Background::As a non-invasive and effective diagnostic method for small intestinal bacterial overgrowth (SIBO), wild-use of breath test (BT) has demonstrated a high comorbidity rate in patients with diarrhea-predominant irritable bowel syndrome (IBS-D) and SIBO. Patients overlapping with SIBO respond better to rifaximin therapy than those with IBS-D only. Gut microbiota plays a critical role in both of these two diseases. We aimed to determine the microbial difference between IBS-D overlapping with/without SIBO, and to study the underlying mechanism of its sensitivity to rifaximin.Methods::Patients with IBS-D were categorized as BT-negative (IBSN) and BT-positive (IBSP). Healthy volunteers (BT-negative) were enrolled as healthy control. The patients were clinically evaluated before and after rifaximin treatment (0.4 g bid, 4 weeks). Blood, intestine, and stool samples were collected for cytokine assessment and gut microbial analyses.Results::Clinical complaints and microbial abundance were significantly higher in IBSP than in IBSN. In contrast, severe systemic inflammation and more active bacterial invasion function that were associated with enrichment of opportunistic pathogens were seen in IBSN. The symptoms of IBSP patients were relieved in different degrees after therapy, but the symptoms of IBSN rarely changed. We also found that the presence of IBSN-enriched genera ( Enterobacter and Enterococcus) are unaffected by rifaximin therapy. Conclusions::IBS-D patients overlapping with SIBO showed noticeably different fecal microbial composition and function compared with IBS-D only. The better response to rifaximin in those comorbid patients might associate with their different gut microbiota, which suggests that BT is necessary before IBS-D diagnosis and use of rifaximin.Registration::Chinese Clinical Trial Registry, ChiCTR1800017911.

In the past ten years, the research and application of microbiome has continued to increase. The microbiome has gradually become the research focus in the fields of life science, environmental science, and medicine. Meanwhile, many countries and organizations around the world are launching their own microbiome projects and conducting a multi-faceted layout, striving to gain a strategic position in this promising field. In addition, whether it is scientific research or industrial applications, there has been a climax of research and a wave of investment and financing, accordingly, products and services related to the microbiome are constantly emerging. However, due to the rapid development of microbiome sequencing and analysis related technologies and methods, the research and application from various countries have not yet unified on the standards of technology, programs, and data. Domestic industry participants also have insufficient understanding of the microbiome. New methods, technologies, and theories have not yet been fully accepted and used. In addition, some of the existing standards and guidelines are too general with poor practicality. This not only causes obstacles in the integration of scientific research data and waste of resources, but also gives related companies unfair competition opportunity. More importantly, China still lacks national standards related to the microbiome, and the national microbiome project is still in the process of preparation. In this context, the experts and practitioners of the microbiome worked together and developed the consensus of experts. It can not only guide domestic scientific research and industrial institutions to regulate the production, learning and research of the microbiome, the application can also provide reference technical basis for the relevant national functional departments, protect the scale and standardized corporate company's interests, strengthen industry self-discipline, avoid unregulated enterprises from disrupting the market, and ultimately promote the benign development of microbiome-related industries.
China ; Consensus ; Humans ; Industry ; Microbiota

Exploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction (FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage (AMD) microbiota, and a complex community as human gut microbiota. Furthermore, we define community structure shaping (CSS) genes as functional genes crucial for shaping the microbial community. We have identified CSS genes in AMD and human gut microbiota samples with FCP model and find that CSS genes change with the conditions. Compared to essential genes for microbes, CSS genes are significantly enriched in the genes involved in mobile genetic elements, cell motility, and defense mechanisms, indicating that the functions of CSS genes are focused on communication and strategies in response to the environment factors. We further find that it is the minority, rather than the majority, which contributes to maintaining community structure. Compared to health control samples, we find that some functional genes associated with metabolism of amino acids, nucleotides, and lipopolysaccharide are more likely to be CSS genes in the disease group. CSS genes may help us to understand critical cellular processes and be useful in seeking addable gene circuitries to maintain artificial self-sustainable communities. Our study suggests that functional genes are important to the assembly of microbial communities.
Gastrointestinal Microbiome ; genetics ; Genes, Microbial ; Humans ; Microbiota ; genetics ; Mining ; Models, Genetic ; Water Pollution

