Characteristics of intestinal flora in patients with cerebral infarction complicated with Type 2 diabetes mellitus / 中南大学学报(医学版)

OBJECTIVES@#The intestinal microbial characteristics of patients with simple cerebral infarction (CI) and CI complicated with Type 2 diabetes mellitus (CI-T2DM) are still not clear. This study aims to analyze the differences in the variable characteristics of intestinal flora between patients simply with CI and CI-T2DM.@*METHODS@#This study retrospectively collected the patients who were admitted to the Affiliated Hospital of Putian University from September 2021 to September 2022. The patients were divided into a CI group (n=12) and a CI-T2DM group (n=12). Simultaneously, 12 healthy people were selected as a control group. Total DNA was extracted from feces specimens. Illumina Novaseq sequencing platform was used for metagenomic sequencing. The Knead Data software, Kraken2 software, and Bracken software were applied for sequencing analysis.@*RESULTS@#At phylum level, the average ratio of Firmicutes, Bacteroidetes, and Proteobacteria in the CI-T2DM group were 33.07%, 54.80%, and 7.00%, respectively. In the CI group, the ratios of each were 14.03%, 69.62%, and 11.13%, respectively, while in the control group, the ratios were 50.99%, 37.67%, and 5.24%, respectively. There was significant differences in the distribution of Firmicutes (F=6.130, P=0.011) among the 3 groups. At the family level, compared with the CI group, the relative abundance of Eubacteriaceae (t=8.062, P<0.001) in the CI-T2DM group was significantly increased, while Corynebacteriaceae (t=4.471, P<0.001), Methanobacteriaceae (t=3.406, P=0.003), and Pseudomonadaceae (t=2.352, P=0.028) were decreased significantly. At the genus level, compared with the CI group, there was a relative abundance of Cutibacterium (t=6.242, P<0.001), Eubacterium (t=8.448, P<0.001), and Blautia (t=3.442, P=0.002) in the CI-T2DM group which was significantly increased. In terms of Methanobrevibacter (t=3.466, P=0.002), Pyramidobacter (t=2.846, P=0.009) and Pseudomonas (t=2.352, P=0.028), their distributions were decreased significantly in the CI-T2DM group. At the species level, compared with the CI group, the relative abundance of Cutibacterium acnes (t=6.242, P<0.001) in the CI-T2DM group was significantly increased, while Pseudomonas aeruginosa (t=2.352, P=0.028) was decreased significantly. Still at the genus level, linear discriminant analysis effect size (LEfSe) analysis showed that the distributions of Pseudomonas and Blautia were determined to be the most significantly different between the CI-T2DM and the CI group. At the species level, the total number of operational taxonomic units (OTUs) in the 3 groups was 1 491. There were 169, 221, and 192 kinds of OTUs unique to the CI-T2DM, CI, and control group, respectively.@*CONCLUSIONS@#From phylum level to species level, the composition of intestinal flora in the patients with CI-T2DM is different from those in the patients simply with CI. The change in the proportion of Firmicutes, Bacteroidetes and Proteus compared with the healthy population is an important feature of intestinal flora imbalance in the patients with CI and with CI-T2DM. Attention should be paid to the differential distribution of Bacteroides monocytogenes and butyrate producing bacteria.

Gut microbiota and immune checkpoint inhibitor treatment of melanoma / 中华皮肤科杂志

A growing number of studies have shown that gut microbiota affects the development of melanoma through various mechanisms, and plays a vital role in the treatment of melanoma. This review summarizes the relationship between gut microbiota and the development of melanoma, the effect of gut microbiota on the checkpoint blockade immunotherapy of melanoma and related adverse effects.

