Culturing and Molecular Approaches for Identifying Microbiota Taxa Impacting Children's Obesogenic Phenotypes Related to Xenobiotic Dietary Exposure.

Integrated data from molecular and improved culturomics studies might offer holistic insights on gut microbiome dysbiosis triggered by xenobiotics, such as obesity and metabolic disorders. Bisphenol A (BPA), a dietary xenobiotic obesogen, was chosen for a directed culturing approach using microbiota specimens from 46 children with obesity and normal-weight profiles. In parallel, a complementary molecular analysis was carried out to estimate the BPA metabolising capacities. Firstly, catalogues of 237 BPA directed-cultured microorganisms were isolated using five selected media and several BPA treatments and conditions. Taxa from Firmicutes, Proteobacteria, and Actinobacteria were the most abundant in normal-weight and overweight/obese children, with species belonging to the genera Enterococcus, Escherichia, Staphylococcus, Bacillus, and Clostridium. Secondly, the representative isolated taxa from normal-weight vs. overweight/obese were grouped as BPA biodegrader, tolerant, or resistant bacteria, according to the presence of genes encoding BPA enzymes in their whole genome sequences. Remarkably, the presence of sporobiota and concretely Bacillus spp. showed the higher BPA biodegradation potential in overweight/obese group compared to normal-weight, which could drive a relevant role in obesity and metabolic dysbiosis triggered by these xenobiotics.

An Ohio State Scenic River Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent.

The entry of antibiotic resistance genes (ARGs) into aquatic systems has been documented for large municipal wastewater treatment plants (WWTPs), but there is less study of the impact of smaller plants that are situated on small rural rivers. We sampled water metagenomes for ARGs and taxa composition from the Kokosing River, a small rural river in Knox County, Ohio, which has been designated an Ohio State Scenic River for retention of natural character. Samples were obtained 1.0 km upstream, 120 m downstream, and 6.4 km downstream from the effluent release of the Mount Vernon WWTP. ARGs were identified in metagenomes using ShortBRED markers from the comprehensive antibiotic resistance database (CARD) screened against UniPROT. Through all seasons, the metagenome just downstream of the WWTP effluent showed a substantial elevation of at least 15 different ARGs, including 6 ARGs commonly associated with Acinetobacter baumannii, such as msrE, mphE (macrolide resistance), and tet(39) (tetracycline resistance). The ARGs most prevalent near the effluent pipe persisted 6.4 km downriver. Using metagenomic phylogenetic analysis (MetaPhlAn2) clade-specific marker genes, the taxa distribution near the effluent showed elevation of reads annotated as Acinetobacter species as well as gut-associated taxa, Bacteroides and Firmicutes. The ARG levels and taxa prevalence showed little dependence on seasonal chlorination of the effluent. Nitrogen and phosphorus were elevated near the effluent pipe but had no consistent correlation with ARG levels. We show that in a rural river microbiome, year-round wastewater effluent substantially elevates ARGs, including those associated with multidrug-resistant A. baumannii. IMPORTANCE Antibiotic resistance is a growing problem worldwide, with frequent transmission between pathogens and environmental organisms. Rural rivers can support high levels of recreational use by people unaware of inputs from treated wastewater, while wastewater treatment plants (WWTPs) can generate a small but significant portion of flow volume into a river surrounded by forest and agriculture. There is little information on the rural impacts of WWTP effluent on the delivery and transport of antibiotic resistance genes. In our study, the river water proximal to wastewater effluent shows evidence for the influx of multidrug-resistant Acinetobacter baumannii, an opportunistic pathogen of concern for hospitals but also widespread in natural environments. Our work highlights the importance of wastewater effluent in management of environmental antibiotic resistance, even in high quality, rural river systems.

Native joint infections caused by Parvimonas micra.

Parvimonas micra is an anaerobic, fastidious, gram positive organism commonly found in the oral cavity and gastrointestinal tract. It has been increasingly reported as the cause of septic arthritis of native joints, often times with delayed diagnosis leading to increased morbidity. Risk factors include immunosuppression, inflammation of the joint, and recent dental procedures or infections. It has been a historically difficult organism to culture. However, the development of and increasing use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has led to increased identification of P. micra. Common antibiotic susceptibilities, as well as data regarding susceptibilities in specific situations, have been reported, but susceptibility testing is required in all cases. Common treatments include clindamycin, penicillin, and metronidazole for six to ten weeks.

