MOBFinder: a tool for mobilization typing of plasmid metagenomic fragments based on a language model.

BACKGROUND: Mobilization typing (MOB) is a classification scheme for plasmid genomes based on their relaxase gene. The host ranges of plasmids of different MOB categories are diverse, and MOB is crucial for investigating plasmid mobilization, especially the transmission of resistance genes and virulence factors. However, MOB typing of plasmid metagenomic data is challenging due to the highly fragmented characteristics of metagenomic contigs. RESULTS: We developed MOBFinder, an 11-class classifier, for categorizing plasmid fragments into 10 MOB types and a nonmobilizable category. We first performed MOB typing to classify complete plasmid genomes according to relaxase information and then constructed an artificial benchmark dataset of plasmid metagenomic fragments (PMFs) from those complete plasmid genomes whose MOB types are well annotated. Next, based on natural language models, we used word vectors to characterize the PMFs. Several random forest classification models were trained and integrated to predict fragments of different lengths. Evaluating the tool using the benchmark dataset, we found that MOBFinder outperforms previous tools such as MOBscan and MOB-suite, with an overall accuracy approximately 59% higher than that of MOB-suite. Moreover, the balanced accuracy, harmonic mean, and F1-score reached up to 99% for some MOB types. When applied to a cohort of patients with type 2 diabetes (T2D), MOBFinder offered insights suggesting that the MOBF type plasmid, which is widely present in Escherichia and Klebsiella, and the MOBQ type plasmid might accelerate antibiotic resistance transmission in patients with T2D. CONCLUSIONS: To the best of our knowledge, MOBFinder is the first tool for MOB typing of PMFs. The tool is freely available at https://github.com/FengTaoSMU/MOBFinder.

Varicella­zoster virus­associated meningitis followed peripheral facial palsy: A case report.

Although central nervous system infection following varicella zoster virus infection is relatively common, subsequent peripheral nervous system infection is comparatively rare. The present case documents a case of meningitis after varicella-zoster virus (VZV) infection, which was then followed by peripheral facial palsy. Specifically, a 54-year-old female patient was first admitted to Shengli Oilfield Central Hospital (Dongying, China) with headache and fever. Physical examination revealed herpes that formed along the intercostal nerve in the left forebreast, armpit and back. Subsequently, neurological examination found cervical resistance in more than three fingers (neck resistance of less than two transverse fingers is not evidence of meningeal irritation; the neck resistance of this patient was approximately three transverse fingers, so the patient was presumed to be positive for meningeal irritation, highly suggestive of meningitis) and Kernig sign was positive. There were no significant abnormalities according to brain MRI and lumbar puncture pressure was 330 mmH2O. In addition, the leukocyte count was 734x106/l, 50% monocyte count, 50% multinucleated cells, chloride levels of 109.1 mmol/l, protein levels of 235 mg/dl and glucose levels of 4.18 mmol/l in the cerebrospinal fluid. DNA and RNA metagenomic detection of pathogenic microorganisms in the cerebrospinal fluid revealed the presence of VZV. The patient was therefore treated with acyclovir, ceftriaxone, mannitol and methylprednisolone, but then developed right peripheral facial palsy at 10 days after treatment. This complication was not found in the literature, and the occurrence of facial neuritis was unexpected. The active period of VZV virus was 21 days, and the patient had herpes 5 days before admission. The active period of the virus was considered to have subsided and the patient was in the recovery period. Moreover, the results of lumbar puncture showed that the white blood cells, the proportion of neutrophils and the protein in cerebrospinal fluid were all decreasing, which also indicated that the patient had entered the recovery period. The patient was discharged 18 days after admission. In conclusion, observations from the present case suggested that the clinical manifestations of VZV infection can be complex and varied, requiring the clinician to have an accurate understanding of its disease progression and treatment.

Immunology of bile acids regulated receptors.

