2021Although imbalanced intestinal flora contributes to the pathogenesis of nonalcoholic fatty liver disease (NAFLD), conflicting results have been obtained for... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Although imbalanced intestinal flora contributes to the pathogenesis of nonalcoholic fatty liver disease (NAFLD), conflicting results have been obtained for patient-derived microbiome composition analyses. A meta-analysis was performed to summarize the characteristics of intestinal microbiota at the species level in NAFLD patients.
METHODS
Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement, a completed search (last update: December 30, 2020) of databases was performed to identify eligible case-control studies detecting gut microbiota in NAFLD patients. The meta-analysis results are presented as the standard mean difference (SMD) and 95% confidence interval (CI). Bias controls were evaluated with the Newcastle-Ottawa Scale (NOS), funnel plot analysis, and Egger's and Begg's tests.
RESULTS
Fifteen studies (NOS score range: 6-8) that detected the gut microbiota in the stools of 1265 individuals (577 NAFLD patients and 688 controls) were included. It was found that Escherichia, Prevotella and Streptococcus (SMD = 1.55 [95% CI: 0.57, 2.54], 1.89 [95% CI: 0.02, 3.76] and 1.33 [95% CI: 0.62, 2.05], respectively) exhibited increased abundance while Coprococcus, Faecalibacterium and Ruminococcus (SMD = - 1.75 [95% CI: - 3.13, - 0.37], - 9.84 [95% CI: - 13.21, - 6.47] and - 1.84 [95% CI, - 2.41, - 1.27], respectively) exhibited decreased abundance in the NAFLD patients compared with healthy controls. No differences in the abundance of Bacteroides, Bifidobacterium, Blautia, Clostridium, Dorea, Lactobacillus, Parabacteroides or Roseburia were confirmed between the NAFLD patients and healthy controls.
CONCLUSIONS
This meta-analysis revealed that changes in the abundance of Escherichia, Prevotella, Streptococcus, Coprococcus, Faecalibacterium and Ruminococcus were the universal intestinal bacterial signature of NAFLD.
Topics: Bacteroides; Bifidobacterium; Case-Control Studies; Clostridium; Dysbiosis; Escherichia; Feces; Gastrointestinal Microbiome; Humans; Lactobacillus; Liver; Non-alcoholic Fatty Liver Disease; Prevotella; Streptococcus
PubMed: 33637088
DOI: 10.1186/s12944-021-01440-w -
Nutrients Mar 2020Altered intestinal microbiota is associated with systemic and intestinal diseases, such as inflammatory bowel disease (IBD). Dysbiotic microbiota with enhanced...
Altered intestinal microbiota is associated with systemic and intestinal diseases, such as inflammatory bowel disease (IBD). Dysbiotic microbiota with enhanced proinflammatory capacity is characterized by depletion of anaerobic commensals, increased proportion of facultatively anaerobic bacteria, as well as reduced diversity and stability. In this study, we developed a high-throughput in vitro screening assay to isolate intestinal commensal bacteria with anti-inflammatory capacity from a healthy fecal microbiota transplantation donor. Freshly isolated gut bacteria were screened for their capacity to attenuate lipopolysaccharide (LPS)-induced interleukin 8 (IL-8) release from HT-29 cells. The screen yielded a number of and isolates, which were identified as , , , , , and using whole genome sequencing. We observed that a cell-cell contact with the epithelium was not necessary to alleviate in vitro inflammation as spent culture media from the isolates were also effective and the anti-inflammatory action did not correlate with the enterocyte adherence capacity of the isolates. The anti-inflammatory isolates also exerted enterocyte monolayer reinforcing action and lacked essential genes to synthetize hexa-acylated, proinflammatory lipid A, part of LPS. Yet, the anti-inflammatory effector molecules remain to be identified. The strains isolated and characterized in this study have potential to be used as so-called next-generation probiotics.
Topics: Adult; Anti-Inflammatory Agents; Bacteroides; Bacteroidetes; Caco-2 Cells; Feces; Female; Gastrointestinal Microbiome; High-Throughput Screening Assays; Homeostasis; Humans; Interleukin-8; Lipopolysaccharides; Probiotics
PubMed: 32230951
DOI: 10.3390/nu12040935 -
PeerJ 2022Southern River Terrapin, , is a freshwater turtle listed as critically endangered on the IUCN Red List since 2000. Many studies suggest that faecal DNA metabarcoding can...
