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.

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.

A guide to human microbiome research: study design, sample collection, and bioinformatics analysis / 中华医学杂志(英文版)

The purpose of this review is to provide medical researchers, especially those without a bioinformatics background, with an easy-to-understand summary of the concepts and technologies used in microbiome research. First, we define primary concepts such as microbiota, microbiome, and metagenome. Then, we discuss study design schemes, the methods of sample size calculation, and the methods for improving the reliability of research. We emphasize the importance of negative and positive controls in this section. Next, we discuss statistical analysis methods used in microbiome research, focusing on problems with multiple comparisons and ways to compare β-diversity between groups. Finally, we provide step-by-step pipelines for bioinformatics analysis. In summary, the meticulous study design is a key step to obtaining meaningful results, and appropriate statistical methods are important for accurate interpretation of microbiome data. The step-by-step pipelines provide researchers with insights into newly developed bioinformatics analysis methods.

Antioxidant effects of celastrol against hydrogen peroxide-induced oxidative stress in the cell model of amyotrophic lateral sclerosis / 生理学报

To investigate the anti-oxidative effect of celastrol on HO-induced oxidative stress in the cell model of amyotrophic lateral sclerosis (ALS) and its molecular mechanism, NSC34 motor neuron-like cells were transfected with EGFP-G93A-SOD1 plasmid and used as in vitro ALS cell model. SOD1transfected NSC34 cells were treated with different doses of HOand celastrol. The survival rate of the cells was detected by CCK-8 assay, and malondialdehyde (MDA) content was detected by corresponding kit. The mRNA expression of glutamate-cysteine ligase catalytic subunit (GCLC) and glutathione S-transferases (GST) were detected by real-time PCR. The activation of intracellular MEK/ERK and PI3K/Akt signal pathways was detected by Western blot. The results showed that pre-incubation of celastrol (50 nmol/L) for 4 h prior to HO(10 μmol/L) co-treatment for another 24 h significantly attenuated HO-induced cell death and MDA level in SOD1transfected NSC34 cells. Real-time PCR showed that the mRNA expressions of GCLC and GST were enhanced with pre-incubation of celastrol. Celastrol quickly induced phosphorylation of ERK1/2 and Akt within 30 min and 1 h respectively in SOD1transfected NSC34 cells. Pharmacological inhibitors of MEK (PD98059, 10 μmol/L) or Akt (MK2206, 10 μmol/L) could reverse the phosphorylation of ERK1/2 and Akt, and abolish up-regulation of GCLC and GST induced by celastrol at mRNA levels. Taken together, we conclude that celastrol exerts a beneficial antioxidant effect in SOD1NSC34 cells, which might be dependent on MEK/ERK and PI3K/Akt signaling pathway activation.

Clinical features and serologic analysis of latent syphilis / 中国医学科学院学报

<p><b>OBJECTIVE</b>To summarize the clinical features and analyze the serologic test results of latent syphilis.</p><p><b>METHODS</b>The clinical data of 601 patients with latent syphilis who were treated in the sexually transmitted disease centre of Peking Union Medical College Hospital between January 2001 and November 2007 were retrospectively analyzed.</p><p><b>RESULTS</b>Of the 601 cases of latent syphilis, there were 174 cases of early latent syphilis(EL), 170 cases of late latent syphilis(LL), and 257 cases of unknown latent syphilis. Male to female ratio was 0.74:1256 males and 345 females, respectively). Patients aged 20-39 years accounted for the largest proportion. Non-marital sexual intercourse was the main route of infection. Forty-six patients (7.65%) were co-infected with other sexually transmitted diseases. A total of 251 cases of latent syphilis (41.76%) were confirmed when the patients were receiving tests for other sexually transmitted diseases or suspected sexually transmitted diseases. Of the 601 patients with EL, LL and unknown latency, the proportion of serum rapid plasma reagin(RPR) titers higher than or equal to 8 were 72.99% (127/174), 52.94% (90/170), and 60.31%(155/257), respectively. Compared with the early syphilis, serological negative conversion rate was significantly lower after treatment for l2 months in the early latent syphilis patients (P=0.044).</p><p><b>CONCLUSION</b>Education and awareness raising on syphilis should be strengthened to lower the prevalence of latent syphilis.</p>

