Culturing Human Gut Microbiomes in the Laboratory.

The human gut microbiota is a complex community of prokaryotic and eukaryotic microbes and viral particles that is increasingly associated with many aspects of host physiology and health. However, the classical microbiology approach of axenic culture cannot provide a complete picture of the complex interactions between microbes and their hosts in vivo. As such, recently there has been much interest in the culture of gut microbial ecosystems in the laboratory as a strategy to better understand their compositions and functions. In this review, we discuss the model platforms and methods available in the contemporary microbiology laboratory to study human gut microbiomes, as well as current knowledge surrounding the isolation of human gut microbes for the potential construction of defined communities for use in model systems.

Combined recovery of polyhydroxyalkanoates and reclaimed water in the mainstream of a WWTP for agro-food industrial wastewater valorisation by membrane bioreactor technology.

The present study investigated the combined production of reclaimed water for reuse purposes and polyhydroxyalkanoates (PHA) from an agro-food industrial wastewater. A pilot plant implementing a two-stage process for PHA production was studied. It consisted of a mainstream sequencing batch membrane bioreactor (SBMBR) in which selection of PHA-accumulating organisms and wastewater treatment were carried out in, and a side-stream fed-batch reactor (FBR) where the excess sludge from the SBMBR was used for PHA accumulation. The performance of the SBMBR was compared with that of a conventional sequencing batch reactor (SBR) treating the same wastewater under different food to microorganisms' ratios (F/M) ranging between 0.125 and 0.650 kgCOD kgTSS-3 d-1. The SBMBR enabled to obtain very high-quality effluent in compliance with the relevant national (Italy) and European regulations (Italian DM 185/03 and EU, 2020/741) in the field of wastewater reclamation, whereas the performances in the SBR collapsed at F/M higher than 0.50 kgCOD kgTSS-1d-1. A maximum intracellular storage of 45% (w/w) and a production yield of 0.63 gPHA L-1h-1 were achieved when the SBMBR system was operated with a F/M ratio close to 0.50 kgCOD kgTSS-1d-1. This resulted approximately 35% higher than those observed in the SBR, since the ultrafiltration membrane avoided the washout of dispersed and filamentous bacteria capable of storing PHA. Furthermore, while maximizing PHA productivity in conventional SBR systems led to process dysfunctions, in the SBMBR system it helped mitigate these issues by reducing membrane fouling behaviour. The results of this study supported the possibility to achieve combined recovery of reclaimed water and high-value added bioproducts using membrane technology, leading the way for agro-food industrial wastewater valorization in the frame of a circular economy model.

Clinical features, treatment and prognosis of patients with endogenous infectious endophthalmitis.

PURPOSE: To investigate whether the clinical characteristics, treatment and prognosis of endogenous infectious endophthalmitis (EIE) have changed over the past 5 years. METHODS: Retrospectively analyze all articles about EIE published in the PubMed, Web of Science, and Embase databases from 2017 to 2021. RESULTS: A total of 128 patients and 147 eyes (46 left and 60 right) were included in the study. The mean age at diagnosis was 51 ± 19 years. The most common risk factors were diabetes and intravenous drug use. From 2017 to 2021, Klebsiella was the most common pathogenic microorganism (22%), and vitreous culture had the highest positivity rate. The most common complaint was blurred vision. The mean visual acuity (logMAR) at onset was 2.84, and the clinical symptoms were vitreal inflammation and opacity (63%), ocular pain (37%), and conjunctival congestion (36%). The ocular inflammation could be reduced by intraocular antibiotics or vitrectomy. However, the visual prognosis, with a mean logMAR of 2.73; only 50% of the eyes reached a visual acuity level of finger count and above. Changes in diagnostics over the past 5 years have mainly manifested as more diverse microorganism culture methods. In addition to conventional culture methods, PCR, sputum culture and aqueous humour culture are also commonly used for the diagnosis of pathogenic bacteria, improving the positive culture rate and visual prognosis. CONCLUSION: The prognosis of EIE is poor. It is recommended to pay attention to the pathogenic bacteria culture results and accompanying systemic diseases and to diagnose and treat patients as soon as possible.

Study on the use of bovine blood protein hydrolysate as a peptone in microbial culture media.

