The COVID-19 pandemic caused by the SARS-CoV-2 virus has resulted in millions of deaths worldwide. The disease presents with various manifestations that can vary in severity and long-term outcomes. Previous efforts have contributed to the development of effective strategies for treatment and prevention by uncovering the mechanism of viral infection. We now know all the direct protein–protein interactions that occur during the lifecycle of SARS-CoV-2 infection, but it is critical to move beyond these known interactions to a comprehensive understanding of the “full interactome” of SARS-CoV-2 infection, which incorporates human microRNAs (miRNAs), additional human protein-coding genes, and exogenous microbes. Potentially, this will help in developing new drugs to treat COVID-19, differentiating the nuances of long COVID, and identifying histopathological signatures in SARS-CoV-2-infected organs. To construct the full interactome, we developed a statistical modeling approach called MLCrosstalk (multiple-layer crosstalk) based on latent Dirichlet allocation. MLCrosstalk integrates data from multiple sources, including microbes, human protein-coding genes, miRNAs, and human protein–protein interactions. It constructs "topics" that group SARS-CoV-2 with genes and microbes based on similar patterns of co-occurrence across patient samples. We use these topics to infer linkages between SARS-CoV-2 and protein-coding genes, miRNAs, and microbes. We then refine these initial linkages using network propagation to contextualize them within a larger framework of network and pathway structures. Using MLCrosstalk, we identified genes in the IL1-processing and VEGFA–VEGFR2 pathways that are linked to SARS-CoV-2. We also found that Rothia mucilaginosa and Prevotella melaninogenica are positively and negatively correlated with SARS-CoV-2 abundance, a finding corroborated by analysis of single-cell sequencing data.
The third instar larvae of Anomala corpulenta and Holotrichia oblita were injected with a standardized dose of spores of Bacillus popilliae Dutky, and the reactions of hemoeytes were examined during the first 24 hours after the injection. Agglomerates of hemoeytes were formed in all the injected larvae and they attached to the fat body and internal surfaces of the body cavity.In the more susceptible larvae of Anomala corpulenta, hemoeytes formed clumps and the cells underwent lysis to yield the melanian acellular substance. The necrotising masses may become encapsulated by plasmatocytes to form capsules with black cores within 5 min., althouth this encapsulation occurred around a few agglomerates. In the nonsusceptible larvae of Holotrichia oblita, most of clumps consisted of spherule hemoeytes, granular hemoeytes and plasmatocytes and the bacteria. The initial aggregetion stage was very rapid, occurring within 5 min., and it was brought about by the release of an adhesive flocculent material by the spherule hemoeytes in contact with the bacteria. Within 24 hours, we did not found any hemocyte lysis and melanization.The result shows that the responses of the hemoeytes of Anomala corpulenta and Holotrichia oblita to the pathogenic Bacillus can give indication of their natural infective rates, and that encapsulation and clump formation can effectively prevent the-development of the bacterial spores.