Bile acids are steroids formed at the interface of host metabolism and intestinal microbiota. While primary bile acids are generated in the liver from cholesterol metabolism, secondary bile acids represent the products of microbial enzymes. Close to 100 different enzymatic modifications of bile acids structures occur in the human intestine and clinically guided metagenomic and metabolomic analyses have led to the identification of an extraordinary number of novel metabolites. These chemical mediators make an essential contribution to the composition and function of the postbiota, participating to the bidirectional communications of the intestinal microbiota with the host and contributing to the architecture of intestinal-liver and -brain and -endocrine axes. Bile acids exert their function by binding to a group of cell membrane and nuclear receptors collectively known as bile acid-regulated receptors (BARRs), expressed in monocytes, tissue-resident macrophages, CD4+ T effector cells, including Th17, T regulatory cells, dendritic cells and type 3 of intestinal lymphoid cells and NKT cells, highlighting their role in immune regulation. In this review we report on how bile acids and their metabolitesmodulate the immune system in inflammations and cancers and could be exploiting for developing novel therapeutic approaches in these disorders.

Composition and metabolic flexibility of hydrocarbon-degrading consortia in oil reservoirs.

Hydrocarbon-degrading consortia (HDC) play an important role in petroleum exploitation. However, the real composition and metabolic mechanism of HDC in the microbial enhanced oil recovery (MEOR) process remain unclear. By combining 13C-DNA stable isotope probing microcosms with metagenomics, some newly reported phyla, including Chloroflexi, Synergistetes, Thermotogae, and Planctomycetes, dominated the HDC in the oil reservoirs. In the field trials, the HDC in the aerobic-facultative-anaerobic stage of oilfields jointly promoted the MEOR process, with monthly oil increments of up to 189 tons. Pseudomonas can improve oil recovery by producing rhamnolipid in the facultative condition. Roseovarius was the novel taxa potentially oxidizing alkane and producing acetate to improve oil porosity and permeability in the aerobic condition. Ca. Bacteroidia were the new members potentially degrading hydrocarbons by fumarate addition in the anaerobic environment. Comprehensive identification of the active HDC in oil reservoirs provides a novel theoretical basis for oilfield regulatory scheme.

Meta-genomic next-generation sequencing in the diagnosis of brucellosis: Five cases from a non-endemic area.

Metagenomic next-generation sequencing (mNGS) in diagnosis of human brucellosis is comparatively unexplored. This report details five human brucellosis cases diagnosed using mNGS based on Illumina sequencing platform, comprising three females and two males, four with epidemiological exposure. In cases 1 and 2, plasma mNGS results showed one positive and one negative for Brucella melitensis, and subsequent blood cultures were both positive. Cases 3, 4 and 5 involved spinal brucellosis, some with paravertebral abscesses. mNGS from infectious tissue samples successfully detected Brucella, with read counts ranging between 30 and 1314, yet cultures were negative in cases 4 and 5. Following antibiotic and surgical treatments, all patients showed clinical improvement. This report shows mNGS testing enhances the detection sensitivity of brucellosis diagnosis.

What is this summary about? Brucella is a type of bacteria that can infect humans and animals. It causes a disease called brucellosis. Symptoms of brucellosis include fever and fatigue, among others. Meta-genomic next-generation sequencing (mNGS) is a tool for sequencing the DNA of bacteria. In this report, we use mNGS to diagnose human brucellosis in five cases.What were the results? Brucella was found in the blood of two infected people, but mNGS found Brucella in only one. Of three people with Brucella infection of the spine, mNGS found Brucella in the infected tissue but Brucella was only cultured in one case. Following antibiotic and surgical treatments, all five patients showed improvement of their symptoms.What do the results of the study mean? mNGS is a relatively rapid and effective diagnostic method that can improve the detection of Brucella in brucellosis.

Transformation and degradation of tebuconazole and its metabolites in constructed wetlands with arbuscular mycorrhizal fungi colonization.

Arbuscular mycorrhizal fungi (AMF) colonization has been used in constructed wetlands (CWs) to enhance treatment performance. However, its role in azole (fungicide) degradation and microbial community changes is not well understood. This study aims to explore the impact of AMF on the degradation of tebuconazole and its metabolites in CWs. Total organic carbon levels were consistently higher with the colonization of AMF (AMF+; 9.63- 16.37 mg/L) compared to without the colonization of AMF (AMF-; 8.79-14.48 mg/L) in CWs. Notably, tebuconazole removal was swift, occurring within one day in both treatments (p = 0.885), with removal efficiencies ranging from 94.10 % to 97.83 %. That's primarily due to rapid substrate absorption at the beginning, while degradation follows with a longer time. Four metabolites were reported in CWs first time: tebuconazole hydroxy, tebuconazole lactone, tebuconazole carboxy acid, and tebuconazole dechloro. AMF decreased the abundance of tebuconazole dechloro in the liquid phase, suggesting an inhibitory effect of AMF on dechlorination processes. Furthermore, tebuconazole carboxy acid and hydroxy were predominantly found in plant roots, with a higher abundance observed in AMF+ treatments. Metagenomic analysis highlighted an increasing abundance in bacterial community structure in favor of beneficial microorganisms (xanthomonadales, xanthomonadaceae, and lysobacter), along with a notable presence of functional genes like codA, NAD, and deaD in AMF+ treatments. These findings highlight the positive influence of AMF on tebuconazole stress resilience, microbial community modification, and the enhancement of bioremediation capabilities in CWs.