Perturbations in gastrointestinal tract microbiota composition and function in individuals with yellow-greasy tongue coating / 数字中医药（英文）

@#【Objective】  To study the composition and function of tongue coating (TC) and gastrointestinal tract (GIT) microbiota in participants with yellow-greasy tongue coating (YGTC), and to explore the representative metabolite markers and pathways in this group. 【Methods】  Subjects with YGTC or thin-white tongue coating (TWTC) were recruited from December 1, 2021 to October 30, 2022, and the TC and fecal samples were collected. Samples were subjected to both whole-genome shotgun (WGS), and 16S rRNA gene sequencing. The α-diversity analysis, principal component analysis (PCA), and Spearman correlation analysis were performed for two groups. Ultra-performance liquid chromatography combined with tandem mass spectrometry (UPLC–MS/MS) analysis was used to analyze metabolomics and enrichment of metabolic pathways. 【Results】  The results revealed 20 YGTC participates and 19 TWTC participates. At the genus level, the dominant bacterial species of TC flora and intestinal flora in the two groups were roughly the same, but the relative kurtosis difference was marked, and the abundance of potentially pathogenic bacteria in TC and fecal samples of YGTC subjects was higher. There were 9 down-regulated microorganisms in the TC samples, 26 down-regulated microorganisms, and 6 up-regulated microorganisms in YGTC subjects. The α-diversity analysis indicated that the Chao and abundance-based coverage estimator (ACE) indices of TC bacteria in the YGTC subjects showed a decreasing trend, but the difference was not statistically significant (P > 0.05). The α-diversity of fecal samples and the Chao and ACE indices decreased significantly (P < 0.05). PCA showed that the microflora structure of TC and fecal samples were significantly different between the two groups. Spearman correlation analysis showed that there was no correlation between TC and fecal microorganisms at phyla and genus levels in the same subjects (P > 0.05). The metabolomics results demonstrated that fumarate reductase, V/A ATPase, and phosphatidylethanolamine were increased, and glycerate-3p, UDP-glucose, and quinone oxidoreductase metabolites were decreased in YGTC TC samples. Inosine monophosphate (IMP), uridine monophosphate (UMP), and gamma-aminobutyric acid(GABA) were increased in YGTC fecal samples, while the contents of ribo-5P, histidine, biotin,and cobalamin were decreased. Metabolic pathway analysis indicated that the abundance of the TC and fecal samples of the YGTC subjects was relatively low in various metabolic pathways, including amino acid metabolism, carbohydrate metabolism, nitrogen metabolism, and energy metabolism. 【Conclusion】  Structural and functional changes in TC and GIT microbiota or metabolite markers could be potential biological bases of YGTC formation.

The best practice for microbiome analysis using R

With the gradual maturity of sequencing technology, many microbiome studies have published, driving the emergence and advance of related analysis tools. R language is the widely used platform for microbiome data analysis for powerful functions. However, tens of thousands of R packages and numerous similar analysis tools have brought major challenges for many researchers to explore microbiome data. How to choose suitable, efficient, convenient, and easy-to-learn tools from the numerous R packages has become a problem for many microbiome researchers. We have organized 324 common R packages for microbiome analysis and classified them according to application categories (diversity, difference, biomarker, correlation and network, functional prediction, and others), which could help researchers quickly find relevant R packages for microbiome analysis. Furthermore, we systematically sorted the integrated R packages (phyloseq, microbiome, MicrobiomeAnalystR, Animalcules, microeco, and amplicon) for microbiome analysis, and summarized the advantages and limitations, which will help researchers choose the appropriate tools. Finally, we thoroughly reviewed the R packages for microbiome analysis, summarized most of the common analysis content in the microbiome, and formed the most suitable pipeline for microbiome analysis. This paper is accompanied by hundreds of examples with 10,000 lines codes in GitHub, which can help beginners to learn, also help analysts compare and test different tools. This paper systematically sorts the application of R in microbiome, providing an important theoretical basis and practical reference for the development of better microbiome tools in the future. All the code is available at GitHub github.com/taowenmicro/EasyMicrobiomeR.