Southern River Terrapin, , is a freshwater turtle listed as critically endangered on the IUCN Red List since 2000. Many studies suggest that faecal DNA metabarcoding can shield light on the host-associated microbial communities that play important roles in host health. Thus, this study aimed to characterise and compare the faecal bacterial community between captive and wild using metabarcoding approaches. A total of seven faeces samples were collected from captive ( = 5) and wild ( = 2) adult aseptically, crossing the East and West coast of peninsular Malaysia. The DNA was extracted from the faeces samples, and the 16S rRNA gene (V3-V4 region) was amplified using polymerase chain reaction (PCR). The amplicon was further analysed using SILVA and DADA2 pipelines. In total, 297 bacterial communities taxonomic profile (phylum to genus) were determined. Three phyla were found in high abundance in all faeces samples, namely Firmicutes (38.69%), Bacteroidetes (24.52%), and Fusobacteria (6.95%). Proteobacteria were detected in all faeces samples (39.63%), except the wild sample, KBW3. Under genus level, was found as the most abundant genus (67.79%), followed by (24.56%) and (21.78%). The uncultured genus had the highest abundance (88.51%) even though not detected in the BK31 and KBW2 samples. The potential probiotic genera (75.00%) were discovered to be more dominant in faeces samples. Results demonstrated that the captive faeces samples have a greater bacterial variety and richness than wild faeces samples. This study has established a starting point for future investigation of the gut microbiota of .
Topics: Animals; Turtles; Rivers; RNA, Ribosomal, 16S; DNA Barcoding, Taxonomic; Bacteria; Bacteroidetes; DNA; Feces
PubMed: 35368336
DOI: 10.7717/peerj.12970 -
Genome Biology Jun 2021The human microbiome plays an important role in cancer. Accumulating evidence indicates that commensal microbiome-derived DNA may be represented in minute quantities in...
BACKGROUND
The human microbiome plays an important role in cancer. Accumulating evidence indicates that commensal microbiome-derived DNA may be represented in minute quantities in the cell-free DNA of human blood and could possibly be harnessed as a new cancer biomarker. However, there has been limited use of rigorous experimental controls to account for contamination, which invariably affects low-biomass microbiome studies.
RESULTS
We apply a combination of 16S-rRNA-gene sequencing and droplet digital PCR to determine if the specific detection of cell-free microbial DNA (cfmDNA) is possible in metastatic melanoma patients. Compared to matched stool and saliva samples, the absolute concentration of cfmDNA is low but significantly above the levels detected from negative controls. The microbial community of plasma is strongly influenced by laboratory and reagent contaminants introduced during the DNA extraction and sequencing processes. Through the application of an in silico decontamination strategy including the filtering of amplicon sequence variants (ASVs) with batch dependent abundances and those with a higher prevalence in negative controls, we identify known gut commensal bacteria, such as Faecalibacterium, Bacteroides and Ruminococcus, and also other uncharacterised ASVs. We analyse additional plasma samples, highlighting the potential of this framework to identify differences in cfmDNA between healthy and cancer patients.
CONCLUSIONS
Together, these observations indicate that plasma can harbour a low yet detectable level of cfmDNA. The results highlight the importance of accounting for contamination and provide an analytical decontamination framework to allow the accurate detection of cfmDNA for future biomarker studies in cancer and other diseases.
Topics: Bacteroides; Cell-Free Nucleic Acids; DNA Contamination; DNA, Bacterial; Faecalibacterium; Feces; Humans; Melanoma; Microbiota; Neoplasm Metastasis; Neoplasm Staging; Polymerase Chain Reaction; RNA, Ribosomal, 16S; Ruminococcus; Saliva; Skin Neoplasms; Symbiosis
PubMed: 34162397
DOI: 10.1186/s13059-021-02401-3 -
Scientific Reports Sep 2023High-throughput sequencing allows for the comprehensive analysis of the human intestinal microbiota. However, extensive association analyses between the microbiome and...
High-throughput sequencing allows for the comprehensive analysis of the human intestinal microbiota. However, extensive association analyses between the microbiome and lifestyle differences in the Chinese population are limited. Here, we carried out an independent cohort study-the Chinese Healthy Gut Project (n = 483)-where correlations between the gut microbiota and dietary and lifestyle variables in a healthy Chinese population are defined. We collected both questionnaire data, including basic information and lifestyle and dietary variables, and fecal stools from the enrolled volunteers. We then performed 16S rRNA sequencing on the microbial DNA isolated from the stools to assess the composition of the intestinal microbiota. We found that Prevotella and Bacteroides were the most abundant genera in the healthy Chinese gut microbiome. Additionally, 9 out of 29 clinical and questionnaire-based phenotype covariates were found to be associated with the variation in the composition of the gut microbiota. Among these lifestyle phenotypes, sleep procrastination, negative mood, and drinking habits had the largest effect size. Additionally, an appreciable effect of urbanization was observed, resulting in decreased intra-individual diversity, increased inter-individual diversity, and an increased abundance of the Bacteroides enterotype. The results of this study provide a foundation for assessing the healthy Chinese gut microbiota community structure at baseline in a healthy Chinese population. Furthermore, this study also provides insights into understanding how distinctive living habits influence the relationships between the Chinese gut microbiome and systemic health state.
Topics: Humans; Bacteroides; Cohort Studies; East Asian People; Gastrointestinal Microbiome; Life Style; RNA, Ribosomal, 16S; Healthy Volunteers; Feces
PubMed: 37660184
DOI: 10.1038/s41598-023-41532-4