Magnetite encapsulated in carbon shell particles (Fe3O4@C) to boost anaerobic methanogenesis of chloramphenicol wastewater.

Magnetite (Fe3O4) is extensively applied to enhance efficacy of anaerobic biological treatment systems designed for refractory wastewater. However, the interaction between magnetite, organic pollutants and microorganisms in digestion solution is constrained by magnetic attraction. To overcome this limitation and prevent magnetite aggregation, the core-shell composite materials with carbon outer layer enveloping magnetite core particles (Fe3O4@C) were developed. The impact of Fe3O4@C with varying Fe3O4 mass ratios on the anaerobic methanogenesis capability in the treatment of chloramphenicol (CAP) wastewater was investigated. Experimental results demonstrated that Fe3O4@C not only enhanced chemical oxygen demand (COD) removal efficiency and biogas production by 2.42-13.18% and by 7.53%-23.25%, respectively, but also reduced the inhibition of microbial activity caused by toxic substances and the secretion of extracellular polymeric substances (EPS) by microorganisms responding to adverse environments. The reinforcing capability of Fe3O4@C increased with the rise in Fe3O4 content. Furthermore, High-throughput pyrosequencing illustrated that Fe3O4@C enhanced the relative abundance of Methanobacterium, a hydrogen-utilizing methanogen capable of participating in direct interspecies electron transfer (DIET), by 5%. Metagenomic analysis indicated that Fe3O4@C improved the decomposition of complex organics into simpler compounds by elevating functional genes encoding key enzymes associated with organic matter metabolism, acetogenesis, and hydrogenophilic methanogenesis pathways. These findings suggest that Fe3O4@C have the potential to strengthen both the hydrogenophilic methanogenesis and DIET processes. This insight offers a novel perspective on the anaerobic bioaugmentation of high-concentration refractory organic wastewater.

Lactobacillus inoculation mediated carboxylates and alcohols production from waste activated sludge fermentation system: Insight into process outcomes and metabolic network.

Producing medium chain fatty acids (MCFAs) from waste activated sludge (WAS) is crucial for sustainable chemical industries. This study addressed the electron donor requirement for MCFAs production by inoculating Lactobacillus at varying concentrations (7.94 × 1010, 3.18 × 1011, and 6.35 × 1011 cell/L) to supply lactate internally. Interestingly, the highest MCFAs yield (∼2000 mg COD/L) occurred at the lowest Lactobacillus inoculation. Higher inoculation concentrations redirected more carbon from WAS towards alcohols production rather than MCFAs generation, with up to 2852 mg COD/L alcohols obtained under 6.35 × 1011 cell/L inoculation. Clostridium dominance and increased genes abundance for substrate hydrolysis, lactate conversion, and MCFAs/alcohol production collectively enhanced WAS-derived MCFAs and alcohols synthesis after Lactobacillus inoculation. Overall, the strategy of Lactobacillus inoculation regulated fermentation outcomes and subsequent carbon recovery in WAS, presenting a sustainable technology to achieve liquid bio-energy production from underutilized wet wastes.

Microbial carbohydrate active enzyme (CAZyme) genes and diversity from Menagesha Suba natural forest soils of Ethiopia as revealed by shotgun metagenomic sequencing.