Livestock blood is a protein-rich waste byproduct produced during meat production processes in slaughterhouses. Its utilization through conversion into value-added products is an intriguing management strategy. In this study, bovine blood was used to obtain the protein hydrolysate for use as a peptone for microbial growth medium. Lyophilized bovine blood was heat treated to make it susceptible to enzymic hydrolysis, and then enzymatically treated with trypsin (bovine pancreas protease) to produce protein hydrolysate. Physico-chemical features were determined for protein hydrolysate and compared to commercial Merck peptone from meat. Amino acid compositions of bovine blood and commercial peptones were subjected to multivariate analysis based on Euclidean similarity matrix using software PAST. Strains of Staphylococcus aureus 25,923, Pseudomonas aeruginosa 27,853, Staphylococcus aureus 6538 P, Enterococcus faecalis 11,700, Escherichia coli 8739, Klebsiella pneumoniae 13,883, Salmonella typhimurium 14,028 and Listeria monocytogenes 13,932 were used as test microbial strains. Growth of bacteria in culture media based on the peptone from bovine protein hydrolysate was compared to that in corresponding reference media based on commercial peptone. The results of these growth tests were comparable. Growth data were depicted and statistically analyzed using R packages ggplot2 and growthcurver, respectively, providing data fitting a standard form of logistic equation.

Is the Medium Still the Message? Culture-Independent Diagnosis of Gastrointestinal Infections.

Infectious diarrhea is caused by a variety of pathogens, including viruses, bacteria, and parasitic organisms. Though the causative agent of diarrhea has historically been evaluated via stool cultures, recently, culture-independent diagnostic tests (CIDT) have been developed and utilized with increasing frequency. Current practice guidelines recommend their use as adjuncts to stool cultures for diagnosing acute and chronic diarrhea. The three principal CIDT are microscopy, enzyme-based immunoassays (EIAs), and molecular based polymerase chain reaction (PCR). This review explores the common causes of infectious diarrhea, the basics of stool culture, the diagnostic utility of these three culture-independent modalities, and the strengths and weaknesses of all currently available clinical techniques. It also outlines considerations for specific populations including returning travelers and those with inflammatory bowel disease.

Impact of Acetate in Reduction of Perchlorate by Mixed Microbial Culture under the Influence of Nitrate and Sulfate.

The biological reduction of slow degradation contaminants such as perchlorate (ClO4-) is considered to be a promising water treatment technology. The process is based on the ability of a specific mixed microbial culture to use perchlorate as an electron acceptor in the absence of oxygen. In this study, batch experiments were conducted to investigate the effect of nitrate on perchlorate reduction, the kinetic parameters of the Monod equation and the optimal ratio of acetate to perchlorate for the perchlorate reducing bacterial consortium. The results of this study suggest that acclimated microbial cultures can be applied to treat wastewater containing high concentrations of perchlorate. Reactor experiments were carried out with different hydraulic retention times (HRTs) to determine the optimal operating conditions. A fixed optimal HRT and the effect of nitrate on perchlorate reduction were investigated with various concentrations of the electron donor. The results showed that perchlorate reduction occurred after nitrate removal. Moreover, the presence of sulfate in wastewater had no effect on the perchlorate reduction. However, it had little effect on biomass concentration in the presence of nitrate during exposure to a mixed microbial culture, considering the nitrate as the inhibitor of perchlorate reduction by reducing the degradation rate. The batch scale experiment results illustrated that for efficient operation of perchlorate reduction, the optimal acetate to perchlorate ratio of 1.4:1.0 would be enough. Moreover, these experiments found the following results: the kinetic parameters equivalent to Y = 0.281 mg biomass/mg perchlorate, Ks = 37.619 mg/L and qmax = 0.042 mg perchlorate/mg biomass/h. In addition, anoxic-aerobic experimental reactor results verify the optimal HRT of 6 h for continuous application. Furthermore, it also illustrated that using 600 mg/L of acetate as a carbon source is responsible for 100% of nitrate reduction with less than 50% of the perchlorate reduction, whereas at 1000 mg/L acetate, approximately 100% reduction was recorded.

Simplified engineering design towards a competitive lipid-rich effluents valorization.