Application value of metagenomic next generation sequencing in the diagnosis of non-tuberculous spinal infection / 中华骨科杂志

Objective:To investigate the application value of metagenomic next generation sequencing (mNGS) in the diagnosis of spinal infectious diseases except tuberculosis and non-tuberculous mycobacterium infection.Methods:According to the inclusion and exclusion criteria, the clinical data of 171 patients with suspected non-tuberculous infectious diseases of spine from January 2019 to November 2020 were analyzed retrospectively. All patients underwent puncture biopsy of spine or surgery to obtain tissue specimens, then tissue biopsy were measured, and Foci purulent blood or lavage fluid was obtained for routine bacterial and mNGS. The differences of reporting time, sensitivity (positive rate) and specificity (true negative rate) were compared between the two methods. The pathogenic microorganism spectrum of spinal infection was analyzed. The effects of specimen collection method, preoperative antibiotic use and specimen type on the detection of pathogenic microorganisms were analyzed.Results:According to the diagnostic criteria of non-tuberculous infectious diseases of the spine, there were 136 cases of infection, among which 111 cases had specific pathogenic microorganism. The average reporting time of traditional culture and mNGS were 81.67+15.52 h and 36.33+11.92 h. There were 43 positive cases and 5 false positive cases in traditional culture, the sensitivity was 31.62%, and the specificity was 85.71%; There were 76 positive cases and 19 false positive cases in mNGS, the sensitivity was 55.88%, and the specificity was 45.71%. There were significant statistical differences in the sensitivity, specificity and reporting time for detection of pathogenic microorganisms by mNGS. The top 3 pathogens of non-specific infection were Staphylococcus aureus and Staphylococcus, Escherichia coli and Streptococcus. Eleven patients with non-tuberculous specific infection were confirmed, including 2 positive cases with traditional culture, 11 positive cases with mNGS. A higher detection rate for rare specific infections were expressed in mNGS. Logistic regression analysis indicated that the standard antibiotic use 4 weeks before surgery and specimen acquisition methods had significant effects on the traditional culture results, while the specimen acquisition methods had no statistically significant effects on the mNGS.Conclusion:Metagenomic next generation sequencing has a higher sensitivity to the detection of pathogenic microorganisms in the diagnosis of non-tuberculous spinal infectious diseases, especially for the detection of rare pathogenic microorganisms, which has a high diagnostic value.

A case of application of metagenomic next generation sequencing technology in a case of Cyanobacteria marneffei infection / 中华检验医学杂志

On September 15, 2020, a patient came in to Peking Union Medical College Hospital after suffering from chest pain, rash and lymphadenopathy for more than 2 years, and expericing general pain for 8 months. He also lost 15 kilograms of weight in the past half a year. For chest pain, cough, and expectoration symptons, cephalosporins and symptomatic treatments were empirically used and the symptoms were relieved. However, drug-induced rash occurred. After anti-allergic treatments, the rash was relieved but the swelling of cervical lymph nodes was not relieved. Diagnostic antituberculosis therapy was employed after biopsy result showed multifocal granulomatous inflammation. The therapy reduced the lymph nodes, but the condition repeated, and the whole body pain appeared. Further examinations showed that lung cancer in the right upper lobe was accompanied by obstructive pneumonia and whole body metastasis to multiple sites. The patient had no history of immunosuppression, and the γ interferon antibody was strongly positive, adult-onset immunodeficiency syndrome was considered. In order to confirm the diagnosis, bone and tissue biopsy were necessary, but the patient failed to cooperate. The histopathological examination results of the right cervical lymph node and the left iliac bone biopsy were weakly acid fast staining positive, Nocardia infection was suspected. The clinical symptoms improved after using sulfanilamide and imipenem empirical treatments against Nocardia. The content of cyanobacteria marneffei, which was detected by metagenomic next generation sequencing, was low. More laboratory pathogenic examinations were actively confirmed for this rare pathogen. The antifungal treatment (amphotericin B plus itraconazole) was used after successfully cultivating the cyanobacteria marneffei pathogen. After two months, the body nodules and masses disappeared and the skin wounds healed. It is of great significance to the diagnosis and treatment of patients to obtain qualified samples, maintain timely communication between the laboratory and the clinic, and construct reasonable interpretations of the results of metagenomic next generation sequencing technology.