BACKGROUND: The global over-reliance on non-renewable fossil fuels has led to the emission of greenhouse gases, creating a critical global environmental challenge. There is an urgent need for alternative solutions like biofuels. Advanced biofuel is a renewable sustainable energy generated from lignocellulosic plant materials, which can significantly contribute to mitigating CO2 emissions. Microbial Carbohydrate Active Enzymes (CAZymes) are the most crucial enzymes for the generation of sustainable biofuel energy. The present study designed shotgun metagenomics approaches to assemble, predict, and annotate, aiming to gain an insight into the taxonomic diversity, annotate CAZymes, and identify carbohydrate hydrolyzing CAZymes from microbiomes in Menagesha suba forest soil for the first time. RESULTS: The microbial diversity based on small subunit (SSU) rRNA analysis revealed the dominance of the bacterial domain representing 81.82% and 92.31% in the studied samples. Furthermore, the phylum composition result indicated the dominance of the phyla Proteobacteria (23.08%, 27.27%), Actinobacteria (11.36%, 20.51%), and Acidobacteria (10.26%, 15.91%). The study also identified unassigned bacteria which might have a unique potential for biopolymer hydrolysis. The metagenomic study revealed that 100,244 and 65,356 genes were predicted from the two distinct samples. A total number of 1806 CAZyme genes were identified, among annotated CAZymes, 758 had a known enzyme assigned to CAZymes. Glycoside hydrolases (GHs) CAZyme family contained most of the CAZyme genes with known enzymes such as ß-glucosidase, endo-ß-1,4-mannanase, exo-ß-1,4-glucanase, α-L-arabinofuranosidase and oligoxyloglucan reducing end-specific cellobiohydrolase. On the other hand, 1048 of the identified CAZyme genes were putative CAZyme genes with unknown enzymatical activity and the majority of which belong to the GHs family. CONCLUSIONS: In general, the identified putative CAZymes genes open up an opportunity for the discovery of new enzymes responsible for hydrolyzing biopolymers utilized for biofuel energy generation. This finding is used as a first-hand piece of evidence to serve as a benchmark for further and comprehensive studies to unveil novel classes of bio-economically valuable genes and their encoded products.

Decolorization and detoxification of direct blue 5B by a Marinobacter-dominated halo-thermoalkalophilic consortium.

Azo dye-containing sewage is commonly detected at high salinity, temperature and pH. In this study, a halo-thermoalkalophilic azo dye decolorization consortium was enriched and named "consortium HL". Consortium HL which was dominated by Marinobacter (84.30%), Desulfocurvibacter (1.89%), and Pseudomonas (1.85%), was able to completely decolorize Direct Blue 5B (DB5) during incubation with the material at 5% salinity, 50 °C, and pH 9 for 30 h. The decolorization mechanism was proposed based on combined metagenomic analysis, GC‒MS, and enzymatic activity detection. The action of the consortium HL showed great tolerance to variations in salinity, temperature and pH. A phytotoxicity study indicated that the metabolic intermediates showed no significant toxicity to the generation of Cucumis sativus and Oryza sativa seeds. This study, in which azo dye decolorization and degradation under high-salt, high-temperature and high-alkalinity conditions were investigated and deeply analyzed by metagenomic information, is the first report regarding the ability of Marinobacter to decolorize azo dyes at high temperatures.

Case Report: Taking action or standing by: managing a preterm neonate at the risk of neonatal varicella by metagenomic next-generation sequencing.

Neonatal varicella is indeed a rare condition, and most infants born to mothers with varicella have a good prognosis. However, in exceptional cases, neonatal varicella can be life-threatening, particularly for preterm infants. Therefore, it is vital to make an early diagnosis or predict the risk of neonatal varicella to ensure prompt treatment and improve prognosis. This report made an effort to early predict neonatal vericalla by using metagenomic next-generation sequencing (mNGS) in a preterm infant who was at risk for vericalla infection. A preterm infant born from a mother with varicella with symptom onset at 8 days before delivery, putting the infant at risk for varicella infection. Importantly, the patient develop pneumonia and pneumothorax, and neonatal vericella was suspected. Fortunately, the use of mNGS for testing the varicella gene in the serum promptly ruled out varicella zoster virus (VZV) infection in the patient, as indicated by a negative mNGS result. Subsequent follow-up, which included a 14-day stay in the hospital followed by an additional 7 days at home, confirmed this finding. Throughout this period, the patient did not exhibit any rash or other symptoms associated with varicella. Therefore, the novel approach of using mNGS allows neonatologists to predict and promptly address potential neonatal infections. This early detection is crucial, as delayed diagnosis or treatment could pose life-threatening risks, as exemplified by the case of neonatal varicella. In such cases, neonatologists can take proactive measures instead of standing by for at-risk neonates. Furthermore, given the severity of neonatal varicella as a life-threatening condition, the early exclusion of subsequent varicella infection by mNGS can offer reassurance to both family members and healthcare professionals.