A tale of two unusual anaerobic bacterial infections in an immunocompetent man: A case report and literature review.

We report a case of an immunocompetent man who presented with Desulfovibrio fairfieldensis bacteremia, followed by an epidural abscess due to Parvimonas micra. Only few cases have described unique clinical features related to both organisms, and this report illustrates two distinct sequential, if not concurrent, syndromes due to these anaerobes.

Late onset prosthetic joint infection caused by Parvimonas micra.

Parvimonas micra (P.micra) is a difficult to culture gram positive anaerobic microorganism, typically found in the human microbiota, specially in the oral cavity. There are limited cases in literature reporting prosthetic joint infection due to this bacteria, although its isolation has been reported in different settings in later years. We present the case of a late onset knee prosthetic joint infection caused by Parvimonas micra in an 87 year old woman treated with antibiotics and two-step surgery with prosthetic material removal, antibiotic-loaded cement spacer placement and new prosthetic material replacement after 2 weeks of intravenous antimicrobial therapy followed by 6 weeks of oral therapy.

Bacteremia caused by Anaerococcus SPP: Is this an underdiagnosed infection?

The objectives of this study were to report 10 episodes of clinically significant bacteremia caused by species of the genus Anaerococcus isolated between July 2018 and February 2021 from the microbiology laboratory of a tertiary hospital in Granada (Spain). None of the isolates were identified by MALDI-TOF MS, and the definitive species identification was performed by 16 S rRNA gene sequencing. No reference spectra of the Anaerococcus species were present in the MALDI-TOF MS database. Eight isolates were finally identified as A. octavius, one isolate as A. tetradius and the other as A. urinomassiliensis. The majority of these infections were seen in patients aged >70 years. Risk factors for anaerobic infection were observed in eight patients, especially diabetes mellitus, surgery, and the presence of cancer. Fever was present in all patients. Three patients died, but only one death was attributed to the infection. Mean detection time of positive blood cultures was 47.5 h (range 24-92 h). Antimicrobial susceptibility to penicillin, amoxicillin-clavulanate, imipenem, moxifloxacin, clindamycin, metronidazole, and piperacillin-tazobactam was tested using the gradient diffusion technique and EUCAST breakpoints (except for moxifloxacin). No resistance to amoxicillin-clavulanate, metronidazole, imipenem, or piperacillin-tazobactam was detected; however, the majority of isolates were resistant to clindamycin. When MALDI-TOF MS does not provide a correct identification at genus or species level, as in some isolates of Gram-positive anaerobic cocci, microbiologists should perform an additional confirmatory technique, such as gene sequencing analysis, to obtain a definitive diagnosis.

Effects of vancomycin-induced gut microbiome alteration on the pharmacodynamics of metformin in healthy male subjects.

Metformin is a major treatment for type 2 diabetes. This study was conducted to investigate the impact of gut microbiome dysbiosis on the pharmacokinetics and antihyperglycemic effects of metformin. Healthy adult males aged 19-45 years with no defecation abnormalities were recruited for this 4-period clinical study: baseline; post-metformin (i.e., multiple oral doses of 1000 mg metformin on days 1-4); post-vancomycin (i.e., multiple oral doses of 500 mg vancomycin on days 11-17 inducing gut microbiome changes); and post-metformin + vancomycin (i.e., multiple oral doses of 1000 mg metformin on days 16-19). In each period, serum glucose and insulin concentrations following an oral glucose tolerance test, fecal samples for gut microbiome composition, and safety data were obtained. Following metformin dosing, plasma and urine samples for pharmacokinetics were collected. Nine subjects completed the study. The pharmacokinetics of metformin remained unchanged, and the antihyperglycemic effect was significantly decreased after vancomycin administration (p value = 0.039), demonstrating the weak relationship between the pharmacokinetics and pharmacodynamics of metformin. Relative abundances of some genus were changed after vancomycin administration, and tended to correlate with the antihyperglycemic effects of metformin (p value = 0.062 for Erysipelatoclostridium; p value = 0.039 for Enterobacter; and p value = 0.086 for Faecalibacterium). Adverse events occurred in all subjects and were resolved without sequelae. In conclusion, a decrease in the antihyperglycemic effect of metformin was observed after concomitant administration with vancomycin, without changes in metformin pharmacokinetics. The antihyperglycemic effect was tended to correlate with the relative abundance of several genus, suggesting that the effect of metformin is partly attributable to the gut microbiome (ClinicalTrials.gov, NCT03809260).