Medium- and long-chain fatty acids and glycerol contained in the oily fraction of many food-industry effluents are excellent candidates to produce biobased high-value triacylglycerides (TAGs) and polyhydroxyalkanoates (PHAs). The typical process configuration for TAGs recovery from lipid-rich streams always includes two steps (culture enrichment plus storage compounds accumulation) whereas, for PHAs production, an additional pretreatment of the substrate for the obtainment of soluble volatile fatty acids (VFAs) is required. To simplify the process, substrate hydrolysis, culture enrichment, and accumulation (TAG and PHA storage) were coupled here in a single sequencing batch reactor (SBR) operated under the double growth limitation strategy (DGL) and fed in pulses with industrial waste fish oil during the whole feast phase. When the SBR was operated in 12 h cycles, it was reached up to 51 wt % biopolymers after only 6 h of feast (TAG:PHA ratio of 50:51; 0.423 CmmolBIOP/CmmolS). Daily storage compound production was observed to be over 25% higher than the reached when enrichment and accumulation stages were carried in separate operational units. Increasing the feast phase length from 6 to 12 h (18 h cycle) negatively affected the DGL strategy performance and hence system storage capacity, which was recovered after also extending the famine phase in the same proportion (24 h cycle). Besides, the carbon influx during the feast phase was identified as a key operational parameter controlling storage compounds production and, together with the C/N ratio, culture selection. The different cycle configurations tested clearly modulated the total fungal abundances without no significant differences in the size of the bacterial populations. Several PHA and TAG producers were found in the mixed culture although the PHA and TAG productions were poorly associated with the increased relative abundances (RAs) of specific operational taxonomic units (OTUs).

The prevalence of Salmonella spp. in working farm dogs and their home-kill raw meat diets in Manawatu, New Zealand.

AIMS: To investigate the prevalence of Salmonella spp. in a convenience sample of working farm dogs and their home-kill raw meat diets in Manawatu, New Zealand. METHODS: Fifty farms in the Manawatu, with at least three working/herding dogs per farm that were fed raw home-killed meat at least fortnightly, were visited. One sample of dog faeces and one sample of food were collected per farm using convenience sampling. If a dog did not defecate, a sample was obtained by digital recovery. Basic descriptive data for all dogs, meat and farm characteristics were recorded. Stomached meat samples and swabs from faecal samples were pre-enriched in buffered peptone water followed by two selective enrichments with agar subculture. Isolates were confirmed to be Salmonella spp. by serology and biochemical characterisation. RESULTS: No Salmonella spp. were isolated from dog faeces or raw meat samples, giving an observed prevalence rate of 0 (95% CI = 0.0-7.1)%. CONCLUSIONS: In this study, there was no evidence that working farm dogs and their home-kill raw meat represent likely sources of infection with Salmonella spp. CLINICAL RELEVANCE: Although this study found no evidence suggesting that farmers should change their feeding practices, it is based on a small sample, from a single region of New Zealand and involved sampling on one occasion for Salmonella spp. only. Currently, although the prevalence of Salmonella spp. carriage appears to be low, feeding raw meat-based diets to working dogs remains a risk and due to the potential zoonotic implications for humans, hygienic measures should be maintained when in contact with dogs and raw meat.

Brain Abscess Apparent Diffusion Coefficient is Associated With Microbial Culture Yields.

BACKGROUND: Obtaining pus for microbial cultures is one of the surgical aims in patients with brain abscess. Predictors of microbial yields are necessary as they help in treatment planning. PURPOSE: To investigate the relationship between microbial culture yields of brain abscesses and their apparent diffusion coefficient (ADC) values and clinical characteristics. STUDY TYPE: Retrospective. SUBJECTS: Eighty-four patients diagnosed with brain abscess by surgery and histopathology (59 with positive abscess cultures). FIELD STRENGTH/SEQUENCE: Diffusion-weighted, T2-weigthed, and contrast-enhanced T1-weighted imaging at 1.5 T and 3 T. ASSESSMENT: Contrast-enhanced T1-weighted images were co-registered to ADC maps. Three neuroradiologists determined abscess imaging characteristics (distribution, location, and ventricular rupture), and two measured abscess volumes and ADC values. Clinical characteristics collected included sex, age, fever, underlying diseases, infection sources, white blood cell count, percentage of segmented neutrophils, C-reactive protein level, regimen and duration of empirical antibiotics, and types of surgery. STATISTICAL TESTS: Interobserver differences were assessed with Fleiss kappa and intraclass correlation coefficients. The differences in clinical and imaging factors between the positive and negative culture groups were compared with Chi-square analysis or Student's t test. All factors were subjected to multivariable logistic regression analysis to assess their associations with microbial culture yields, and factors with statistical significance were evaluated with receiver operating characteristic curve analysis to assess their diagnostic performance in discriminating the two groups. RESULTS: Mean ADC (×10-6  mm2 /s) of culture-negative abscesses (841 ± 173) was significantly higher (P < 0.05) than that of culture-positive abscesses (536 ± 90). On multivariable analysis, mean ADC was the only significant factor (P < 0.05) related to culture yields. With 660 as the cutoff value, the sensitivity, specificity, and accuracy of ADC for discriminating culture yields were 93.2%, 88.0%, and 91.7%, respectively. DATA CONCLUSION: ADC could be used to discriminate between culture-positive and culture-negative abscesses. EVIDENCE LEVEL: 4 TECHNICAL EFFICACY: Stage 2.