Whole-Genome Metagenomic Analysis of the Oral Microbiota in Patients with Obstructive Sleep Apnea Comorbid with Major Depressive Disorder.

Background: Obstructive sleep apnea (OSA) patients commonly experience high rates of depression. This study aims to examine the oral microbiota characteristics of OSA and those with comorbid major depressive disorder (OSA+MDD) patients. Methods: Participants were enrolled from Aug 2022 to Apr 2023. Polysomnography, psychiatrist interviews, and scales were used to diagnose OSA and MDD. Oral samples were collected from participants by rubbing swabs on buccal mucosa, palate, and gums. Oral microbiota was analyzed via whole-genome metagenomics and bioinformatic analysis followed sequencing. Venous blood was drawn to detect plasma inflammatory factor levels. Results: The study enrolled 33 OSA patients, 28 OSA+MDD patients, and 28 healthy controls. Significant differences were found in 8 phyla, 229 genera, and 700 species of oral microbiota among the three groups. Prevotellaceae abundance in the OSA and OSA+MDD groups was significantly lower than that in healthy controls. Linear discriminant analysis effect size (LEfSe) analysis showed that Streptococcaceae and Actinobacteria were the characteristic oral microbiota of the OSA and OSA+MDD groups, respectively. KEGG analysis indicates 30 pathways were changed in the OSA and OSA+MDD groups compared with healthy controls, and 23 pathways were changed in the OSA group compared with the OSA+MDD group. Levels of IL-6 in the OSA+MDD group were significantly higher than in the healthy group, correlating positively with the abundance of Schaalia, Campylobacter, Fusobacterium, Alloprevotella, and Candidatus Nanosynbacter in the oral, as well as with Hamilton Anxiety Rating Scale and Hamilton Depression Rating Scale scores. Conclusion: Significant differences in oral microbiota populations and gene function were observed among the three groups. OSA patients were characterized by a decreased abundance of Prevotellaceae and an increased abundance of Streptococcaceae. OSA+MDD patients had an increased abundance of Actinobacteria. IL-6 might regulate the relationship between depression and the oral microbiota in OSA+MDD patients.

Nitrogen removal pathways in lake restoration using microalgal-bacterial granular sludge: Unraveling influence of organics and C/N.

This study investigated the performance of microalgal-bacterial granular sludge (MBGS) in the restoration of Qingling Lake and Huangjia Lake, focusing on nitrogen removal under varying water quality conditions. Significant color changes in MBGS and differences in granule characteristics were observed, with Qingling Lake demonstrating superior removal efficiencies for ammonia nitrogen, nitrate nitrogen, and total nitrogen compared to Huangjia Lake. Stoichiometric analysis revealed that when the chemical oxygen demand (COD) and carbon-to-nitrogen (C/N) ratios were less than 20 mg/L and 20, respectively, assimilatory nitrate reduction was positively correlated with both, whereas denitrification was negatively correlated. Gene function analysis showed that Qingling Lake had a more active microbial community supporting efficient nitrogen metabolism. The findings highlighted the enormous potential of MBGS in lake restoration, demonstrating its ability to adapt to different COD concentrations and C/N ratios by altering its nitrogen removal pathways.

The dynamic relationship between skin microbiomes and personal care products: A comprehensive review.

Healthy skin reflects a healthy microbiome and vice versa. The contemporary society, marked by a sharp increase in skin irritation cases, has compelled researchers, dermatologists, and the cosmetics industry to investigate the correlation between skin microbiomes and the use of skincare products. Different cosmetics can change skin's normal flora to a varying degree -some changes can be detrimental, there are also instances where these alterations aid in restoring the skin microbiome. Previous studies using artificial skin models, metagenomic analysis, and culture-based approaches have suggested that skincare products play an important role in skin microbial alteration. This article assessed current knowledge on microbial shifts from daily use of various personal and skincare products. We have also introduced a readily applicable framework, synthesized from various observations, which can be employed to identify the normal skin microbiome and evaluate the impact of personal care and skincare products on it. We also discussed how lifestyle choice remake skin microbial makeup. Future studies are warranted to examine the effect of personal and skincare product usage on skin microbiome across various age groups, genders, and body sites with a multi-study approach.