Multiple hepatic and brain abscesses caused by Parvimonas micra: A case report and literature review.

Gram-positive anaerobic cocci (GPAC) are responsible for 30% of anaerobic infections. Parvimonas micra is an emergent pathogen that is part of the oral and gastrointestinal commensal flora, and its role in several infection processes has recently emerged thanks to the improvement of diagnostic techniques. P. micra bacteraemia is reported in immunocompromised patients and is often complicated by abscesses. Here, we present a case study of multiple hepatic and brain abscesses caused by P. micra bacteraemia in a patient with complicated diverticulitis.

Antimicrobial treatment of Erysipelatoclostridium ramosum invasive infections: a systematic review.

The aim of this systematic review was to determine the causal role of Erysipelatoclostridium ramosum in specific invasive infections in humans, and to assess the clinical outcome of antibiotic therapy used to treat them. Several electronic databases were systematically searched for clinical trials, observational studies or individual cases on patients of any age and gender with a systemic inflammatory response syndrome (SIRS) due to E. ramosum isolated from body fluids or tissues in which it is not normally present. Only reports identifying E. ramosum as the only microorganism isolated from a patient with SIRS were included. This systematic review included 15 studies reporting 19 individual cases in which E. ramosum caused invasive infections in various tissues, mainly in immunocompromised patients. E. ramosum was most often isolated by blood cultures and identified by specific biochemical tests. Severe infections caused by E. ramosum were in most cases effectively treated with antibiotics, except in two patients, one of whom died. More than one isolate of E. ramosum exhibited 100% susceptibility to metronidazole, amoxicillin/clavulanate and piperacillin/tazobactam. On the other hand, individual resistance of this bacterium to penicillin, ciprofloxacin, clindamycin, imipenem and ertapenem was reported. This systematic review confirmed the clinical relevance of E. ramosum as a cause of a number of severe infections mainly in immunocompromised inpatients. Metronidazole and meropenem appear to be the antibiotics of choice that should be used in combination or as monotherapy to treat E. ramosum infections, depending on the type and severity of the infection.

Bactericidal activity of a substituted thiazole against multidrug-resistant Eggerthia catenaformis isolated from patients with dental abscess.

Human infections caused by the anaerobic bacterium Eggerthia catenaformis are rare. However, a growing number of case reports have presented the bacterium as the causative agent in many serious complications. This study provides data on the isolation and antibiotic susceptibility profiles of E. catenaformis from dental abscess. Identification of isolates was performed using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). We also investigated the antibacterial activity of 5-acetyl-4-methyl-2-(3-pyridyl) thiazole (AMPT) on E. catenaformis isolates. Minimum inhibitory concentrations (MICs) were determined by an agar dilution method and bactericidal activity was evaluated by a time-kill assay. Moreover, the mechanism of action of AMPT was also explored by cell membrane disruption assay and scanning electron microscopy (SEM). MALDI-TOF MS results revealed unambiguous identification of all isolates with score values between 2.120 and 2.501. Isolates NY4 and NY9 (20% of isolates) were found resistant to multiple antibiotics judged by MIC values. As multidrug-resistant strains of E. catenaformis were not reported to date, we then confirmed the identity of NY4 and NY9 based on 16S rRNA gene sequence. Favorably, all isolates were susceptible to AMPT with an MIC range of 0.25-1 mg/L. Time-kill kinetics of AMPT indicated that it exhibited potent bactericidal activity against the multidrug-resistant isolates NY4 and NY9. Furthermore, this study also hypothesizes that AMPT exerts its antibacterial effect through damaging the cell membrane and thereby induce the release of intracellular components. AMPT could therefore be considered as a therapeutic option for infections caused by multidrug-resistant bacteria.