Current status and challenges of pathogen metagenomic high-throughput sequencing testing implemented in a clinical laboratory affiliated to a hospital / 中华检验医学杂志

Pathogen metagenomic next-generation sequencing (mNGS) testing is highly sophisticated. Its requirements for laboratory environment, equipment, and technical capabilities of personnel are very high. How to orderly develop, standardize management, and application of mNGS technology in hospitals is a scientific topic that practitioners must treat with caution. In this article, the establishment mode of the mNGS detection system in clinical laboratories, the analytical and clinical validation of the detection system, the risk management (which from biological factors, detection procedures, and the bioinformatics analysis and information transmission), as well as the requirements for pathogen databases, bioinformatics analysis talents, and diagnostic reports, have been professionally considered and discussed. It is expected to provide scientific advice for the completely implementation of mNGS testing in a clinical laboratory affiliated to a hospital, promoting the standardized application and healthy development of this technology in hospitals.

Application of nanopore sequencing in environmental microbiology research / 生物工程学报

The development of high-throughput sequencing techniques enabled a deeper and more comprehensive understanding of environmental microbiology. Specifically, the third-generation sequencing techniques represented by nanopore sequencing have greatly promoted the development of environmental microbiology research due to its advantages such as long sequencing reads, fast sequencing speed, real-time monitoring of sequencing data, and convenient machine carrying, as well as no GC bias and no PCR amplification requirement. This review briefly summarized the technical principle and characteristics of nanopore sequencing, followed by discussing the application of nanopore sequencing techniques in the amplicon sequencing, metagenome sequencing and whole genome sequencing of environmental microorganisms. The advantages and challenges of nanopore sequencing in the application of environmental microbiology research were also analyzed.

Comprehensive Evaluation and Application of Experimental Sources of Variation in Gut Microbiome Sequencing Studies / 中国生物化学与分子生物学报

Gut microbiome sequencing studies have great potential to translate microbial analysis outcomes into human health research. Sequencing strategies of 16S amplicon and whole-metagenome shotgun (WMS) are two main methods in microbiome research with respective advantages. However, how sample heterogeneity, sequencers and library preparation protocols affect the sequencing reproducibility of gut microbiome needs further investigation. This study aims to provide a reference for the selection of sequencing technologies by comparing differences in microbial composition from different sampling sites. The results of three widely adopted sequencers showed that the technical repetition correlation (r= 0. 94) was high in WMS method, while the biological repetition correlation (r = 0. 69) was low. Bray-Curtis distance identified that dissimilarity from biological replicates was larger than that of technical replicates (P<0. 001). In addition, dissimilarity and specific taxonomic profiles were observed between 16S and WMS datasets. Our results imply that homogenization is a necessary step before sample DNA extraction. The sequencers contributed less to taxonomic variation than the library preparation protocols. We developed an empirical Bayes approach that " borrowed information" in calculations and analyzed batch effect parameters using standardized data and prior distributions of (non-) parameters, which may improve population comparability between 16S and WMS and provide a basis for further application to fusion analysis of published 16S and microbial datasets.