Metagenomic analysis demonstrates distinct changes in the gut microbiome of Kawasaki diseases children.

Background: Kawasaki disease (KD) has been considered as the most common required pediatric cardiovascular diseases among the world. However, the molecular mechanisms of KD were not fully underlined, leading to a confused situation in disease management and providing precious prognosis prediction. The disorders of gut microbiome had been identified among several cardiovascular diseases and inflammation conditions. Therefore, it is urgent to elucidate the characteristics of gut microbiome in KD and demonstrate its potential role in regulating intravenous immunoglobulin (IVIG) resistance and coronary artery injuries. Methods: A total of 96 KD children and 62 controls were enrolled in the study. One hundred forty fecal samples had been harvested from KD patients, including individuals before or after IVIG treatment, with or without early coronary artery lesions and IVIG resistance. Fecal samples had been collected before and after IVIG administration and stored at -80°C. Then, metagenomic analysis had been done using Illumina NovaSeq 6000 platform. After that, the different strains and functional differences among comparisons were identified. Results: First, significant changes had been observed between KD and their controls. We found that the decrease of Akkermansia muciniphila, Faecalibacterium prausnitzii, Bacteroides uniformis, and Bacteroides ovatus and the increase of pathogenic bacteria Finegoldia magna, Abiotrophia defectiva, and Anaerococcus prevotii perhaps closely related to the incidence of KD. Then, metagenomic and responding functional analysis demonstrated that short-chain fatty acid pathways and related strains were associated with different outcomes of therapeutic efficacies. Among them, the reduction of Bacteroides thetaiotaomicron, the enrichment of Enterococcus faecalis and antibiotic resistance genes had been found to be involved in IVIG resistance of KD. Moreover, our data also revealed several potential pathogenetic microbiome of that KD patients with coronary artery lesions. Conclusion: These results strongly proved that distinct changes in the gut microbiome of KD and the dysfunction of gut microbiomes should be responsible for the pathogenesis of KD and significantly impact the prognosis of KD.

Severe community-acquired pneumonia caused by Chlamydia abortus in China: a case report.

Background: Chlamydia abortus causes abortions in ruminants; it can also cause miscarriages and stillbirths in pregnant women. However, it rarely causes pneumonia in humans. Here, we report a case of severe community-acquired pneumonia caused by C. abortus. Case presentation: On admission to our hospital, a 74-year-old woman reported that she had had a fever, cough, phlegm in her throat, and shortness of breath for 10 days. In the local hospital, she was initially diagnosed with community-acquired pneumonia and treated with piperacillin-tazobactam for 4 days. However, her condition worsened, and she was therefore transferred to our hospital. On arrival at our emergency department, she was diagnosed with severe community-acquired pneumonia and treated with a high-flow nasal cannula and meropenem; she was then transferred to the Department of Respiratory Medicine. There, her condition continued to worsen despite continued treatment with the high-flow nasal cannula and omadacycline. After 24 h and emergency tracheal intubation, the patient was sent to the intensive care unit (ICU) for further treatment. The doctors in the ICU again adjusted the treatment, this time to meropenem along with mechanical ventilation; they also instituted methylprednisolone, ulinastatin, nadroparin calcium, and human immunoglobulin. In addition, bronchoalveolar lavage fluid was sent for metagenomic next-generation sequencing (mNGS). Subsequent mNGS suggested the presence of C. abortus, sequence number 5072; we therefore discontinued the meropenem and implemented a combination of doxycycline and moxifloxacin. After 8 days of treatment in the ICU, the patient's condition improved; she was then extubated and, 3 days later, transferred back to the respiratory medicine department. The respiratory physician continued to administer doxycycline and moxifloxacin for 4 days, after which the patient was discharged with medication. A month later, a repeat computed tomography (CT) scan of the chest suggested that the lesions in both lungs had been largely absorbed. Conclusion: C. abortus can occasionally cause pneumonia in humans and, rarely, severe, life-threatening pneumonia. mNGS is uniquely suited for the early detection of this unusual infection. The combination of doxycycline and quinolones has been shown to be effective in severe pneumonia caused by C. abortus.

A case report of acute Q fever with low-read detection of Coxiella burnetii genome by next-generation metagenomic sequencing.

The case presents a 47-year-old man with sudden abdominal pain and fever, but the cause was uncertain. Through metagenomic next-generation sequencing (mNGS) and detecting Q fever antibodies in serum, along with the patient's clinical and epidemiological history, a precise diagnosis was made, enabling timely and proper treatment.