The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with sepsis.

BACKGROUND: In this study, we aimed to perform a comprehensive analysis on the metagenomic next-generation sequencing for the etiological diagnosis of septic patients, and further to establish optimal read values for detecting common pathogens. METHODS: In this single-center retrospective study, septic patients who underwent pathogen detection by both microbial culture and metagenomic next-generation sequencing in the intensive care unit of the Second People's Hospital of Shenzhen from June 24, 2015, to October 20, 2019, were included. RESULTS: A total of 193 patients with 305 detected specimens were included in the final analysis. The results of metagenomic next-generation sequencing showed significantly higher positive rates in samples from disparate loci, including blood, bronchoalveolar lavage fluid, and cerebrospinal fluid, as well as in the determination of various pathogens. The optimal diagnostic reads were 2893, 1825.5, and 892.5 for Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, respectively. CONCLUSIONS: The metagenomic next-generation sequencing is capable of identifying multiple pathogens in specimens from septic patients, and shows significantly higher positive rates than culture-based diagnostics. The optimal diagnostic reads for frequently detected microbes might be useful for the clinical application of metagenomic next-generation sequencing in terms of timely and accurately determining etiological pathogens for suspected and confirmed cases of sepsis due to well-performed data interpretation.

Unambiguous Stereochemical Assignment of Cyclo(Phe-Pro), Cyclo(Leu-Pro), and Cyclo(Val-Pro) by Electronic Circular Dichroic Spectroscopy.

2,5-diketopiperazines (DKPs) are cyclic dipeptides ubiquitously found in nature. In particular, cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro) are frequently detected in many microbial cultures. Each of these DKPs has four possible stereoisomers due to the presence of two chirality centers. However, absolute configurations of natural DKPs are often ambiguous due to the lack of a simple, sensitive, and reproducible method for stereochemical assignment. This is an important problem because stereochemistry is a key determinant of biological activity. Here, we report a synthetic DKP library containing all stereoisomers of cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro). The library was subjected to spectroscopic characterization using mass spectrometry, NMR, and electronic circular dichroism (ECD). It turned out that ECD can clearly differentiate DKP stereoisomers. Thus, our ECD dataset can serve as a reference for unambiguous stereochemical assignment of cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro) samples from natural sources. The DKP library was also subjected to a biological screening using assays for E. coli growth and biofilm formation, which revealed distinct biological effects of cyclo(D-Phe-L-Pro).

Comparison of bacterial culture results collected via direct corneal ulcer vs conjunctival fornix sampling in canine eyes with presumed bacterial ulcerative keratitis.

OBJECTIVE: To compare aerobic bacterial culture results between samples obtained from the corneal ulcer versus lower conjunctival fornix in eyes with presumed bacterial ulcerative keratitis. ANIMALS STUDIED: Fifty five client-owned dogs diagnosed with ulcerative keratitis. PROCEDURES: Ophthalmic examinations were performed on each dog including slit-lamp biomicroscopy and indirect ophthalmoscopy. Microbial swabs were collected by direct sampling of the infected corneal ulcer as well as the lower conjunctival fornix, of the same eye, using a sterile rayon-tipped swab. Samples were submitted to an outside reference laboratory for aerobic bacterial culture and sensitivity. RESULTS: One hundred twelve samples were obtained from 56 eyes (55 dogs). Sixty-eight samples yielded bacterial growth. Positive growth from both sites was obtained in 31 eyes (55%). Six eyes yielded bacterial growth from the conjunctival fornix but not from the cornea. No bacterial growth was obtained from either sampling site in 19 eyes. Overall, 31/56 (55%) corneal samples were positive and 37/56 (66%) conjunctival fornix samples were positive. Comparison of organisms isolated from the two collection sites of the same eye revealed an exact correlation in 42/56 (75%) eyes and differed in 14/56 (25%) eyes. Twenty different bacterial isolates were obtained from 68 positive samples. Gram-positive (71%) organisms were more common than Gram-negative (29%). The most commonly isolated organisms were Staphylococcus pseudintermedius (25%), beta-hemolytic Streptococcus spp. (23%), and Pseudomonas aeruginosa (12%). Methicillin-resistant organisms were isolated in 9% of samples. CONCLUSION: Sampling from the conjunctival fornix may be a suitable alternative to direct ulcer sampling in eyes with compromised corneal structural integrity.

