Assay for estimating total bacterial load: relative qPCR normalisation of bacterial load with associated clinical implications

Stool Microbiome Features and Weight Change Response to Treatment for cancer cachexia

BACKGROUND AND AIMS

Cancer cachexia is characterised by significant weight loss and muscle wasting that adversely affects patient outcomes. Nutritional interventions in cancer cachexia leads to improved outcomes, including improved weight change. However, there are wide variations in weight response to dietary interventions. Thus, it remains difficult to predict response to a given increase in dietary intake at an individual patient level. This study aimed to identify gut microbiome features that could serve as potential predictive biomarkers for response to individualized dietary intervention in patients with cancer cachexia attending the McGill Cancer Nutrition-Rehabilitation Program at the Jewish General Hospital (CNR-JGH).

METHODS

Participants were recruited from CNR-JGH clinic. Interventions included individualized nutritional counselling by a registered dietitian, to increase energy and protein intake to meet recommended levels. Stool DNA samples were collected at baseline (V1) and visit 2 (V2), and gut microbiome profiles were analysed to assess microbial diversity and identify differentially abundant genera in patients who lost weight (WL, N = 8) vs. maintained/gained weight (WSG, N = 29) at subsequent CNR-JGH clinic visits.

RESULTS

Greater alpha-diversity and higher Lachnospira genus abundance at baseline predicted higher likelihood that patients would have good response to CNR-JGH intervention (WSG at V2). Though predictors of poor response to nutritional intervention (WL at V2) were not identified, subjects in the WL group exhibited lower alpha-diversity and greater microbial population instability after CNR-JGH interventions.

CONCLUSIONS

In this cohort of patients with cancer-related weight loss attending a cancer cachexia clinic, certain gut microbiome features were associated with response to dietary interventions. Patients who lost weight after CNR-JGH intervention also developed a less diverse and less stable gut microbiome. Lachnospira genus abundance is a potential predictor of positive weight change response to dietary intervention as part of multimodal care for cancer cachexia, and further confirmatory studies are warranted. In addition, targeted dietary approaches to maintain diversity and gut microbiome population stability may have a role in improving the response to dietary interventions in cancer cachexia.

Microbiota and metabolome dynamics induced by Shiga toxin-producing E. coli in an in vitro model of an infant's colon

Shiga toxin-producing Escherichia coli (STEC) is a major food-borne pathogen causing human diseases ranging from diarrhea to life-threatening complications, mainly in young children. Colonization, virulence, and interactions of STEC strains with human gut microbiota are pivotal during infection but remain poorly described, particularly in children, the most affected population. In this work, we evaluated changes in the microbiota and metabolome composition in the in vitro gut model: Toddler ARtificial COLon (T-ARCOL) infected with EHEC O157:H7 strain EDL 933. Stool samples collected from children with STEC-positive diarrhea and stool from the same children after recovery from the diarrheal episode (n=5) were used to inoculate the T-ARCOL model. STEC colonization was progressively reduced throughout fermentation in T-ARCOL with diarrhea or recovery fecal samples. Beta diversity showed that the diarrhea-associated microbiota was significantly distinct from the recovery microbiota and exhibited a lower α-diversity. In contrast to recovery conditions, diarrheal conditions were characterized by an increased abundance of potential pathobionts such as members of the Clostridiaceae family and higher acetate, succinate, and N-acetylneuraminic acid levels. Our results provide new evidence of the impact of EHEC in the microbiota and metabolome dynamics in an in vitro gut model that could be useful in understanding their physiopathology in this at-risk population, considering inter-individual variabilities in gut microbiota.

Detection of colorectal-cancer-associated bacterial taxa in fecal samples using next-generation sequencing and 19 newly established qPCR assays