Objective: To study the intestinal flora specific differences with different lesional stages of metabolic (disorder) associated fatty liver disease (MAFLD), namely simple steatosis and steatohepatitis, so as to provide a new direction for MAFLD-related intestinal flora transplantation and targeted therapy. Methods: Mice were fed with normal diet, methionine-choline deficient diet (MCD) and a high-fat high-fructose diet (HFHF) for 12 weeks to construct simple steatosis and steatohepatitis models. HE and Sirius scarlet staining was performed to observe the liver pathological changes. The qPCR method was used to evaluate inflammation and liver fibrosis factors. A fully automatic biochemical analyzer was used to detect changes in liver transaminase and blood lipids. 16S rRNA sequencing method was used to observe the intestinal flora differences in the feces of each group of mice. The comparison of means between two groups was performed by t-test, and the comparison of means between multiple groups was performed by one-way analysis of variance. Kruskal-Wallis rank sum test was used for non-normally distributed data. Results: NAFLD scores were determined with pathological sections (HE and Sirius scarlet staining) of mice liver, which showed that the inflammation and liver fibrosis scores of the MCD and HFHF groups were 2.12 ± 0.18 and 1.06 ± 0.24, and 2.22 ± 0.16 and 0.46 ± 0.10, respectively. The degree of liver inflammation and fibrosis was significantly higher in the MCD than the HFHF group (P < 0.001 and P < 0.01). Lipid deposition was higher in the HFHF than the MCD group (P < 0.001), and the scores were 2.36 ± 0.17 and 1.60 ± 0.24 respectively. Simultaneously, the inflammatory [tumor necrosis factor-A (TNF-a), chemokine factor-2 (CXCL-2)] and hepatic fibrosis indicators [vascular smooth muscle actin alpha (a-SMA) and connective tissue growth factor (CTGF)] had confirmed the above-mentioned results at the transcription level. Moreover, the intestinal flora diversity was reduced (P < 0.05) in the MCD group than the HFHF group, and the Simpson and Shannon index were 0.31 ± 0.10 and 0.42 ± 0.05, and 2.03 ± 0.33 and 1.70 ± 0.28, respectively, and the differences were significant between different intestinal flora groups. The levels of Desulfovibrio, Odoribacter, and Roseburia flora were significantly increased in the HFHF than the MCD group, and the levels of Faecalibaculum, Parasutterella, Alipis, Butyricimonas_virosa, Turicibacter_sp, and Romboutsia_ilealis were significantly increased in the MCD than the HFHF group, and the difference was statistically significant (P < 0.05). Conclusion: There are significant differences in intestinal flora diversity between simple steatosis and steatohepatitis models. Therefore, clarifying the difference between the two may provide a new direction for the stage manner treatment of MAFLD.目的： 研究代谢（紊乱）相关脂肪性肝病(MAFLD）不同病变阶段，即单纯性脂肪肝和脂肪性肝炎病变阶段中肠道菌群的具体差异，为MAFLD相关的肠道菌群移植及靶向肠道菌群治疗提供新的方向。 方法： 分别以正常饮食、蛋氨酸-胆碱缺乏饮食（MCD）和高脂高果糖饮食（HFHF）喂养小鼠12周，构建单纯性脂肪肝和脂肪性肝炎模型；通过肝脏HE染色和天狼猩红染色观察其病理改变，应用qPCR方法对炎症和肝纤维化因子进行评估，全自动生化仪检测转氨酶及血脂变化，同时用16S rRNA测序观察各组小鼠粪便中肠道菌群的差异。两组间均数比较采用t检验，多组间均数比较采用单因素方差分析，非正态分布数据采用Kruskal-Wallis秩和检验。 结果： 通过小鼠肝脏HE病理切片和天狼猩红染色进行非酒精性脂肪性肝病活动度评分可知，MCD和HFHF组的炎症评分分别为2.12±0.18和1.06±0.24，肝纤维化评分为2.22±0.16和0.46±0.10，MCD饮食组小鼠肝脏炎症及纤维化程度明显重于HFHF饮食组（P < 0.001及P < 0.01）；HFHF组的脂质沉积重于MCD饮食组（P < 0.001），其评分值分别为2.36±0.17和1.60±0.24。同时炎症指标肿瘤坏死因子-a、趋化因子-2和肝纤维化指标血管平滑肌肌动蛋白、结缔组织生长因子在转录水平上对上述结果得到了验证。除此之外，相对于HFHF组，MCD组小鼠肠道菌群多样性降低（P < 0.05），其Simpson指数分别为0.31±0.10和0.42±0.05，Shannon指数为2.03±0.33和1.70±0.28，不同分组间菌群存在明显差异。相对于MCD饮食组，HFHF组中Desulfovibrio、Odoribacter、Roseburia菌群水平明显升高；相对于HFHF组，MCD饮食组小鼠Faecalibaculum、Parasutterella、Alistipes、Butyricimonas_virosa、Turicibacter_sp、Romboutsia_ilealis菌群水平升高，差异具有统计学意义（P < 0.05）。 结论： 单纯性脂肪肝和脂肪性肝炎模型中肠道菌群差别显著，明确两者差异可能为分阶段治疗MAFLD提供新的方向。.
Thermoanaerobacterium aotearoense SCUT27, isolated from a hot spring in China, is a strictly anaerobic, thermophilic bacterium capable of degrading xylan and converting both pentose and hexose to ethanol with high yields. Here, we report the draft genome sequence of SCUT27, which reveals insights into the mechanisms of carbon source coutilization and xylan degradation in this thermophilic microorganism.
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