Progress on correlation between intestinal flora and mental diseases / 中国药理学通报

The impact of intestinal flora on human and animal health and diseases has attracted much attention both at home and abroad in recent years. The intestinal flora constitutes the intestinal microecosystem and plays an important role in physiological activities such as nutrition, metabolism, growth and development, barrier protection, and immunity. In this article, the relationship between intestinal dysbiosis and psychiatric diseases has been reviewed from two aspects:metagenomic characterization of intestinal microflora diversity in neurological diseases and validation of the relationship between intestinal flora and psychiatric diseases by fecal bacteria transplantation in germ-free mice. In addition, the microbial-gut-brain axis theory has been proposed in recent years, which links the nerve-endocrine-immune system to form a two-way signaling pathway. Intestinal flora plays an important role in regulating the central nervous system by promoting neurotransmitter release, endocrine, and immunity. The system plays an important role. Changes in intestinal flora mainly affect the host's nervous system through vagus nerve pathways, endocrine pathways, immune pathways, etc, thereby triggering or aggravating depression, autism, Alzheimer's disease, schizophrenia, Parkinson's disease, etc. This article reviews the relationships between host-related neurological abnormalities, intestinal flora imbalance and mental diseases, and discusses the research methods, research progress, and mechanism of the correlation between intestinal flora imbalance and mental diseases to research progress on microbe-gut-brain axis.

Microbiome analysis of gut bacterial communities of healthy and diseased Malaysian mahseer (Tor tambroides) using 16S rRNA metagenomics approach

Aims@#The gut microbiota is referred to as an ‘extra organ’ and is critical in assisting the host in terms of nutrition and immunity. Environmental stressors could alter the gut microbial community and cause gut inflammation. This study aimed to investigate and compare the gut microbiota community between healthy and diseased Tor tambroides.@*Methodology and results@#In this study, such gut microbial alterations were explored using NGS-based 16S rDNA targeted sequencing on the Malaysian mahseer (T. tambroides). Three healthy adult and three diseased adult Malaysian mahseers (showing signs of exophthalmia, coelomic distension and petechial haemorrhage) were obtained from LTT Aquaculture Sdn Bhd. Our results revealed significant differences in microbial diversity, composition and function between both populations of T. tambroides. Alpha diversity analysis depicts lower diversity of gut microbiota composition in diseased T. tambroides as compared to the healthy group. In particular, Enterobacteriaceae, Aeromonas, Bacteroides, Vibrio and Pseudomonas were found within gut microbiota of the diseased fishes. In addition, cellulosedegrading bacteria and protease-producing bacteria were identified from the gut of T. tambroides.@*Conclusion, significance and impact of study@#Thus, our findings emphasized on the association between the alteration in gut microbiota composition and infectious abdominal dropsy (IAD) in T. tambroides. This finding is important to provide basic information for further diagnosis, prevention and treatment of intestinal diseases in fish.

Chlamydia psittaci pneumonia complicated with rhabdomyolysis: a clinical analysis of 5 cases / 中华全科医师杂志

The clinical data of patients with chlamydia psitsiti pneumonia confirmed by metagenomic next-generation sequencing (mNGS) who were admitted to the Huizhou Municipal Central Hospital from January 2020 to November 2021 were retrospectively analyzed. Among 21 patients, the serum creatine kinase (CK) was elevated in 10 cases, and 5 cases was complicated with rhabdomyolysis (RM). The symptoms of patients with Chlamydia psittaci pneumonia-induced RM were severe, including high fever, dyspnoea, headache and myalgia; 2 case were complicated by acute kidney injury (AKI) and neurological symptoms. Laboratory testing showed a marked increase in CK, myoglobin (Mb), high sensitivity C-reactive protein (hs-CRP), interleukin-6 (IL-6) and D-dimer levels in all 5 patients. The chest CT revealed large areas of pulmonary consolidation, ground-glass opacity in 1 case and a small amount of pleural effusion in 2 cases. One patient died from multiple organ failure, and the other 4 patients were discharged with considerable improvement. Patients with psittacosis pneumonia are prone to developing rhabdomyolysis, early detection and early treatment can effectively improve the prognosis of patients.