We have previously identified increased levels of distinct bacterial taxa within mucosal biopsies from colorectal cancer (CRC) patients. Following prior research, the aim of this study was to investigate the detection of the same CRC-associated bacteria in fecal samples and to evaluate the suitability of fecal samples as a non-invasive material for the detection of CRC-associated bacteria. Next-generation sequencing (NGS) of the 16S ribosomal RNA (rRNA) V4 region was performed to evaluate the detection of the CRC-associated bacteria in the fecal microbiota of cancer patients, patients with adenomatous polyp and healthy controls. Furthermore, 19 novel species-specific quantitative PCR (qPCR) assays were established to detect the CRC-associated bacteria. Approximately, 75% of the bacterial taxa identified in biopsies were reflected in fecal samples. NGS failed to detect low-abundance CRC-associated taxa in fecal samples, whereas qPCR exhibited high sensitivity and specificity in identifying all targeted taxa. Comparison of fecal microbial composition between the different patient groups showed enrichment of Fusobacterium nucleatum, Parvimonas micra, and Gemella morbillorum in cancer patients. Our findings suggest that low-abundance mucosa-associated bacteria can be detected in fecal samples using sensitive qPCR assays.

No microorganism was detected in amniotic fluid of healthy pregnancies from the second trimester to the delivery

BACKGROUND

The early colonization and establishment of the microbiome in newborns is a crucial step in the development of the immune system and host metabolism. However, the exact timing of initial microbial colonization remains a subject of ongoing debate. While numerous studies have attempted to determine the presence or absence of intrauterine bacteria, the majority of them have drawn conclusions based on sequencing data from maternal or infant samples taken at a single time point. In this study, we aimed to investigate the microbial population in amniotic fluid (AF) from the second trimester until the time of delivery using multiple microbiological methods.

METHODS

AF samples were collected during the second trimester (19-21 gestational weeks) and at the time of delivery. Cohort 1 included 51 women who underwent the term and elective cesarean section, with both their second trimester and delivery AF samples (n = 55, respectively) analyzed. Cohort 2 contained 22 women who experienced infection-related adverse pregnancy outcomes (including preterm birth, histological chorioamnionitis, and stillbirth), with only their second trimester AF samples (n = 24) examined. Additionally, multiple procedural negative controls and technical positive controls were applied to this study to remove potential contamination. Microbial profiles were assessed through cultivation, quantitative real-time polymerase chain reaction, 16S ribosomal RNA gene sequencing, and cytokine analysis.

RESULTS

In cohort 1, the bacterial load and community structure in the second trimester AF samples were indistinguishable from negative controls. Although marginally higher bacterial loads and different bacterial communities were observed in the delivery AF samples compared to negative controls, these bacterial DNA were not considered biologically functional due to the absence of maternal inflammatory responses. In cohort 2, the bacterial load and community structure of the second trimester AF samples differed significantly from those of negative controls, with Ureaplasma and Lactobacillus identified as the most prevalent genera against negative controls.

CONCLUSIONS

Our study demonstrates that no microorganisms were detected in the AF of healthy pregnancies from the second trimester to the delivery. The presence of Ureaplasma and Lactobacillus in the second trimester AF may be associated with infection-related adverse pregnancy outcomes. Video Abstract.

Potential New Methods to Analyze Basal and Total Endogenous Protein Losses of Host and Bacterial Origin in Pigs

BACKGROUND

Current systems for assessing protein quality such as the Digestible Indispensable Amino Acid Score correct apparent amino acid (AA) digestibility for basal endogenous protein losses (bEPL), ignoring the potential influence of the diet on these losses. However, the quantification of total endogenous protein losses (tEPL) poses a challenge.

OBJECTIVES

To evaluate different methods for quantifying tEPL and bEPL, and to assess their potential in discriminating between tEPL originating from bacteria and host.

METHODS

Using an incomplete Youden square design, 12 ileal cannulated pigs received 10 different protein sources, and a nitrogen-free (NF) diet. Ileal digesta were collected on days 6 and 7 of each 1-wk feeding period, to quantify endogenous protein losses (EPL) and analyze apparent ileal digestibility. Ileal EPL were estimated based on 1) 16S-+18S gene copy quantitative polymerase chain reaction, 2) diaminopimelic acid (DAPA)+18S, 3) differential AA profiles in digesta, EPL, and bacteria, equaling tEPL, and 4) an NF diet and 5) whey protein isolate (WPI), equaling bEPL.

RESULTS

Ileal bEPL based on the NF and WPI method correlated moderately to highly (r = 0.69, P < 0.05), but the NF method probably underestimated bEPL. In pigs fed the WPI diet, EPL based on the WPI and AA profile method were highly correlated (r = 0.88, P < 0.01). Overall, tEPL based on the AA profile method were moderately correlated with the 16S+18S method (r = 0.58, P < 0.001), and DAPA+18S (r = 0.57, P < 0.001). Low correlations were observed between bacterial tEPL based on the AA profile method and 16S or DAPA. Host tEPL based on the AA profile method and 18S were weakly correlated (r = 0.39, P < 0.001).

CONCLUSIONS

The AA profile method seems the most appropriate method for tEPL quantification, whereas the WPI method is preferred for bEPL quantification. Despite challenges in distinguishing between bacterial and host EPL, it is evident that bacterial proteins substantially (on average 37%-83%, depending on method) contribute to the EPL.

Oxygen-induced evolution of anammox granular sludge explains its unique responses during preservation

Anammox granular sludge (AnGS) preservation is indispensable for the application of anammox technology. Oxygen is a common and crucial factor for anammox, yet its long-term effects on AnGS during preservation remain incomplete clarification. This study investigated the effect of oxygen on AnGS in two simulated preservation systems with open and sealed conditions, and the mechanism was discussed. The results showed that the open system was in an oxidized state with an average dissolved oxygen (DO) concentration and oxidation-reduction potential (ORP) of (3.10 ± 1.36) mg·L-1 and (112.58 ± 46.78) mV, while a reduced state for the sealed system with no detected DO and a lower average ORP of (-153.96 ± 64.32) mV. Both systems showed declines in AnGS activity, while with different responses of AnGS demonstrated by the evolution in terms of granular morphology and structure, bacterial communities, bacteria survival, and bacteria antioxidation. In the open system, reactive oxygen species were generated and destroyed the unsaturated fatty acids in the cell membrane, further leading to the destructed cell structure and declined activity. However, in the sealed system, AnAOB tended to enter a dormant state after long-term preservation, contributing to better conditions in granular morphology and structure, higher AnAOB abundance, and higher live cell ratio. The findings of this study are expected to offer vital information and guidelines for the preservation technologies of AnGS.

The Effects of Electrolytic Technology Toothbrush Application on the Clinical Parameters and Bacteria Associated with Periodontal Disease in Dogs

The aim of this study was to compare the effects of electrolytic and nonelectrolytic toothbrushing on dogs' oral health and the presence of common bacteria associated with periodontal disease. Periodontal disease in dogs is a common problem worldwide. A toothbrushing procedure is recommended to prevent periodontal disease, with additional benefits if electrolytic toothbrushes are used in dog oral hygiene practices. A total of 26 dogs were enrolled in this eight-week study and were divided into two groups-treatment and control. Daily toothbrushing was performed on all dogs using the same dog toothbrush, with the power source disengaged in the control group. Oral examination was conducted on anesthetized dogs before and at 4 and 8 weeks after commencing the study, with sampling for bacterial analysis. This study was designed to be blind for owners, veterinarians, and laboratory staff. Improvements in the average gingival index (from 0.55 to 0.31) and calculus index (from 0.55 to 0.38) in the treatment group were recorded. In the control group, after an initial improvement in the plaque index (from 0.97 to 0.53), at week 8, it significantly rose to 1.21 (p < 0.05). Relative bacterial abundance revealed a reduction in all four tested bacteria in the treatment group, while in the control group, Campylobacter rectus levels rose by 3.67 log2 compared to before the study and at week 8. No adverse effects were recorded in either group.

Species-level verification of Phascolarctobacterium association with colorectal cancer