The Biological Threat: The Threat of Planetary Quarantine Failure as a Result of Outer Space Exploration by Humans.

The paper presents the results of experiments with spore-forming bacteria and microscopic fungi performed in the framework of the Russian Research Program outside the International Space Station. It has been found that microorganisms not only survive in this extreme environment, but also retain reproductive ability. Moreover, most microorganisms exhibit an increase in biochemical activity and resistance to antimicrobial agents, specifically antibiotics. These findings are of obvious interest to the developers of both planetary quarantine methods and biomedical safety systems for manned space exploration missions. In addition, they demonstrate the necessity of experiments on the exposure of bio-objects to simulated environmental factors beyond Earth's magnetosphere.

Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study.

BACKGROUND: The human small intestine plays a central role in the processes of digestion and nutrient absorption. However, characterizations of the human gut microbiome have largely relied on stool samples, and the associated methodologies are ill-suited for the viscosity and low microbial biomass of small intestine samples. As part of the REIMAGINE study to examine the specific roles of the small bowel microbiome in human health and disease, this study aimed to develop and validate methodologies to optimize microbial analysis of the small intestine. RESULTS: Subjects undergoing esophagogastroduodenoscopy without colon preparation for standard of care were prospectively recruited, and ~ 2 ml samples of luminal fluid were obtained from the duodenum using a custom sterile aspiration catheter. Samples of duodenal aspirates were either untreated (DA-U, N = 127) or pretreated with dithiothreitol (DA-DTT, N = 101), then cultured on MacConkey agar for quantitation of aerobic gram-negative bacteria, typically from the class Gammaproteobacteria, and on blood agar for quantitation of anaerobic microorganisms. DA-DTT exhibited 2.86-fold greater anaerobic bacterial counts compared to DA-U (P = 0.0101), but were not statistically different on MacConkey agar. DNA isolation from DA-U (N = 112) and DA-DTT (N = 43) samples and library preparation for 16S rRNA gene sequencing were also performed using modified protocols. DA-DTT samples exhibited 3.81-fold higher DNA concentrations (P = 0.0014) and 4.18-fold higher 16S library concentrations (P < 0.0001) then DA-U samples. 16S rRNA gene sequencing revealed increases in the detected relative abundances of obligate and facultative anaerobes in DA-DTT samples, including increases in the genera Clostridium (false discovery rate (FDR) P = 4.38E-6), Enterococcus (FDR P = 2.57E-8), Fusobacterium (FDR P = 0.02) and Bacteroides (FDR P = 5.43E-9). Detected levels of Gram-negative enteropathogens from the phylum Proteobacteria, such as Klebsiella (FDR P = 2.73E-6) and Providencia (FDR P < 0.0001) (family Enterobacteriaceae) and Pseudomonas (family Pseudomonadaceae) (FDR P = 0.04), were also increased in DA-DTT samples. CONCLUSIONS: This study validates novel DTT-based methodology which optimizes microbial culture and 16S rRNA gene sequencing for the study of the small bowel microbiome. The microbial analyses indicate increased isolation of facultative and obligate anaerobes from the mucus layer using these novel techniques.

Medium Chain Carboxylic Acids from Complex Organic Feedstocks by Mixed Culture Fermentation.