Flammulina velutipes polysaccharide improves C57BL/6 mice gut health through regulation of intestine microbial metabolic activity.

Flammulina velutipes polysaccharides (FVP) can improve gut health through gut microbiota and metabolism regulation. In this study, the 28-days fed experiment was used to investigate gut microbime and metabolic profiling induced by FVP. After treatment, intestinal tissue section showed the higher villus height and villus height/crypt depth (V/C) value in FVP-treated group. The 16 s rRNA gene sequencing revealed microbiota composition alteration caused by FVP, as the Firmicutes phylum increased while Bacteroidetes phylum slightly decreased. The metabolic profiling was detected by LC/MS and results showed 56 and 99 compounds were dramatically changed after FVP treatment in positive and negative ion mode, respectively. Annotation in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways displayed the adjustment of energy metabolism, amino acid metabolism, nucleotide metabolism and other related basic pathways after FVP treatment. Our study suggested that FVP can be developed as a dietary supplement for intestine health promotion.

An uncommon case of native joint septic arthritis by Parvimonas micra.

Parvimonas micra is an anaerobic, Gram-positive coccus found in the oral cavity and gastrointestinal tract. We report a case of a 77-year-old male with right knee pain after a recent dental procedure and fall. Arthrocentesis was notable for Parvimonas micra which was successfully treated with metronidazole.

Dietary corn-resistant starch suppresses broiler abdominal fat deposition associated with the reduced cecal Firmicutes.

This study investigated the effects of dietary corn-resistant starch on lipid metabolism of broilers and its potential relationship with cecal microbiota modulation. A total of three hundred twenty 1-day-old male broilers were randomly assigned into 5 dietary treatments: 1 normal corn-soybean (NC) diet, 1 corn-soybean-based diet supplementation with 20% corn starch (CS), and 3 corn-soybean-based diets supplementation with 4, 8, and 12% corn resistant starch (RS) (identified as 4%RS, 8%RS, and 12%RS, respectively). Each group had 8 replicates with 8 broilers per replicate. The experiment lasted 21 d. The results showed that the abdominal fat percentage were lower in birds from 8%RS and 12%RS groups (0.75 and 0.58%, respectively) than those from NC and CS groups (1.20 and 1.28%, respectively; P < 0.05). The birds from 8%RS and 12%RS groups exhibited lower concentrations of blood triglyceride and nonestesterified fatty acid than those in the NC and CS groups (P < 0.05). Moreover, birds fed diets supplementation with 12% RS decreased the relative mRNA expressions of peroxisome proliferator-activated receptor gamma, ATP citrate-lyase, fatty acid synthase, and acetyl-CoA carboxylase in liver, and glycerol-3-phosphate acyltransferase in abdominal adipose tissue (P < 0.05). Microbiota analysis revealed that birds fed diets supplementation with 8 and 12% RS decreased the abundance of cecal Firmicutes by 23.08 and 20.47% and increased the proportion of Bacteroidetes by 24.33 and 21.92%, respectively, compared with the NC group (P < 0.05). In addition, correlation analysis revealed that many Firmicutes members had highly positive relationship with blood lipid levels and fat storage capacity, which might contribute to the lower abdominal fat phenotype. Overall, broilers receiving diets containing a higher concentration of RS harbor less Firmicutes, which decreased liver fatty acid synthesis and suppress abdominal fat deposition of birds during the starter phase. These findings provide a profound understanding about the relationship between gut microbial composition and lipid metabolism in broilers.

Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats.

In this study, the self-extracted constipation treatment of traditional Chinese medicine extracts was applied to constipated rats. To explore the mechanism and role of the Chinese medicine for the treatment of constipation, the 16S rRNA sequencing and qRT-PCR technology were used to analyze the intestinal flora. We found that the relative abundance of Firmicutes with constipation was significantly higher accounted for 86.7%, while the gut microbiota was significantly changed after taking a certain dose of Chinese medicine, greatly increased the relative abundance of Lactobacillus accounted for 23.1%, enhanced the symbiotic relationships of Lactobacillus with other intestinal flora. The total copies of intestinal bacteria in the constipated rats decreased after taking the traditional Chinese medicine. Finally, this study results provides a theoretical basis for the treatment and understand the mechanism and effect of traditional Chinese medicine on rate constipation.