Clinicopathological analysis of 56 cases of swimming pool granuloma / 中华皮肤科杂志

Objective:To investigate clinicopathological features of swimming pool granuloma.Methods:From January 2018 to January 2021, 56 patients with swimming pool granuloma were collected from Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, and their clinical and pathological characteristics were retrospectively analyzed.Results:Among the 56 patients, 16 were males and 40 were females, with an average age of 60.84 years. The most common exposure type among these patients was handling of infected fishes or seafood by aquaculture workers and residents in daily cooking (31/56) , the average incubation period was 4.58 weeks, and the average time to diagnosis was 3.19 months. All skin lesions were located at the upper extremities, mainly manifesting as erythema and papular nodules, and sometimes as pustules, ulcers, granulomas or verrucous plaques. Eleven patients presented with solitary skin lesions, 36 with sporotrichoid skin lesions, and 6 with bilateral sporotrichoid lesions. Histopathologically, infectious granulomas were observed in all patients except 4 without specific changes, and 37 presented with characteristic exudative necrosis, with varying amounts of fibrinoid exudative or necrotic elements in the center, and a large number of neutrophils, histiocytes and multinucleated giant cells infiltrating inside or around it. Sequences of Mycobacterium marinum were identified in all 56 cases by metagenomic DNA sequencing of pathogenic microorganisms. Conclusion:In Tianjin area, swimming pool granuloma mostly affected elderly females, handling of infected fishes or seafood was the main type of exposure, and skin lesions were histopathologically characterized by exudative necrotic granulomas.

Clinical characteristics of Chlamydia psittaci pneumonia: an analysis of 13 cases / 中华全科医师杂志

Objective:To analyze the clinical characteristics of pneumonia caused by Chlamydia psittaci (C. psitttaci). Methods:A retrospective analysis was performed on the clinical data of 13 consecutive patients with C. psitttaci pneumonia admitted to the First Affiliated Hospital of Xiamen University from November 2018 to February 2021. Results:All 13 cases had symptoms of fatigue and 6 cases had headache. At consultation, the ΔSequential Organ Failure Assessment (SOFA) scores of all patients were ≥2 points. According to the Pneumonia Severity Index (PSI) score, 2 patients were grade Ⅱ and the other 11 patients were grade Ⅳ or Ⅴ. Laboratory tests showed that C-reactive protein (CRP) and procalcitonin (PCT) levels were elevated in all patients; CRP≥100 mg/L was found in 11 cases and PCT≥0.5 ng/ml was found in 9 cases.There were 12 cases with respiratory failure and 12 cases with elevated transaminase. Chest CT scans showed multiple patchy exudative shadow, focal consolidation and air bronchial sign; and the lesions were mainly in the lower lungs (8 cases). C. psitttaci infections were confirmed by metagenomics next-generation sequencing (mNGS) and the patients′ conditions improved rapidly after timely adjustment of doxycycline based drug treatment and active organ support. The lesions were completely absorbed without residual fibrous cord changes and the prognosis was good. Conclusions:Pneumonia caused by C. psitttaci usually presents sepsis, and the disease progresses rapidly. The mNGS is of value for the early diagnosis of C. psitttaci pneumonia. Timely adjustment of antibiotics treatment after etiological diagnosis can lead to a good prognosis.

Changes of gut microbiota and its effect on glucose tolerance in a novel mice model of insulin resistance (eLtaS trans) / 中华内分泌代谢杂志

Objective:To investigate the correlation between insulin resistance and alterations in gut microbiota using the animal model of insulin resistance(eLtaS transgenic mice).Methods:Glucose tolerance was measured in eLtaS trans mice and wild-type (WT) mice. Faecal samples of mice were collected for metagenomics and 16S rDNA sequencing. Alterations of gut microbiota in eLtaS trans mice were further analyzed. Faeces from eLtaS trans mice were transplanted into WT mice by " dirty cage" sharing experiment, and glucose tolerance of mice was measured at different time points after transplantation. Results:Significant differences in composition and function of gut microbiota were observed between eLtaS trans mice and WT mice( P=0.028). Compared with WT mice, the diversity of gut microbiota in eLtaS trans mice increased evidently, moreover the relative abundance of Phylum Firmicutes in eLtaS trans mice significantly increased( P<0.001). However, the relative abundance of Phylum Bacteroides and Phylum Verrucomicrobia decreased visibly( P=0.042, P=0.033). The relative abundance of Akkermansia muciniphila and Parabacterides distasonis related to metabolic diseases decreased significantly in eLtaS trans mice( P=0.033, P=0.013). The gut microbiota of eLtaS trans mice was clearly different from that of WT mice in carbohydrate metabolism, lipid metabolism, biosynthesis of other secondary metabolites, metabolism of other amino acids, energy production and transformation. The glucose tolerance of WT mice was impaired at 7th, 8th and 9th week after faecal transplantation, and recovered at 1 week after cessation of faecal transplantation. Conclusion:Insulin resistance leads to obvious changes of gut microbiota in mice, meanwhile the gut microbiota of insulin resistance mice can further induce impaired glucose tolerance.