Environmental pressures caused by population growth and consumerism require the development of resource recovery from waste, hence a circular economy approach. The production of chemicals and fuels from organic waste using mixed microbial cultures (MMC) has become promising. MMC use the synergy of bio-catalytic activities from different microorganisms to transform complex organic feedstock, such as by-products from food production and food waste. In the absence of oxygen, the feedstock can be converted into biogas through the established anaerobic digestion (AD) approach. The potential of MMC has shifted to production of intermediate AD compounds as precursors for renewable chemicals. A particular set of anaerobic pathways in MMC fermentation, known as chain elongation, can occur under specific conditions producing medium chain carboxylic acids (MCCAs) with higher value than biogas and broader applicability. This review introduces the chain elongation pathway and other bio-reactions occurring during MMC fermentation. We present an overview of the complex feedstocks used, and pinpoint the main operational parameters for MCCAs production such as temperature, pH, loading rates, inoculum, head space composition, and reactor design. The review evaluates the key findings of MCCA production using MMC, and concludes by identifying critical research targets to drive forward this promising technology as a valorisation method for complex organic waste.

[Diagnostic performance of pathology, culture and ROSE of lung biopsy for suspected pulmonary infectious diseases].

Objective: To explore the diagnostic performance of CT guided percutaneous lung biopsy (PTLB) with pathology, culture and rapid on-site evaluation (ROSE) in patients with pulmonary infectious diseases. Methods: From January 2016 to June 2018, a retrospective study was implemented in the Department of Pulmonary and Critical Care Medicine of the First Affiliated Hospital of Wenzhou Medical University. Patients who received PTLB, suspected with lung infection were included. The basic information, clinical symptoms, imaging findings, diagnostic methods, complications, and changes in treatment of cases were collected. The diagnostic sensitivity of histopathology, microbial culture, and ROSE were evaluated at the same time. Results: A total of 529 cases were enrolled, including 354 males and 175 females, (59±14) years old in average. Tuberculosis was identified in 197 cases, non-tuberculosis mycobacteria (NTM) pulmonary disease in 8, cryptococcosis in 95, pulmonary aspergillosis in 27, filamentous fungal pneumonia in 3, talaromyces marneffei pulmonary infection in 3 and pulmonary candidiasis in 1, bacterial pneumonia in 39, and pathogen were unknown in 156 cases. A total of 417 cases were submitted for histopathology and microbial culture at the same time, the diagnostic value of pathology and microbial culture were 35.0% (146/417) and 45.6% (190/417), respectively. Combined pathology with microbial culture, the diagnostic value increased to 62.8% (262/417). The diagnostic accuracy of ROSE was 51.8% (71/137). The most common complication of PTLB was pneumothorax 26.1% (138/529). 56.1% (297/529) of the patients received targeted treatment after the diagnosis was confirmed, and 43.9% (232/529) maintained the original treatment. Conclusion: The pathology, microbial culture, and ROSE of PTLB have relative high diagnostic value for pulmonary infectious diseases.

Co-digestion of Biowastes to Enhance Biological Hydrogen Process by Defined Mixed Bacterial Cultures.

Co-digestion of biowastes for hydrogen (H2) production using defined mixed cultures can overcome the high risk of failure due to contamination and imbalanced nutrient status. H2 production from biowastes-pea-shells, potato peels (PP), onion peels (OP) and apple pomace, either individually or in various combinations was evaluated by hydrolyzing with defined hydrolytic mixed bacterial culture (MHC5) and subjecting the hydrolysate to mixture of defined H2 producers (MMC6). Co-digestion of OP and PP hydrolysate supplemented at H2 production stage with GM-2 and M-9 media resulted in 95 and 102 l H2/kg of Total solids (TS), respectively compared to 84 l H2/kg of TS in control. Upscaling the process by digesting 4.0 l slurry (16-fold) resulted in 88.5 and 95 l H2/kg of TS, respectively compared to 72 l H2/kg of TS in control. Thus, H2 production by co-digestion of biowastes could be improved through the supplementation with very dilute medium (0.1 ×) and selection of suitable biowastes under unsterile conditions. The overall efficiency can be further enhanced by integrating it with bioprocesses for biopolymers such as polyhydroxyalkanoates and or biofuels like methane production.

The diagnosis of chronic endometritis in infertile asymptomatic women: a comparative study of histology, microbial cultures, hysteroscopy, and molecular microbiology.