We have previously demonstrated an association between increased abundance of Phascolarctobacterium and colorectal cancer (CRC) and adenomas in two independent Norwegian cohorts. Here we seek to verify our previous findings using new cohorts and methods. In addition, we characterize lifestyle and sex specificity, the functional potential of the Phascolarctobacterium species, and their interaction with other microbial species. We analyze Phascolarctobacterium with 16S rRNA sequencing, shotgun metagenome sequencing, and species-specific qPCR, using 2350 samples from three Norwegian cohorts-CRCAhus, NORCCAP, and CRCbiome-and a large publicly available data set, curatedMetagenomicData. Using metagenome-assembled genomes from the CRCbiome study, we explore the genomic characteristics and functional potential of the Phascolarctobacterium pangenome. Three species of Phascolarctobacterium associated with adenoma/CRC were consistently detected by qPCR and sequencing. Positive associations with adenomas/CRC were verified for Phascolarctobacterium succinatutens and negative associations were shown for Phascolarctobacterium faecium and adenoma in curatedMetagenomicData. Men show a higher prevalence of P. succinatutens across cohorts. Co-occurrence among Phascolarctobacterium species was low (<6%). Each of the three species shows distinct microbial composition and forms distinct correlation networks with other bacterial taxa, although Dialister invisus was negatively correlated to all investigated Phascolarctobacterium species. Pangenome analyses showed P. succinatutens to be enriched for genes related to porphyrin metabolism and degradation of complex carbohydrates, whereas glycoside hydrolase enzyme 3 was specific to P. faecium.IMPORTANCEUntil now Phascolarctobacterium has been going under the radar as a CRC-associated genus despite having been noted, but overseen, as such for over a decade. We found not just one, but two species of Phascolarctobacterium to be associated with CRC-Phascolarctobacterium succinatutens was more abundant in adenoma/CRC, while Phascolarctobacterium faecium was less abundant in adenoma. Each of them represents distinct communities, constituted by specific microbial partners and metabolic capacities-and they rarely occur together in the same patients. We have verified that P. succinatutens is increased in adenoma and CRC and this species should be recognized among the most important CRC-associated bacteria.

Spread and persistence of antimicrobial resistance genes in wastewater from human and animal sources in São Paulo, Brazil

The spread of antimicrobial resistance (AMR) through multiple reservoirs is a global concern. Wastewater is a critical AMR dissemination source, so this study aimed to assess the persistence of resistance genetic markers in wastewater using a culture-independent approach. Raw and treated wastewater samples (n = 121) from a wastewater treatment plant (WWTP), a human hospital, a veterinary hospital, and a pig farm were monthly collected and concentrated by filtration. DNA was extracted directly from filter membranes, and PCR was used in the qualitative search of 32 antimicrobial resistance genes (ARGs). Selected genes (blaCTX-M, blaKPC, qnrB, and mcr-1) were enumerated by quantitative real-time PCR (qPCR). Twenty-six ARGs were detected in the qualitative ARGs search, while quantitative data showed a low variation of the ARG's relative abundance (RA) throughout the months, especially at the human hospital and the WWTP. At the WWTP, despite significantly reducing the absolute number of gene copies/L after each treatment stage (p < 0.05), slight increases (p > 0.05) in the RAs of genes blaCTX-M, qnrB, and mcr-1 were observed in reused water (tertiary treatment) when compared with secondary effluent. Although the increase is not statistically significant, it is worth noting that there was some level of ARGs concentration after the disinfection process. No significant absolute or relative after-treatment quantification reductions were observed for any ARGs at the veterinary hospital or the pig farm. The spread of ARGs through sewage needs to be continuously addressed, because their release into natural environments may pose potential risks of exposure to resistant bacteria and impact local ecosystems.

Dietary resistant starch supplementation increases gut luminal deoxycholic acid abundance in mice

Bile acids (BA) are among the most abundant metabolites produced by the gut microbiome. Primary BAs produced in the liver are converted by gut bacterial 7-α-dehydroxylation into secondary BAs, which can differentially regulate host health via signaling based on their varying affinity for BA receptors. Despite the importance of secondary BAs in host health, the regulation of 7-α-dehydroxylation and the role of diet in modulating this process is incompletely defined. Understanding this process could lead to dietary guidelines that beneficially shift BA metabolism. Dietary fiber regulates gut microbial composition and metabolite production. We tested the hypothesis that feeding mice a diet rich in a fermentable dietary fiber, resistant starch (RS), would alter gut bacterial BA metabolism. Male and female wild-type mice were fed a diet supplemented with RS or an isocaloric control diet (IC). Metabolic parameters were similar between groups. RS supplementation increased gut luminal deoxycholic acid (DCA) abundance. However, gut luminal cholic acid (CA) abundance, the substrate for 7-α-dehydroxylation in DCA production, was unaltered by RS. Further, RS supplementation did not change the mRNA expression of hepatic BA producing enzymes or ileal BA transporters. Metagenomic assessment of gut bacterial composition revealed no change in the relative abundance of bacteria known to perform 7-α-dehydroxylation. P. ginsenosidimutans and P. multiformis were positively correlated with gut luminal DCA abundance and increased in response to RS supplementation. These data demonstrate that RS supplementation enriches gut luminal DCA abundance without increasing the relative abundance of bacteria known to perform 7-α-dehydroxylation.

Bacteria from gut microbiota associated with diarrheal infections in children promote virulence of Shiga toxin-producing and enteroaggregative Escherichia coli pathotypes

Background

Diarrheagenic E. coli (DEC) pathogenicity relies on the interaction of bacteria with the host’s gut environment, which is regulated by the resident microbiota. Previously, we identified indicative bacterial species of gut microbiota in DEC-positive stool samples from children. Here, we evaluated the role of two indicative species, Citrobacter werkmanii (CW) and Escherichia albertii (EA), in the virulence of two DEC pathotypes, Shiga toxin-producing (STEC) and enteroaggregative (EAEC) Escherichia coli.

Methods

We determined the effect of supernatants obtained from CW and EA cultures on the gene expression of STEC strain 86-24 and EAEC strain 042 by RNA-seq analysis. We evaluated IL-8 secretion from T84 cells infected with these DEC strains in the presence or absence of the supernatant from EA. The effect of the supernatant from EA on the growth and adherence of STEC and EAEC to cells was also evaluated. Finally, we studied the effect of the EA supernatant on the STEC-induced inflammation mediated by the long polar fimbriae (Lpf) in T84 cells and the expression of plasmid-encoded toxin (Pet) in EAEC.

Results

RNA-seq analysis revealed that several virulence factors in STEC and EAEC were upregulated in the presence of supernatants from CW and EA. Interestingly, an increase in the secretion of IL-8 was observed in cells infected with STEC or EAEC in the presence of a supernatant from EA. Similar results were observed with the supernatants obtained from clinical strains of E. albertii. The supernatant from EA had no effect on the growth of STEC and EAEC, or on the ability of these DEC strains to adhere to cells. We found that Pet toxin in EAEC was upregulated in the presence of a supernatant from EA. In STEC, using mutant strains for Lpf fimbriae, our data suggested that these fimbriae might be participating in the increase in IL-8 induced by STEC in cells in the presence of a supernatant from EA.

Conclusion

Supernatant obtained from an indicative species of DEC-positive diarrhea could modulate gene expression in STEC and EAEC, and IL-8 secretion induced by these bacteria. These data provide new insights into the effect of gut microbiota species in the pathogenicity of STEC and EAEC.

Assessing Microbial Monitoring Methods for Challenging Environmental Strains and Cultures

This paper focuses on the comparison of microbial biomass increase (cell culture growth) using field-relevant testing methods and moving away from colony counts. Challenges exist in exploring the antimicrobial growth of fastidious strains, poorly culturable bacteria and bacterial communities of environmental interest. Thus, various approaches have been explored to follow bacterial growth that can be efficient surrogates for classical optical density or colony-forming unit measurements. Here, six species grown in pure culture were monitored using optical density, ATP assays, DNA concentrations and 16S rRNA qPCR. Each of these methods have different advantages and disadvantages concerning the measurement of growth and activity in complex field samples. The species used as model systems for monitoring were: Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, Geoalkalibacter subterraneus, Pseudomonas putida and Thauera aromatica. All four techniques were found to successfully measure and detect cell biomass/activity differences, though the shape and accuracy of each technique varied between species. DNA concentrations were found to correlate the best with the other three assays (ATP, DNA concentrations and 16S rRNA-targeted qPCR) and provide the advantages of rapid extraction, consistency between replicates and the potential for downstream analysis. DNA concentrations were determined to be the best universal monitoring method for complex environmental samples.