Potential regulatory mechanisms of thyroid iodine metabolism by gut microbiota / 中华核医学与分子影像杂志

Iodine is an essential trace element in the human body, and the gastrointestinal tract is the main way for the body to intake iodine. The intestinal tract contains trillions of microorganisms that have important impacts on the substance-energy metabolism and the genetic information processing in the human body. Gut microbiota or their metabolites can act on the thyroid through the circulatory system (namely the " gut-thyroid axis" ), thus potentially regulating iodine metabolism in thyroid. This article reviews the effects of gut microbiota on intestinal iodine uptake, as well as the effects of gut microbiota and their metabolites on the expression and activity of sodium iodide symporter (NIS) in thyroid cells, thus exploring the potential regulatory mechanisms of gut microbiota that involved in thyroid iodine metabolism. Potential factors affecting thyroid iodine metabolism by gut microbiota include the direct and the indirect factors. The direct factors include lipopolysaccharides, short-chain fatty acids, microbial peptides, and microbial proteins, which may affect the expression or activity of NIS in thyroid by regulating the nuclear factor kappa-B pathway, histone acetylation modifications, or antigen-antibody reactions. The indirect factors include the altered cellular environment that effected by gut microbiota which can further affect the transport of iodine ions in thyroid cells by manners like regulating the levels of thyroid-specific transcription factors and regulating the signal pathways mediated by thyroid-stimulating hormone and its receptor.

Application of metagenomic next-generation sequencing in patients with Herpes simplex pneumonia mixed infection / 中国医师杂志

Objective:To explore the application value of next-generation sequencing (mNGS) technology in patients with Herpes simplex pneumonia mixed infection.Methods:The clinical data of pneumonia patients who underwent alveolar lavage fluid mNGS technology and traditional pathogen detection in the Affiliated Hospital of Yangzhou University from June 2018 to January 2021 were retrospectively collected.Results:A total of 41 patients with mNGS Herpes simplex type 1 (HSV-1) test (4 HSV-1 carriers, 37 HSV-1 infections) were enrolled in this study, including 22 males and 19 females. The age ranged from 46 to 83 years old, with a median age of 67 years. The higher proportion of pathogens in 25 cases of HSV-1 co-infection detected by mNGS were Pneumocystis jiroveci (6 cases, 24.0%), Acinetobacter baumannii (4 cases, 16.0%), and Klebsiella pneumoniae (4 cases, 16.0%), and Aspergillus fumigatus (3 cases, 12.0%). The difference in the Simpson's diversity index in the HSV-1carrier group, HSV-1 single infection group and HSV-1 mixed infection group was statistically significant ( P<0.05). Compared with 12 cases of HSV-1 single infection, the time for body temperature to return to normal for 25 cases of HSV-1 mixed infection was [(5.16±2.04)days vs (3.75±1.29)days], and course of antibiotic treatment was longer [(10.60±2.18)d vs (8.92±1.98)d]. Conclusions:The mNGS technology has obvious advantages in identifying HSV-1 mixed infections, which is beneficial to physicians to treat them accurately.

A practical guide to amplicon and metagenomic analysis of microbiome data

Advances in high-throughput sequencing (HTS) have fostered rapid developments in the field of microbiome research, and massive microbiome datasets are now being generated. However, the diversity of software tools and the complexity of analysis pipelines make it difficult to access this field. Here, we systematically summarize the advantages and limitations of microbiome methods. Then, we recommend specific pipelines for amplicon and metagenomic analyses, and describe commonly-used software and databases, to help researchers select the appropriate tools. Furthermore, we introduce statistical and visualization methods suitable for microbiome analysis, including alpha- and beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, and common visualization styles to help researchers make informed choices. Finally, a step-by-step reproducible analysis guide is introduced. We hope this review will allow researchers to carry out data analysis more effectively and to quickly select the appropriate tools in order to efficiently mine the biological significance behind the data.

Comparative study on anti-depressant effect of Zhizichi Decoction and its solid fermentation product on CUMS rats / 中国中药杂志

Chronic unpredicted mild stress(CUMS) combined with isolated feeding was used to induce depressed rat model. The anti-depressant effects of Zhizichi Decoction(ZZCD) and its solid fermented product(ZZC) were analyzed by behavioral test and comparison of pathological tissues of hippocampus and liver, metabolic characteristics of intestinal flora, and relative abundance of species. The results showed that ZZC could increase sucrose preference, shorten the immobility time in the forced swim test and tail suspension test(P<0.05), and repair damaged hippocampus and liver tissues, and the effect was superior to that of ZZCD. The results of Biolog ECO plates showed that the average well color development(AWCD) of intestinal flora in the model group significantly decreased and the metabolic levels of sugar and amino acids were reduced, while the AWCD of the treatment groups increased. The metabolic levels of the two carbon sources were improved in the ZZC group, while only sugar metabolic level was elevated in the ZZCD group. Metagenomic analysis of intestinal flora showed that the ratio of Firmicutes/Bacteroidetes was 3.87 in the control group, 21.77 in the model group, 5.91 in the ZZC group, and 18.48 in the ZZCD group. Lactobacillus increased by 3.28 times, and Prevotella and Bacteroidetes decreased by 75.59% and 76.39%, respectively in the model group as compared with that in the control group. Lactobacillus decreased by 31.13%, and Prevotella and Bacteroidetes increased by more than three times in the ZZC group as compared with that in the model group, while the corresponding changes in the ZZCD group were not significant. ZZC could improve depression-like beha-viors by regulating the structure of intestinal flora and metabolic functions and repairing damaged hippocampus and liver tissues in depressed rats, showing an anti-depressant effect superior to that of ZZCD. This study is expected to provide a basis for the development of new anti-depressant food products.

Shotgun metagenome sequencing of Chinese gut microbiota: a review / 生物工程学报

The research on the relationship between gut microbiota and human health continues to be a hot topic in the field of life science. Culture independent 16S rRNA gene high-throughput sequencing is the current main research method. However, with the reduction of sequencing cost and the maturity of data analysis methods, shotgun metagenome sequencing is gradually becoming an important method for the study of gut microbiome due to its advantages of obtaining more information. With the support from the human microbiome project, 30 805 metagenome samples were sequenced in the United States. By searching NCBI PubMed and SRA databases, it was found that 72 studies collecting about 10 000 Chinese intestinal samples were used for metagenome sequencing. To date, only 56 studies were published, including 16 related to metabolic diseases, 16 related to infectious and immune diseases, and 12 related to cardiovascular and cerebrovascular diseases. The samples were mainly collected in Beijing, Guangzhou, Shanghai and other cosmopolitan cities, where great differences exist in sequencing platforms and methods. The outcome of most studies are based on correlation analysis, which has little practical value in guiding the diagnosis and treatment of clinical diseases. Standardizing sampling methods, sequencing platform and data analysis process, and carrying out multi center parallel research will contribute to data integration and comparative analysis. Moreover, insights into the functional verification and molecular mechanism by using the combination of transcriptomics, proteomics and culturomics will enable the gut microbiota research to better serve the clinical diagnosis and treatment.