Decreasing light exposure increases the abundance of antibiotic resistance genes in the cecum and feces of laying hens.

The gut microbiome plays a crucial role in maintaining animal health and is influenced by various factors, including light exposure; however, the response in laying hens of the gut microbiome to intermittent light regimes and the related impact on antibiotic resistance genes (ARGs) remain poorly understood. In this study, we divided 20-week-old laying hens into two groups. These groups were exposed to either continuous normal light or intermittent light for 8 weeks. The feces and cecal contents of laying hens were collected for analysis. Metagenomic analysis of both feces and cecal content samples revealed significant shifts in the microbial composition and abundance of ARGs under intermittent light exposure compared to normal light exposure (P < 0.05). Furthermore, metabolomic analysis of the cecal contents revealed substantial alterations in the abundance and composition of ARGs and mobile genetic elements (MGEs) in response to intermittent light exposure (P < 0.05). Network analysis revealed intricate co-occurrence patterns among bacterial communities, metabolites, and ARGs, highlighting correlations between Bacteroidetes species, ARGs, and metabolites. Although certain bacterial species showed differential associations, the dominant bacteria carrying ARGs or MGEs had relatively low numbers, suggesting that other bacterial communities may have had a greater influence on ARG dissemination. Moreover, our observations highlight the crucial role of metabolites as mediators between bacterial communities and ARGs, providing novel insights into the dynamics of antibiotic resistance development. Our findings underscore the impact of intermittent light exposure on ARG proliferation in poultry farming and emphasize interconnections among ARGs, bacterial communities, and metabolic pathways. The results underscore the importance of considering both microbial communities and metabolic processes to understand antibiotic resistance in agricultural settings.

Sequencing Methods to Study the Microbiome with Antibiotic Resistance Genes in Patients with Pulmonary Infections.

Various antibiotic-resistant bacteria (ARB) are known to induce repeated pulmonary infections and increase morbidity and mortality. A thorough knowledge of antibiotic resistance is imperative for clinical practice to treat resistant pulmonary infections. In this study, we used a reads-based method and an assembly-based method according to the metagenomic next-generation sequencing (mNGS) data to reveal the spectra of ARB and corresponding antibiotic resistance genes (ARGs) in samples from patients with pulmonary infections. A total of 151 clinical samples from 144 patients with pulmonary infections were collected for retrospective analysis. The ARB and ARGs detection performance was compared by the reads-based method and assembly-based method with the culture method and antibiotic susceptibility testing (AST), respectively. In addition, ARGs and the attribution relationship of common ARB were analyzed by the two methods. The comparison results showed that the assembly-based method could assist in determining pathogens detected by the reads-based method as true ARB and improve the predictive capabilities (46% > 13%). ARG-ARB network analysis revealed that assembly-based method could promote determining clear ARGbacteria attribution and 101 ARGs were detected both in two methods. 25 ARB were obtained by both methods, of which the most predominant ARB and its ARGs in the samples of pulmonary infections were Acinetobacter baumannii (ade), Pseudomonas aeruginosa (mex), Klebsiella pneumoniae (emr), and Stenotrophomonas maltophilia (sme). Collectively, our findings demonstrated that the assembly-based method could be a supplement to the reads-based method and uncovered pulmonary infection-associated ARB and ARGs as potential antibiotic treatment targets.

The Relationship between Microbial Communities in Coffee Fermentation and Aroma with Metabolite Attributes of Finished Products.

Coffee is a critical agricultural commodity and is used to produce premium beverages enjoyed by people worldwide. The microbiome of coffee beans has proven to be an essential tool that improves the flavor profile of coffee by creating aromatic flavor compounds through natural fermentation. This study investigated the natural microbial consortium during the wet process fermentation of coffee onsite in Thailand in order to identify the correlation between microbial diversity and biochemical characteristics including flavor, aroma, and metabolic attributes. Our study found 64 genera of bacteria and 59 genera of yeast/fungi present during the fermentation process. Group of microbes, mainly yeast and lactic acid bacteria, that predominated in the process were significantly correlated with preferable flavor and aroma compounds, including linalyl formate, linalool, cis-isoeugenol, trans-geraniol, and (-)-isopulegol. Some of the detected metabolites were found to be active compounds which could play a role in health.