Accurate quantification of bacterial abundance in metagenomic DNAs accounting for variable DNA integrity levels

The quantification of the total microbial content in metagenomic samples is critical for investigating the interplay between the microbiome and its host, as well as for assessing the accuracy and precision of the relative microbial composition which can be strongly biased in low microbial biomass samples. In the present study, we demonstrate that digital droplet PCR (ddPCR) can provide accurate quantification of the total copy number of the 16S rRNA gene, the gene usually exploited for assessing total bacterial abundance in metagenomic DNA samples. Notably, using DNA templates with different integrity levels, as measured by the DNA integrity number (DIN), we demonstrated that 16S rRNA copy number quantification is strongly affected by DNA quality and determined a precise correlation between quantification underestimation and DNA degradation levels. Therefore, we propose an input DNA mass correction, according to the observed DIN value, which could prevent inaccurate quantification of 16S copy number in degraded metagenomic DNAs. Our results highlight that a preliminary evaluation of the metagenomic DNA integrity should be considered before performing metagenomic analyses of different samples, both for the assessment of the reliability of observed differential abundances in different conditions and to obtain significant functional insights.

Sample Adequacy Control (SAC) Lowers False Negatives and Increases the Quality of Screening: Introduction of "Non-Competitive" SAC for qPCR Assays

Sample Adequacy Control (SAC) has critical analytical, clinical and epidemiological value that increases confidence in a negative test result. The SAC is an integral qPCR assay control, which ensures that all pre-analytical and analytical steps are adequate for accurate testing and reporting. As such, a negative SAC with a negative result on pathogen screen specifies that the result should be reported as inconclusive instead of negative. Despite this, many regulatory approved tests do not incorporate SAC into their assay design. Herein, we emphasize the universal value of SAC and offer for the first time, a simple technical strategy to introduce non-competitive SAC which does not interfere with the limit of detection for the screened pathogen. Integration of SAC can provide key benefits towards identifying, isolating, quarantining and contact tracing infected individuals and in turn can improve worldwide efforts in infection control.

Interindividual Differences in Human Intestinal Microbial Conversion of (-)-Epicatechin to Bioactive Phenolic Compounds

To quantify interindividual differences in the human intestinal microbial metabolism of (-)-epicatechin (EC), in vitro anaerobic incubations with fecal inocula from 24 healthy donors were conducted. EC-derived colonic microbial metabolites were qualitatively and quantitively analyzed by liquid chromatography triple quadrupole mass spectrometry (LC-TQ-MS) and liquid chromatography time-of-flight mass spectrometry (LC-TOF-MS). Quantitative microbiota characterization was achieved by 16S rRNA analysis. The results obtained show 1-(3',4'-dihydroxyphenyl)-3-(2″,4″,6″-dihydroxyphenyl)-2-propanol (3,4-diHPP-2-ol) and 5-(3',4'-dihydroxyphenyl)-γ-valerolactone (3,4-diHPV) to be key intermediate microbial metabolites of EC and also revealed the substantial interindividual differences in both the rate of EC conversion and the time-dependent EC metabolite pattern. Furthermore, substantial differences in microbiota composition among different individuals were detected. Correlations between specific microbial phylotypes and formation of certain metabolites were established. It is concluded that interindividual differences in the intestinal microbial metabolism of EC may contribute to interindividual differences in potential health effects of EC-abundant dietary foods or drinks.

Laboratory-developed test for detection of acute Clostridium difficile infections with the capacity for quantitative sample normalization

We describe a laboratory-developed test intended for the detection of acute Clostridium difficile infections (CDI) with the capacity for quantitative sample normalization. The test is based on the detection of the tcdB gene. However, this biomarker is also present among people without symptoms, implying that individuals with diarrhea, not caused by C. difficile may nonetheless test positive. Therefore, clinical diagnosis based on this format of testing can be challenging. In order to improve diagnostic assays capability, tcdB-based quantification methods were suggested as a potential solution, however they did not increase clinical specificity. We report methodology for a dual biomarker monitoring (total bacterial load and tcdB assay), allowing for the calculation of the relative presence of tcdB in the total bacterial population in the tested samples. We believe that this approach is clinically relevant to current assays and can improve CDI testing algorithms.

Detection of Fusobacterium nucleatum in stool and colonic tissues from Norwegian colorectal cancer patients

Norway has one of the world's highest incidences of colorectal cancer (CRC). Accumulating research suggests that the intestinal microbiota may have an important role in initiation and progression of colorectal cancer. In order to evaluate microbiome-based biomarkers for non-invasive detection of CRC, the levels of Fusobacterium nucleatum and selected Escherichia coli toxin genes in stool and mucosa from a small cohort of Norwegian patients were investigated. The study cohort included 72 patients scheduled for colonoscopy. The patients were divided into three groups upon their examinations: cancer, polyp, and control groups. Levels of F. nucleatum in stool samples were significantly higher in the cancer group compared with the control group and the polyp group. High levels of F. nucleatum in stool reflected detection of F. nucleatum in the tumor tissues of colorectal cancer patients. However, no difference in the levels of E. coli toxin genes in neither stool nor biopsy samples between the patient groups was observed. This study suggests that a quantitative PCR assay targeting F. nucleatum in stool samples has the potential to be included in a larger panel of biomarkers for non-invasive testing for colorectal cancer.

Akkermansia muciniphila as a Model Case for the Development of an Improved Quantitative RPA Microbiome Assay

Changes in the population levels of specific bacterial species within the gut microbiome have been linked to a variety of illnesses. Most assays that determine the relative abundance of specific taxa are based on amplification and sequencing of stable phylogenetic gene regions. Such lab-based analysis requires pre-analytical sample preservation and storage that have been shown to introduce biases in the characterization of microbial profiles. Recombinase polymerase amplification (RPA) is an isothermal nucleic acid amplification method that employs commercially available, easy-to-use freeze-dried enzyme pellets that can be used to analyze specimens rapidly in the field or clinic, using a portable fluorometer. Immediate analysis of diverse bacterial communities can lead to a more accurate quantification of relative bacterial abundance. In this study, we discovered that universal bacterial 16S ribosomal DNA primers give false-positive signals in RPA analysis because manufacturing host Escherichia coli DNA is present in the RPA reagents. The manufacturer of RPA reagents advises against developing an RPA assay that detects the presence of E. coli due to the presence of contaminating E. coli DNA in the reaction buffer (www.twistdx.co.uk/). We, therefore, explored four strategies to deplete or fragment extraneous DNA in RPA reagents while preserving enzyme activity: metal-chelate affinity chromatography, sonication, DNA cleavage using methylation-dependent restriction endonucleases, and DNA depletion using anti-DNA antibodies. Removing DNA with anti-DNA antibodies enabled the development of a quantitative RPA microbiome assay capable of determining the relative abundance of the physiologically-important bacterium Akkermansia muciniphila in human feces.

iNOS- and NOX1-dependent ROS production maintains bacterial homeostasis in the ileum of mice

The intestinal epithelial cells constitute the first line of defense against gut microbes, which includes secretion of various antimicrobial substances. Reactive oxygen species (ROS) are well characterized as part of the innate phagocytic immunity; however, a role in controlling microorganisms in the gut lumen is less clear. Here, we show a role for nitric oxide synthase (iNOS)- and NOX1-produced ROS in maintaining homeostasis of the gut microbiota. In vivo imaging revealed distinctly high levels of ROS in the ileum of normal healthy mice, regulated in accordance with the amount of gut bacteria. The ROS level was dependent on the nitric oxide and superoxide producers iNOS and NOX1, respectively, suggesting peroxynitrite as the effector molecule. In the ileum of iNOS- and NOX1-deficient mice, the bacterial load is increased and the composition is more cecum like. Our data suggest a unique role of ileum in maintaining homeostasis of gut microbes through production of ROS with potential importance for preventing reflux from the large intestine, bacterial overgrowth, and translocation.

Rectal swab screening assays of public health importance in molecular diagnostics: Sample adequacy control

Rectal swabs are routinely used by public health authorities to screen for multi-drug resistant enteric bacteria including vancomycin-resistant enterococci (VRE) and carbapenem-resistant enterobacteriaceae (CRE). Screening sensitivity can be influenced by the quality of the swabbing, whether performed by the patient (self-swabbing) or a healthcare practitioner. One common exclusion criterion for rectal swabs is absence of "visible soiling" from fecal matter. In our institution, this criterion excludes almost 10% of rectal swabs received in the microbiology laboratory. Furthermore, over 30% of patients in whom rectal swabs are cancelled will not be re-screened within the next 48h, resulting in delays in removing infection prevention measures. We describe two quantitative polymerase chain reaction (qPCR)-based assays, human RNAse P and eubacterial 16S rDNA, which might serve as suitable controls for sampling adequacy. However, lower amounts of amplifiable human DNA make the 16s rDNA assay a better candidate for sample adequacy control.