A rare case of polymicrobial chronic maxillary sinusitis due to concurrent isolation of Parvimonas micra and Fusobacterium nucleatum.

Parvimonas micra and Fusobacterium nucleatum are commensal pathogens very rarely isolated simultaneously in clinical specimens. We report a case of chronic maxillary sinusitis caused by these two pathogens, presumably resulting from a co-existing dental infection.

Enrichment of microbial communities for hexavalent chromium removal using a biofilm reactor.

Given the toxicity and widespread occurrence of hexavalent chromium [Cr(VI)] in aquatic environments, we investigated the feasibility of a down-flow hanging sponge (DHS) biofilm reactor for the enrichment of microbial communities capable of Cr(VI) removal. In the present study, a laboratory-scale DHS reactor fed with a molasses-based medium containing Cr(VI) was operated for 112 days for the investigation. The enrichment of Cr(VI)-removing microbial communities was evaluated based on water quality and prokaryotic community analyses. Once the DHS reactor began to operate, high average volumetric Cr(VI) removal rates of 1.21-1.45 mg L-sponge-1 h-1 were confirmed under varying influent Cr(VI) concentrations (approximately 20-40 mg L-1). 16S rRNA gene amplicon sequencing analysis suggested the presence of phylogenetically diverse prokaryotic lineages, including phyla that contain well-known Cr(VI)-reducing bacteria (e.g., Bacteroidetes, Firmicutes, and Proteobacteria) in the polyurethane sponge media of the DHS reactor. Therefore, our findings indicate that DHS reactors have great potential for the enrichment of Cr(VI)-removing microbial communities.

First case report of Solobacterium moorei bacteremia due to acute cholangitis in South Korea.

Solobacterium moorei is an anaerobic gram-positive bacillus that rarely causes bacteremia. Herein, we report a case of S. moorei bacteremia associated with acute cholangitis in a patient without malignancy. The patient had a history of chronic pancreatitis with pancreaticogastrostomy and presented with fever and abdominal pain. Computed tomography scans showed acute cholangitis and S. moorei identified in blood cultures were confirmed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and 16S rRNA sequencing. The patient was successfully treated with endoscopic retrograde biliary drainage and antibiotics including meropenem and piperacillin-tazobactam.

Integrated omics analysis unraveled the microbiome-mediated effects of Yijin-Tang on hepatosteatosis and insulin resistance in obese mouse.

BACKGROUND: Gut microbiota play important roles in insulin homeostasis and the pathogenesis of non-alcoholic fatty liver diseases (NAFLD). Yijin-Tang (YJT), a traditional Korean and Chinese medicine, is used in the treatment of gastrointestinal diseases and obesity-related disorders such as insulin resistance (IR) and NAFLD. PURPOSE: Our aim was to identify the microbiome-mediated effects of YJT on IR and associated NAFLD by integrating metagenomics and hepatic lipid profile. METHODS: C57BL/6J mice were fed a normal chow diet (NC) or high-fat/high-cholesterol (HFHC) diet with or without YJT treatment. Hepatic lipid profiles were analyzed using liquid chromatography/mass spectrometry, and the composition of gut microbiota was investigated using 16S rRNA sequencing. Then, hepatic lipid profiles, gut microbiome, and inflammatory marker data were integrated using multivariate analysis and bioinformatics tools. RESULTS: YJT improved NAFLD, and 39 hepatic lipid metabolites were altered by YJT in a dose-dependent manner. YJT also altered the gut microbiome composition in HFHC-fed mice. In particular, Faecalibaculum rodentium and Bacteroides acidifaciens were altered by YJT in a dose-dependent manner. Also, we found significant correlation among hepatic phosphatidylglycerol metabolites, F. rodentium, and γδ-T cells. Moreover, interleukin (IL)-17, which is secreted by the γδ-T cell when it recognizes lipid antigens, were elevated in HFHC mice and decreased by YJT treatment. In addition, YJT increased the relative abundance of B. acidifaciens in NC or HFHC-fed mice, which is a gut microbiota that mediates anti-obesity and anti-diabetic effects by modulating the gut environment. We also confirmed that YJT ameliorated the gut tight junctions and increased short chain fatty acid (SCFA) levels in the intestine, which resulted in improved IR. CONCLUSION: These data demonstrated that gut microbiome and hepatic lipid profiles are regulated by YJT, which improved the IR and NAFLD in mice with diet-induced obesity.