BACKGROUND: Chronic endometritis is a persistent inflammation of the endometrial mucosa caused by bacterial pathogens such as Enterobacteriaceae, Enterococcus, Streptococcus, Staphylococcus, Mycoplasma, and Ureaplasma. Although chronic endometritis can be asymptomatic, it is found in up to 40% of infertile patients and is responsible for repeated implantation failure and recurrent miscarriage. Diagnosis of chronic endometritis is based on hysteroscopy of the uterine cavity, endometrial biopsy with plasma cells being identified histologically, while specific treatment is determined based on microbial culture. However, not all microorganisms implicated are easily or readily culturable needing a turnaround time of up to 1 week. OBJECTIVE: We sought to develop a molecular diagnostic tool for chronic endometritis based on real-time polymerase chain reaction equivalent to using the 3 classic methods together, overcoming the bias of using any of them alone. STUDY DESIGN: Endometrial samples from patients assessed for chronic endometritis (n = 113) using at least 1 or several conventional diagnostic methods namely histology, hysteroscopy, and/or microbial culture, were blindly evaluated by real-time polymerase chain reaction for the presence of 9 chronic endometritis pathogens: Chlamydia trachomatis, Enterococcus, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Mycoplasma hominis, Neisseria gonorrhoeae, Staphylococcus, and Streptococcus. The sensitivity and specificity of the molecular analysis vs the classic diagnostic techniques were compared in the 65 patients assessed by all 3 recognized classic methods. RESULTS: The molecular method showed concordant results with histological diagnosis in 30 samples (14 double positive and 16 double negative) with a matching accuracy of 46.15%. Concordance of molecular and hysteroscopic diagnosis was observed in 38 samples (37 double positive and 1 double negative), with an accuracy of 58.46%. When the molecular method was compared to microbial culture, concordance was present in 37 samples (22 double positive and 15 double negative), a matching rate of 56.92%. When cases of potential contamination and/or noncultivable bacteria were considered, the accuracy increased to 66.15%. Of these 65 patients, only 27 patients had consistent histological + hysteroscopic diagnosis, revealing 58.64% of nonconcordant results. Only 13 of 65 patients (20%) had consistent histology + hysteroscopy + microbial culture results. In these cases, the molecular microbiology matched in 10 cases showing a diagnostic accuracy of 76.92%. Interestingly, the molecular microbiology confirmed over half of the isolated pathogens and provided additional detection of nonculturable microorganisms. These results were confirmed by the microbiome assessed by next-generation sequencing. In the endometrial samples with concordant histology + hysteroscopy + microbial culture results, the molecular microbiology diagnosis demonstrates 75% sensitivity, 100% specificity, 100% positive and 25% negative predictive values, and 0% false-positive and 25% false-negative rates. CONCLUSION: The molecular microbiology method describe herein is a fast and inexpensive diagnostic tool that allows for the identification of culturable and nonculturable endometrial pathogens associated with chronic endometritis. The results obtained were similar to all 3 classic diagnostic methods together with a degree of concordance of 76.92% providing an opportunity to improve the clinical management of infertile patients with a risk of experiencing this ghost endometrial pathology.

Nanoparticles in Biological Hydrogen Production: An Overview.

Biological hydrogen (H2) production enhancement through the use of nanoparticles (NPs) supplement in the media is being recognized as a promising approach. The NPs, including those of metal and metal oxides have shown a significant improvement in the BHP. A number of organisms as pure or mixed cultures can produce H2 in presence of NPs from pure sugars and biowaste as a feed. However, their H2 production efficiencies have been found to vary significantly with the type of NPs and their concentration. In this review article, the potential role of NPs in the enhancement of H2 production has been assessed in dark- and photo-fermentative organisms using sugars and biowaste materials as feed. Further, the integrative approaches for commercial applications of NPs in BHP have been discussed.

Letter to the editor on 'The necessity of overhaul in perception of microbiological culture methods'.

Unarguably, clinical microbiology has got a boost from NGS technology, but in the process of this transition it has suffered a huge setback. Computational biology can find the microbial genomic variations and can link it to drug resistance, but it has so far underestimated the crucial role of microbial culture medium. The constituents and growth conditions of the medium have been documented to shuffle genomic, epigenetic and metabolic aspects of the bacterial pathogens. Ignoring these in vitro-driven evolutions and attributing the variations as normal bacterial features, responsible for drug resistance is a huge mistake. Unfortunately, it has been the trend since the inception of NGS in microbiology arena. No wonder, drug resistance is spreading unrestrained like wildfire and drug discovery is lagging behind. The urgent need to standardize culture medium by simulating it to human physiological conditions can salvage the situation and result in correct interpretations.