Objective To observe the changes of inflammatory factors in acute lung injury (ALI) in mice induced by lipopolysaccharide (LPS), and to explore the influence of different doses of LPS on ALI onset and progress at different time points. Methods Intratracheally, LPS at the dosages of 2.5, 5.0, 7.5 and 10.0 mg/kg were administered to a total of 210 C57BL/6 mice, and according to the difference in dosage, they were divided into four groups. The ALI model was replicated by intratracheally dropping of LPS. And a normal control group and a normal saline control group were established (each, n=10). The changes of index of pathological lung tissue and lung tissue wet/dry (W/D) ratio were observed at 1, 2, 4, and 8 hours after injury, and simultaneously, the levels of norepinephrine (NE), tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and protein in serum and bronchoalveolar lavage fluid (BALF) were detected. Results ①The degree of lung injury induced by LPS was dose-and time-dependent.②With the increase of LPS dosage and prolongation of time, in LPS group, the lung W/D ratio and the index of pathological lung tissue were increased;additionally, the levels of NE, TNF-α, IL-6 and protein in serum or BALF were also significantly increased. The critical occurrence point of acute respiratory distress syndrome (ARDS) with specific characteristics was at 5.0 mg/kg of LPS acting for 4 hours [lung W/D ratio: 4.97±0.41, index of pathological changes of lung tissue (score): 5.60±1.52; serum NE (ng/L): 379.99±27.65, TNF-α (ng/L): 159.15±20.62, IL-6 (ng/L): 177.15±29.13;BALF NE (mg/kg):105.85±13.66, TNF-α(mg/kg):227.22±48.01, IL-6 (mg/kg):251.55±54.08, total protein (g/L):1.59±0.37]. The injury induced by LPS acting for 8 hours in the dosage group 10.0 mg/kg was the most significant in comparisons with other groups of dosages at the same time points [lung W/D ratio:5.10±0.18 vs. 5.01±0.43, 5.01±0.19, 4.91±0.30; index of pathological changes of lung tissue (score): 9.20±1.48 vs. 8.00±1.00, 6.00±1.22, 4.40±0.89;serum NE (ng/L): 447.43±34.63 vs. 419.23±30.62, 391.16±54.91, 372.59±51.52; TNF-α(ng/L): 205.99±31.31 vs. 181.01±25.11, 161.01±13.98, 138.83±28.95; IL-6 (ng/L): 233.76±34.84 vs. 206.21±26.68, 186.58±26.54, 156.99±28.83;BALF NE (mg/kg):190.82±41.75 vs. 153.30±35.42, 122.64±25.15, 80.23±13.69;TNF-α(mg/kg):305.24±72.99 vs. 292.77±38.07, 249.60±35.20, 193.63±10.83; IL-6 (mg/kg): 354.81±67.79 vs. 303.02±54.24, 272.43±32.34, 197.64±12.35;total protein (g/L):2.31±0.30 vs. 2.02±0.26, 1.62±0.19, 1.10±0.24, P<0.05 or P<0.01]. Conclusions The severity of ALI induced by LPS in mice was positively correlated to LPS dosage and duration of its action. After administration of LPS 5 mg/kg for 4 hours, remarkable characteristic manifestations of ARDS occur in mice, reaching the critical point.

ObjectiveTo compare the efficacy and tolerability of 1-week 1％ terbinafine hydrochloride cream, 1- and 4-week 2％ miconazole nitrate cream in the treatment of interdigital tinea pedis, and to observe the relapse in patients treated with these regimens. MethodsA multi-center, randomized, double-blind and parallel group study was conducted. By using a stratified randomization protocol, patients were divided into 3 groups to apply terbinafine cream twice daily for 1 week and inert cream(placebo) for the next 3 weeks (1week terbinafine group), miconazole cream twice daily for 1 week and inert cream(placebo) for the next 3 weeks (1-week miconazole group), and miconazole cream twice daily for 4 weeks (4-week miconazole group),respectively. Clinical and mycological assessment was made on week 1, 3, 4, 6, 9 and 12 after the initiation of treatment. ResultsA total of 152 patients with positive baseline mycological culture were eligible for the efficacy analysis. After 4-week treatment, the mycological cure rates were 94.7％, 87.8％ and 82.6％, global effective rates 89.5％, 81.6％ and 63.0％, respectively for the 1-week terbinafine group, 4-week miconazole group and 1-week miconazole group. On week 12, the mycological relapse rates in 1-week terbinafine, 4-week miconazole and 1-week miconazole group were 13％, 14％ and 21％ respectively, and the incidence of adverse reaction was 2.38％, 2.38％ and 3.57％, respectively. ConclusionsAs far as the efficacy and recurrence in patients are concerned, the 1-week terbinafine cream regimen is similar to the 4-week miconazole cream regimen for the treatment of interdigital tinea pedis.