Clinical Next Generation Sequencing Outperforms Standard Microbiological Culture for Characterizing Polymicrobial Samples

BACKGROUND

Humans suffer from infections caused by single species or more complex polymicrobial communities. Identification of infectious bacteria commonly employs microbiological culture, which depends upon the in vitro propagation and isolation of viable organisms. In contrast, detection of bacterial DNA using next generation sequencing (NGS) allows culture-independent microbial profiling, potentially providing important new insights into the microbiota in clinical specimens.

METHODS

NGS 16S rRNA gene sequencing (NGS16S) was compared with culture using (a) synthetic polymicrobial samples for which the identity and abundance of organisms present were precisely defined and (b) primary clinical specimens.

RESULTS

Complex mixtures of at least 20 organisms were well resolved by NGS16S with excellent reproducibility. In mixed bacterial suspensions (10⁷ total genomes), we observed linear detection of a target organism over a 4-log concentration range (500-3 × 10⁶ genomes). NGS16S analysis more accurately recapitulated the known composition of synthetic samples than standard microbiological culture using nonselective media, which distorted the relative abundance of organisms and frequently failed to identify low-abundance pathogens. However, extended quantitative culture using selective media for each of the component species recovered the expected organisms at the proper abundance, validating NGS16S results. In an analysis of sputa from cystic fibrosis patients, NGS16S identified more clinically relevant pathogens than standard culture.

CONCLUSIONS

Biases in standard, nonselective microbiological culture lead to a distorted characterization of polymicrobial mixtures. NGS16S demonstrates enhanced reproducibility, quantification, and classification accuracy compared with standard culture, providing a more comprehensive, accurate, and culture-free analysis of clinical specimens.

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

BACKGROUND

Next-generation 16S ribosomal RNA gene sequencing is widely used to determine the relative composition of the mammalian gut microbiomes. However, in the absence of a reference, this does not reveal alterations in absolute abundance of specific operational taxonomic units if microbial loads vary across specimens.

RESULTS

Here we suggest the spiking of exogenous bacteria into crude specimens to quantify ratios of absolute bacterial abundances. We use the 16S rDNA read counts of the spike-in bacteria to adjust the read counts of endogenous bacteria for changes in total microbial loads. Using a series of dilutions of pooled faecal samples from mice containing defined amounts of the spike-in bacteria Salinibacter ruber, Rhizobium radiobacter and Alicyclobacillus acidiphilus, we demonstrate that spike-in-based calibration to microbial loads allows accurate estimation of ratios of absolute endogenous bacteria abundances. Applied to stool specimens of patients undergoing allogeneic stem cell transplantation, we were able to determine changes in both relative and absolute abundances of various phyla, especially the genus Enterococcus, in response to antibiotic treatment and radio-chemotherapeutic conditioning.

CONCLUSION

Exogenous spike-in bacteria in gut microbiome studies enable estimation of ratios of absolute OTU abundances, providing novel insights into the structure and the dynamics of intestinal microbiomes.

Intricacies of assessing the human microbiome in epidemiologic studies

PURPOSE

In the past decade, remarkable relationships have been documented between dysbiosis of the human microbiota and adverse health outcomes. This review seeks to highlight some of the challenges and pitfalls that may be encountered during all stages of microbiota research, from study design and sample collection, to nucleic acid extraction and sequencing, and bioinformatic and statistical analysis.

METHODS

Literature focused on human microbiota research was reviewed and summarized.

RESULTS

Although most studies have focused on surveying the composition of the microbiota, fewer have explored the causal roles of these bacteria, archaea, viruses, and fungi in affecting disease states. Microbiome research is in its relatively early years and many aspects remain challenging, including the complexity and personalized aspects of microbial communities, the influence of exogenous and often confounding factors, the need to apply fundamental principles of ecology and epidemiology, the necessity for new software tools, and the rapidly evolving genomic, technological, and analytical landscapes.

CONCLUSIONS

Incorporating human microbiome research in large epidemiologic studies will soon help us unravel the intricate relationships that we have with our microbial partners and provide interventional opportunities to improve human health.