Analysis of 1125 syphilis cases / 中国医学科学院学报

<p><b>OBJECTIVE</b>To summarize the epidemiological, clinical and serological features of syphilis.</p><p><b>METHOD</b>The clinical data of 1125 patients with syphilis were retrospectively analyzed.</p><p><b>RESULTS</b>Non-marital sexual intercourse is the main route of infection. The 129 cases of primary syphilis were featured by extragenital chancres and the 357 cases of secondary syphilis were featured by scaling macules on the palms and soles and condylomata lata. Early latent syphilis were detected in 178 cases, late latent syphilis in 174 cases, and latent syphilis of unknown duration in 285 cases. Concurrent infection with other sexually transmitted diseases were noted in 107 cases (9.51%). Most patients were treated with benzathine penicillin, and only 31 patients (2.75%) were allergic to this therapy. Except for the primary syphilis, the sensitivity of syphilis serological tests (including rapid plasma regain test, treponema pallidum particle agglutination, treponema pallidum hemagglutination assay, and fluorescent treponemal antibody-absorption) were higher than 97%.</p><p><b>CONCLUSIONS</b>The incidence of latent syphilis is high, while the incidence of late syphilis is low. Penicillin remains the treatment of choice for syphilis.</p>

5-aminolaevulinic acid-photodynamic therapy for the treatment of cervical condylomata acuminata / 中国医学科学杂志(英文版)

<p><b>OBJECTIVE</b>To investigate the efficacy and safety of photodynamic therapy (PDT) with topical 5-aminolaevulinic acid (ALA) on cervical condylomata acuminata.</p><p><b>METHODS</b>Patients with cervical condylomata (n=30) were allocated into primary and recurrent group, and were given topical ALA under occlusive dressing for 3 hours followed by irradiation with semiconductor laser at a dose of 100 Jcm(-2) and a power of 100 mW. The treatment was repeated 7 days later if the lesion was not completely removed after the first treatment. Complete response rate and recurrence rate of wart lesions as well as rate of adverse reaction were analyzed.</p><p><b>RESULTS</b>The total complete response rate of PDT was 100% and the total recurrence rate was 5% after 3 months of follow-up. Recurrence rate of recurrent group was significantly lower than that of prior managements (100%, P<0.01). The side effects of PDT in patients mainly included mild burning and/or stinging restricted to the illuminated areas, and was significant lower than their own control (25% vs. 100%, P<0.05).</p><p><b>CONCLUSION</b>Compared with conventional therapies, topical application of ALA-PDT is a simple, effective, safe, well-tolerated, and low recurrence rate treatment for cervical condylomata acuminata.</p>

Incidence of seroresistance of syphilis and its relevant factors / 中国医学科学院学报

<p><b>OBJECTIVE</b>To investigate the incidence of seroresistance of syphilis and analyze its relevant factors.</p><p><b>METHODS</b>The clinical data of 131 patients with syphilis were retrospectively analyzed. The incidence of seroresistance was investigated and the correlation between seroresistance and factors including age, gender, original titer, disease course, and medications were analyzed.</p><p><b>RESULTS</b>The incidence of seroresistance was not significantly different among patients with different ages and genders, but was significantly different among patients with different disease courses, antibody titers, and medications. Patients with a baseline serum rapid plasma reagin (RPR) titer of greater than 1: 8, a latent course, or a macrolide therapy history had higher incidences of seroresistance (i. e., 61%, 45.6%, and 72.7% respectively) than those who had a lower RPR titer, a primary course, or a benzathine penicillin therapy history.</p><p><b>CONCLUSION</b>Syphilis patients with a high baseline RPR titer, a latent course, and a macrolides therapy are prone to be seroresistant.</p>

Detection of cholesterol ester transfer protein in semen of infertile patients / 中华男科学杂志

<p><b>OBJECTIVES</b>To detect the cholesterol ester transfer protein (CETP) levels in semen of infertile patients and evaluate the correlation between CETP in semial plasma and infertility.</p><p><b>METHODS</b>One hundred and sixty-three infertile patients and fifteen fertile males were selected randomly. The routine examination of ejaculates was fulfilled by computer aided semen analysis (CASA). The CETP levels in all seminal plasma samples and fifty-five serum samples were detected by ELISA method.</p><p><b>RESULTS</b>The CETP levels in infertile patients and fertile males were (2.21 +/- 1.23) microgram/L and (1.40 +/- 0.45) microgram/L, respectively. There were no significant differences between the two groups(P > 0.05). And there were no significant differences of CETP levels in seminal plasma among groups of azoospermia(n = 29), oligoasthenozoospermia (n = 58), oligospermia(n = 15), asthenozoospermia(n = 44) and normozoospermia(n = 17) in the infertile patients(P > 0.05). The CETP in seminal plasma and serum were detected in 55 infertile patients, and there was no correlation between CETP levels in seminal plasma and serum using Spearman analysis(r = 0.009, P > 0.05). The mean CETP level in seminal plasma was almost 1/1,000 of that in serum.</p><p><b>CONCLUSIONS</b>The CETP level in seminal plasma is extremely low and has no relation with the changes of sperm density or motility. It may ensure the integrity of sperm membrane before the sperm enters into female genital tract.</p>