Comparison of culture-independent and dependent approaches for identification of native arsenic-resistant bacteria and their potential use for arsenic bioremediation.

Arsenic is a common contaminant in gold mine soil and tailings. Microbes present an opportunity for bio-treatment of arsenic, since it is a sustainable and cost-effective approach to remove arsenic from water. However, the development of existing bio-treatment approaches depends on isolation of arsenic-resistant microbes from arsenic contaminated samples. Microbial cultures are commonly used in bio-treatment; however, it is not established whether the structure of the cultured isolates resembles the native microbial community from arsenic-contaminated soil. In this milieu, a culture-independent approach using Illumina sequencing technology was used to profile the microbial community in situ. This was coupled with a culture-dependent technique, that is, isolation using two different growth media, to analyse the microbial population in arsenic laden tailing dam sludge based on the culture-independent sequencing approach, 4 phyla and 8 genera were identified in a sample from the arsenic-rich gold mine. Firmicutes (92.23%) was the dominant phylum, followed by Proteobacteria (3.21%), Actinobacteria (2.41%), and Bacteroidetes (1.49%). The identified genera included Staphylococcus (89.8%), Pseudomonas (1.25), Corynebacterium (0.82), Prevotella (0.54%), Megamonas (0.38%) and Sphingomonas (0.36%). The Shannon index value (3.05) and Simpson index value (0.1661) indicated low diversity in arsenic laden tailing. The culture dependent method exposed significant similarities with culture independent methods at the phylum level with Firmicutes, Proteobacteria and Actinobacteria, being common, and Firmicutes was the dominant phylum whereas, at the genus level, only Pseudomonas was presented by both methods. It showed high similarities between culture independent and dependent methods at the phylum level and large differences at the genus level, highlighting the complementarity between the two methods for identification of the native population bacteria in arsenic-rich mine. As a result, the present study can be a resource on microbes for bio-treatment of arsenic in mining waste.

Long-term effects of antimicrobial drugs on the composition of the human gut microbiota.

INTRODUCTION: Antimicrobial drugs are known to have effects on the human gut microbiota. We studied the long-term temporal relationship between several antimicrobial drug groups and the composition of the human gut microbiota determined in feces samples. METHODS: Feces samples were obtained from a community-dwelling cohort of middle-aged and elderly individuals (Rotterdam Study). Bacterial DNA was isolated and sequenced using V3/V4 16 S ribosomal RNA sequencing (Illumina MiSeq). The time between the last prescription of several antimicrobial drug groups and the day of sampling was categorized into 0-12, 12-24, 24-48 and >48 months. The effects of the antimicrobial drug groups on the Shannon alpha-diversity (diversity), the Bray-Curtis beta-diversity (community structure), the Firmicutes/Bacteroidetes (F/B) ratio and individual genera were determined. RESULTS: We studied the gut microbiota of 1413 individuals (57.5% female, median age 62.6 years). The alpha-diversity was significantly lower up to 4 years after prescriptions of macrolides and lincosamides. It was also lower in the first year after the use of beta-lactams. The community structure (beta-diversity) of the microbiota was significantly different up to 4 years for macrolides and lincosamides, the first year for beta-lactams and at least the first year for quinolones. For the F/B ratio, drugs with a high anaerobic activity shifted the ratio toward Firmicutes in the first year whereas other antimicrobial drugs shifted the ratio toward Bacteroidetes. CONCLUSION: Use of antimicrobial drugs is associated with a shift in the composition of the gut microbiota.These effects differ in strength and duration, depending on the antimicrobial drug group used. These findings should be considered when prescribing antimicrobial drugs.