Accurate prediction of the translation initiation site (TIS) is an important issue for prokaryotic genome annotation. However, it is still a challenge for the existing methods to predict the TIS in the genomes over a wide variety of GC content. Besides, the existing methods have not yet undergone a comprehensive evaluation, leaving prediction reliability as a largely open problem. A new algorithm MED-StartPlus, a tool that predicts TIS in prokaryotic genomes with a wide variety of GC content was presented. It makes several efforts to model the nucleotide composition bias, the regulatory motifs upstream of the TIS, the sequence patterns around the TIS, and the operon structure. Tests on hundreds of reliable data sets, with TISs confirmed by experiments or having annotated functions, show that the new method achieves a totally high accuracy of TIS prediction. Compared with existing TIS predictors, the method reports a totally higher performance, especially for genomes that are GC-rich or have complex initiation mechanisms. The potential application of the method to improve the TIS annotation deposited in the public database was also proposed.

Light, auxin and brassinosteroid play important roles in plant growth and development. Genetic analysis has demonstrated complex interactions between their signaling pathways, but the gene regulatory mechanisms connecting these pathways are poorly understood. CYP72B1 and AUR3 are two important genes responsive to light, auxin and brassinosteroid at transcription level. To understand the regulation mechanism of the two genes, a new tool called OCMMat was developed for identifying cis-elements, OCMMat combines both the over-representation property of regulatory elements in co-expressed genes and the conservation property in orthologous genes, for the latter, it was estimated by an enrichment score of regulatory element in orthologous promoter sequences. Using this tool, 3 regulatory motifs shared by genes CYP72B1 and AUR3 were reported, motif GAGACA which is the same as a known cis-element AuxRE, motif AAGAAAAA containing the sequence of GT element and the third ATCATG which is a new one named EDIB element. The space and the order of AAGAAAAA and EDIB show the same pattern in promoters of both the co-expressed genes and the orthologs of CYP72B1. Based on the sequence analysis and the literature knowledge to date, a model was proposed for describing the transcriptional regulatory mechanism of CYP72B1 and AUR3 in response to light, auxin and brassinosteroid. The model presents how the signaling pathways of light, auxin and brassinosteroid are interplaying at gene transcription level. In response to light, the transcription factors GT factor and an unknown protein repress the expression of CYP72B1 and AUR3, the hormone pathways are not interfered and thus work in their own way. While in the absence of light stimulation, CYP72B1 and AUR3 are expressed and the products, in turn, inhibit both the auxin pathway and the brassinosteroid pathways. On the other side, at high hormone level, gene expression is up-regulated through ARF binding, the gene products inhibit the hormone pathways in a feedback manner, and meanwhile, rescues the light signal through the photoreceptor phyB.

This article discusses the ethical problems about Senile patients of dermatosis and venereal disease in the diagnosis and treatment.The problems mainly include:(1)moral responsibility is not strong and skills are not taken into account when inquiring history;(2)it is not careful enough and personality of patients may be hurt when making medical examination;(3)attitude is not solemn and operation not normative;(4)treatment is not normative and charcteristics of senile patients are not considered.We bring forward some suggestions including of:(1)moral responsibility must be strong enough and skills should be taken into account when inquiring history;(2)it must be careful engough and personality of patients may be respected when making medical examination;(3)attitude must be solemn and operation must be normative;(4)characteristics of senile patients must be considered and treatment should be reasonable;(5)life of senile patients should be respected and cherished,the quality of life should be attached importance to:

To discuss the ethical factors influencing the standard diagnosis and treatment of sexual transmitted diseases(STDs) on special population including senile patients,pregnant and lying-in women and children.The senile patients with STDs had a decline of physiological function and might have foundational diseases,some of these patients had the psychological characteristics such as unclear talk,uncertain memory,stronger self-esteem,and had a decline of life quality.Therefore hte main ethical measures during the senile patients with STDs should include considering the pathophysiological and psychological characteristics,adopting individual diagnosis and treatment,making the skill of inquiring and physical examination,and attaching importance to the improvement of life quality.The main ethical measures during the pregnant and lying-in women with STDs should include attaching importance to the marriage examination and pregnant examination,finding potential STDs as soon as possible,and weighing potential medical risk.The main ethical measures during the children with STDs should include paying attention to the infection of family members or sex-aggression,making the protective medicine,doing well the propaganda and education,and making the children away from STDs.

This article discusses the ethical problems about Senile patients of dermatosis and venereal disease in the diagnosis and treatment.The problems mainly include:(1)moral responsibility is not strong and skills are not taken into account when inquiring history;(2)it is not careful enough and personality of patients may be hurt when making medical examination;(3)attitude is not solemn and operation not normative;(4)treatment is not normative and charcteristics of senile patients are not considered.We bring forward some suggestions including of:(1)moral responsibility must be strong enough and skills should be taken into account when inquiring history;(2)it must be careful engough and personality of patients may be respected when making medical examination;(3)attitude must be solemn and operation must be normative;(4)characteristics of senile patients must be considered and treatment should be reasonable;(5)life of senile patients should be respected and cherished,the quality of life should be attached importance to: