Research progress of gut microbiota in diabetic retinopathy / 中华眼底病杂志

The concept of "Microbe-gut-eye axis" holds that metabolites of the gut microbiota are involved in the pathogenesis of various eye diseases. The composition and diversity of gut microbiota in diabetic retinopathy (DR) patients are significantly different from those in non-DR patients. Metabolites of the gut microbiota such as lipopolysaccharide, short-chain fatty acid, bile acids and branched-chain amino acid aggravate or attenuate the progression of DR by regulating the release of inflammatory cytokines, mitochondrial function, insulin sensitivity, immune response, and autophagy of retinal cells. Therefore, gut microbiota and their metabolites play a role in the occurrence and development of DR through multiple pathways. The participation of gut microbiota may open up a new way to prevent and treat DR in the future.

Research advances in the role of gastrointestinal microbe in pancreatic cancer / 中华肝胆外科杂志

In recent years, there have been increasing studies on the role of microorganisms in pancreatic cancer which show that bacteria and fungi are closely associated with pancreatic cancer. In the past, the pancreas has usually been considered as a sterile organ. Recent studies, however, show that microbiome exists in the pancreas. Bacteria can migrate from the intestine to the pancreas. Changing the composition of the microbiome may have positive effects on treatment of pancreatic cancer. This article reviews the relationship between gastrointestinal microbiome and pancreatic cancer.

PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing datasets as illustrated by application to COVID-19 / 医学前沿

Pathogenic microbes can induce cellular dysfunction, immune response, and cause infectious disease and other diseases including cancers. However, the cellular distributions of pathogens and their impact on host cells remain rarely explored due to the limited methods. Taking advantage of single-cell RNA-sequencing (scRNA-seq) analysis, we can assess the transcriptomic features at the single-cell level. Still, the tools used to interpret pathogens (such as viruses, bacteria, and fungi) at the single-cell level remain to be explored. Here, we introduced PathogenTrack, a python-based computational pipeline that uses unmapped scRNA-seq data to identify intracellular pathogens at the single-cell level. In addition, we established an R package named Yeskit to import, integrate, analyze, and interpret pathogen abundance and transcriptomic features in host cells. Robustness of these tools has been tested on various real and simulated scRNA-seq datasets. PathogenTrack is competitive to the state-of-the-art tools such as Viral-Track, and the first tools for identifying bacteria at the single-cell level. Using the raw data of bronchoalveolar lavage fluid samples (BALF) from COVID-19 patients in the SRA database, we found the SARS-CoV-2 virus exists in multiple cell types including epithelial cells and macrophages. SARS-CoV-2-positive neutrophils showed increased expression of genes related to type I interferon pathway and antigen presenting module. Additionally, we observed the Haemophilus parahaemolyticus in some macrophage and epithelial cells, indicating a co-infection of the bacterium in some severe cases of COVID-19. The PathogenTrack pipeline and the Yeskit package are publicly available at GitHub.

Intestinal microbiome changes in patients with postpartum depression / 西安交通大学学报(医学版)

【Objective】 To analyze the changes of gut microbes in patients with postpartum depression so as to explore the relationship between postpartum depression and gut microbes. 【Methods】 A total of 60 postpartum subjects were recruited to participate in this study. The depression status of the participants was scored using the Edinburgh Postpartum Depression Scale (EPDS). Those with a score ≥13 were included in the postpartum depression group (PPD group), while those with a score less than 13 were included in the postpartum healthy control group (PPHC group). The feces of these 60 subjects were collected, and the fecal whole genome DNA was extracted for 16S rDNA sequencing. The data of changes in the bacterial diversity between the groups were obtained, and the possible correlation between the changes of intestinal microbes and postpartum depression was analyzed. 【Results】 The number of microorganisms in PPD patients was significantly reduced (P<0.001); the Chao1 index (P<0.001) and ACE index (P<0.001) of α diversity decreased significantly. There were also significant differences in β diversity between the two groups. Analysis of the bacteria in the groups showed that Acetanaerobacterium, Adlercreutzia, Allobaculum, Alloprevotella, Bifidobacterium, Christensenella, Escherichia, Eubacterium, Faecalicatena, Fusobacterium, Haemophilus, Intestinimonas, Lactobacillus, Megamonas, Monoglobumus, Muribaculum, Oscillospira, Paraprevotella, Streptococcus, Raoultibacter, Ruminococcus and Stomatobaculum were significantly enriched in PPHC group. In contrast, Kineothrix, Lachnoclostridium, Acinetobacter, Aquisphaera, Enterococcus, and Mucispirillum were enriched in PPD group. RDA/CCA analysis showed that EPDS was positively correlated with Prevotella, Kineothrix, and Alistipes, but negatively correlated with Lachnospira. 【Conclusion】 This study found that the intestinal flora of patients with postpartum depression was significantly disrupted, and there was a correlation between the intestinal flora and postpartum depression symptom score. Therefore, intestinal microbial markers may contribute to the diagnosis and treatment of patients with postpartum depression.

Correlation analysis between continuous cropping obstacle of Gastrodia elata and Ilyonectria fungi and relieving strategy / 中国中药杂志

The continuous cropping obstacle of Gastrodia elata is outstanding, but its mechanism is still unclear. In this study, microbial changes in soils after G. elata planting were investigated to explore the mechanism correlated with continuous cropping obstacle. The changes of species and abundance of fungi and bacteria in soils planted with G. elata after 1, 2, and 3 years were compared. The pathogenic fungi that might cause continuous cropping diseases of G. elata were isolated. Finally, the prevention and control measures of soil-borne fungal diseases of G. elata were investigated with the rotation planting pattern of "G. elata-Phallus impudicus". The results showed that G. elata planting resulted in the decrease in bacterial and fungal community stability and the increase in harmful fungus species and abundance in soils. This change was most obvious in the second year after G. elata planting, and the soil microbial community structure could not return to the normal level even if it was left idle for another two years. After G. elata planting in soils, the most significant change was observed in Ilyonectria cyclaminicola. The richness of the Ilyonectria fungus in soils was significantly positively correlated with the incidence of G. elata diseases. When I. cyclaminicola was inoculated in the sterile soil, the rot rate of G. elata was also significantly increased. After planting one crop of G. elata and one to three crops of P. impudicus, the fungus community structure in soils gradually recovered, and the abundance of I. cyclaminicola decreased year by year. Furthermore, the disease rate of G. elata decreased. The results showed that the cultivation of G. elata made the Ilyonectria fungi the dominant flora in soils, and I. cyclaminicola served as the main pathogen of continuous cropping diseases of G. elata, which could be reduced by rotation planting with P. impudicus.

Advances of miRNA-mediated regulatory roles in plant-microbe interaction / 生物工程学报

There are many bidirectional communication and crosstalk between microbes and host plants. The plant-pathogen interaction directly affects the survival of host plants, while the interaction between plants and their probiotics benefits both. Plant miRNA responds quickly to pathogenic or beneficial microbes when they enter the plant tissues, while microbes also produce miRNA-like RNA (milRNA) to affect plant health. These means miRNA or milRNA is an important fast-responding molecular mediator in plant-microbe interactions, and these internal mechanisms have been better understood in recent years. This review summarized the regulatory roles of miRNA in plant-pathogens and plant-probiotics interaction. The regulatory role of miRNA in disease resistance of host plants during plant-pathogens interaction, and the regulatory role of miRNA in promoting host growth and development during plant-probiotics interaction, as well as the cross-kingdom regulatory role of milRNA in host plants, were discussed in-depth.

Research progress of microbe gut brain axis / 中国综合临床

The emergence of gut microbes has become one of the key regulatory factors of gut brain function, and has made people realize the importance of microbe gut brain axis.The gut microbiota and brain are interconnected through immune system, tryptophan metabolism, vagus nerve and endocrine system.Many factors can affect the composition of gut microbiota, including infection, mode of delivery, use of antibiotics, stress, and host genetics.Recent studies have shown that gut microbiota may be associated with many diseases, including autism, irritable bowel syndrome and so on.Future research will focus on understanding the underlying mechanisms of the microbial gut brain axis and attempt to elucidate microbial based intervention and treatment strategies for neuropsychiatric diseases.

Progress in enhancing electron transfer rate between exoelectrogenic microorganisms and electrode interface / 生物工程学报

Exoelectrogenic microorganisms are the research basis of microbial electrochemical technologies such as microbial fuel cells, electrolytic cells and electrosynthesis. However, their applications are restricted in organic degradation, power generation, seawater desalination, bioremediation, and biosensors due to the weak ability of biofilm formation and the low extracellular electron transfer (EET) efficiency between exoelectrogenic microorganisms and electrode. Therefore, engineering optimization of interaction between exoelectrogenic microorganisms and electrode interface recently has been the research focus. In this article, we review the updated progress in strategies for enhancing microbe-electrode interactions based on microbial engineering modifications, with a focus on the applicability and limitations of these strategies. In addition, we also address research prospects of enhancing the interaction between electroactive cells and electrodes.

The research progress of novel anxiolytics / 中国药理学通报

Anxiety disorder holds the highest prevalence among adults in China, whereas the research and development of its therapeutic drugs are relatively backward. At present, the commonly used anxiolytics in clinical practice are some benzodiazepines, non-benzodiazepines, and antidepressants, most of which have unpleasant side effects. By searching the literature in Pubmed, we here summarized the research progress of novel anxiolytics in recent years from the following aspects: endocannabinoid system, gut-microbe-brain axis, and GABA

Changes in Cold and Hot Syndrome and Gastrointestinal Bacterial Community Structure in Mice by Intervention with Food of Different Nature / 中国结合医学杂志

OBJECTIVE@#To reveal the effect of foods with different natures on cold or hot syndrome and gastrointestinal bacterial community structure in mice.@*METHODS@#Forty-five 6-week-old male ICR Kunming mice of clean grade were divided into 5 groups, 9 per group, including the control (CK), hot nature herbs (HM), Hong Qu glutinous rice wine (RW), tea rice wine (TW), and cold nature herbs (CM) groups. Distilled water or corresponding herbs were administered to mice (0.01 mL/g body weight) in the 5 groups by gastric infusion respectively, once daily for 28 d. Appearance, behavior, and serum biochemical indicators, including 5-hydroxytryptamine (5-HT), thyroid stimulating hormone (TSH), noradrenaline (NE), cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), the hot nature index, as well as the gastrointestinal bacterial community structure were analyzed in all groups after treatment.@*RESULTS@#After supplementation for 28 d, CM and TW mice showed different degrees of cold syndrome, and HM and RW mice showed different degrees of hot syndrome. Compared with the HM and RW mice, the TSH, NE, cAMP levels and hot nature indices in the CM and TW mice were significantly decreased and 5-HT and cGMP levels were significantly increased (P<0.05). There was no obvious change in appearance or behavior in CK mice. Results of clustering analysis showed that the gastrointestinal bacterial community structures were highly similar in TW and CM mice as well as in RW and HM mice, and that they were from the same branch, respectively, when the distance was 0.02. The key microbes associated with cold syndrome were Lachnospiraceae uncultured, Lactococcus, etc., and the key microbes associated with hot syndrome were S24-7 norank, Ruminococcaceae uncultured, etc. CONCLUSION: The interventions with different nature foods could change cold or hot syndrome in mice, leading to changes in gastrointestinal bacterial community structure.

Detection of intestinal microbial changes in rotenone-induced Parkinson' s disease model mice / 解剖学报

[Abstract] Objective To investigate the changes of intestinal microbes in rotenone-induced Parkinson' s disease (PD) mice based on 16S rRNA gene sequencing. Methods Fourteen 8-week-old male C57BL/6J mice were randomly divided into two groups: 6 mice in the control group and 8 mice in the model group. The model mice were injected subcutaneously with rotenone (3 mg/kg) for 5 weeks, and the bod)' weight was measured once a week. After 5 weeks, behavioral tests were perfonned, including the rotating rod test and the open field test. The contents of the tract were used for intestinal microbial detection analysis. Results After 5 weeks of rotenone treatment, the weight of PD mice was significantly lower than that of the control mice(P 0. 05), but the microbial species showed significant differences. Among them, the PD mice showed a significant decrease in the intestinal Turicibacter (P < 0 . 0 1), a significant increase in norank f Lachnospiraceae (P < 0. 01), a significant decrease in norank_f Erysipelotrichaceae(P<0. 01), and a significant increase in Lachnoclostridium{ P<0. 0 1) . Conclusion Intestinal microbes in PD mice are disordered, and these intestinal flora ma)' be involved in the development of dyskinesia in PD mice.

Antepenultimate residue at the C-terminus of NADPH oxidase RBOHD is critical for its function in the production of reactive oxygen species in Arabidopsis / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Production of reactive oxygen species (ROS) is a conserved immune response primarily mediated by NADPH oxidases (NOXs), also known in plants as respiratory burst oxidase homologs (RBOHs). Most microbe-associated molecular patterns (MAMPs) trigger a very fast and transient ROS burst in plants. However, recently, we found that lipopolysaccharides (LPS), a typical bacterial MAMP, triggered a biphasic ROS burst. In this study, we isolated mutants defective in LPS-triggered biphasic ROS burst (delt) in Arabidopsis, and cloned the DELT1 gene that was shown to encode RBOHD. In the delt1-2 allele, the antepenultimate residue, glutamic acid (E919), at the C-terminus of RBOHD was mutated to lysine (K). E919 is a highly conserved residue in NADPH oxidases, and a mutation of the corresponding residue E568 in human NOX2 has been reported to be one of the causes of chronic granulomatous disease. Consistently, we found that residue E919 was indispensable for RBOHD function in the MAMP-induced ROS burst and stomatal closure. It has been suggested that the mutation of this residue in other NADPH oxidases impairs the protein’s stability and complex assembly. However, we found that the E919K mutation did not affect RBOHD protein abundance or the ability of protein association, suggesting that the residue E919 in RBOHD might have a regulatory mechanism different from that of other NOXs. Taken together, our results confirm that the antepenultimate residue E is critical for NADPH oxidases and provide a new insight into the regulatory mechanisms of RBOHD.

Advances in research on relationship between osteoporosis and intestinal microbe / 上海交通大学学报（医学版）

Osteoporosis, one of the severest diseases in the middle-aged and elderly population, is the result of the disorder of the normal bone turnover process. At present, many studies have shown that bone turnover is closely related to the microbial environment in the human body. The largest microbiota in the human body exists in the intestine and plays an important role in the normal physiological activities of the body, such as nutrition, metabolism, immunity and barrier. Intestinal microbe can regulate endocrine and immune system through a series of processes, thereby affecting the process of bone turnover in the body. This article briefly reviews the current research about the effects of intestinal microbe on the process of bone turnover in the body. It is expected to provide new ideas for the treatment of osteoporosis by exploring the relationship between osteoporosis and intestinal microbe.

Antepenultimate residue at the C-terminus of NADPH oxidase RBOHD is critical for its function in the production of reactive oxygen species in Arabidopsis / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Production of reactive oxygen species (ROS) is a conserved immune response primarily mediated by NADPH oxidases (NOXs), also known in plants as respiratory burst oxidase homologs (RBOHs). Most microbe-associated molecular patterns (MAMPs) trigger a very fast and transient ROS burst in plants. However, recently, we found that lipopolysaccharides (LPS), a typical bacterial MAMP, triggered a biphasic ROS burst. In this study, we isolated mutants defective in LPS-triggered biphasic ROS burst (delt) in Arabidopsis, and cloned the DELT1 gene that was shown to encode RBOHD. In the delt1-2 allele, the antepenultimate residue, glutamic acid (E919), at the C-terminus of RBOHD was mutated to lysine (K). E919 is a highly conserved residue in NADPH oxidases, and a mutation of the corresponding residue E568 in human NOX2 has been reported to be one of the causes of chronic granulomatous disease. Consistently, we found that residue E919 was indispensable for RBOHD function in the MAMP-induced ROS burst and stomatal closure. It has been suggested that the mutation of this residue in other NADPH oxidases impairs the protein's stability and complex assembly. However, we found that the E919K mutation did not affect RBOHD protein abundance or the ability of protein association, suggesting that the residue E919 in RBOHD might have a regulatory mechanism different from that of other NOXs. Taken together, our results confirm that the antepenultimate residue E is critical for NADPH oxidases and provide a new insight into the regulatory mechanisms of RBOHD.

Deep in shadows: Epigenetic and epigenomic regulations of medicinal plants / 中草药·英文版

Around 60% of the extant plants have medicinal and health-promoting values. Genuine medicinal material (geoherb) is produced in particular geographic regions, that is defined ecological environment and cultivation pipeline. The clinical efficacy of a geoherb is superior to that of the same medicinal plant growing in other regions. The special medicinal features of a plant are determined by its genome, while the proper ecological conditions have major effects on the formation of a geoherb, which is at least partially mediated by the epigenetics. By epigenetics/epigenomics, researchers uncover the complexities of the influence of the environment on the expression of genes that control medicinal plant growth, development, stress responses, and medicinal phytometabolite yield, and put the other “omics layers” in a meaningful biological context. The unique phenotypes of geoherb are closely related to the growth, development, and stress responses of medicinal plants. In addition to the commonly known genetic control, epigenetic machineries, active at the population level, play an essential role in the formation of geoherbs. This contribution gives a comprehensive overview of the epigenetic regulation of medicinal plants, and the associated microbes, and the role of DNA methylation, small non-coding RNA, transposable elements, and histone modifications in the gene expression regulation of geoherbs and relevant microbiota. The epigenetic and epigenomic mechanisms should be highlighted in the study of specific phenotype and indigenousness of geoherbalism. Revealing the correlation between epigenetics and geoherbs could shed light on the quality assessment, authentication, molecular breeding, and sustainable utilization of medicinal plants and the associated microbes.

Research progress on the etiology, clinical examination and treatment of peri-implantitis / 口腔疾病防治

@#Peri-implantitis is an inflammatory disease that occurs around dental implants and damages both soft and hard tissues, the characteristic feature of which is bone loss. The major etiology of peri-implantitis is dental plaque, including implant overload implants, a history of periodontitis, smoking and diabetes as risk factors. The standards for the clinical diagnosis of peri-implantitis are bleeding on probing, suppuration, a peri-implant pocket depth ≥5 mm, and X-ray evidence. Treatment includes mechanical debridement, drug therapy, laser treatment and surgical treatment. Regular supportive peri-implant therapy can be effective for curing and preventing peri-implantitis. In this paper, the etiology, clinical examination and treatment of periodontitis are reviewed.

Historical story on natural medicinal chemistry: Rapamycin / 中草药

The study on natural product chemistry plays an important role in drug development and microbe is one of the main sources of new drugs. Rapamycin is isolated from the bacterium ensconced in a sample of Easter Island's soil, the compound has led to several approved immunosuppressant and anticancer drugs. The researchers studying on the target of rapamycin have got the "Nobel-class" achievements. In this paper, the discovery and study on rapamycin is summarized to provide the references for future related research.

Bile-resistant Gram-negative bacteria effect of different kinds of root decoction pieces / 中国中药杂志

To investigate the microbial contamination in Chinese herbal decoction pieces with different functional types by studying the total aerobic microbial count (TAMC), and total yeast and mould count (TYMC) in 40 samples of 8 types of root decoction pieces; further evaluate the contamination load of bile-resistant Gram-negative bacteria, and identify the Gram-negative bacteria by using biochemical identification system for Gram-negative bacteria. Our results showed that the TAMC value was more than 1 000 CFU•g⁻¹ in 85% (34/40) samples, and was more than 100 CFU•g⁻¹ in 30% (12/40) samples; the contamination of bile-resistant Gram-negative bacteria was detected in 45% (18/40) of the samples. The bile-resistant Gram-negative bacteria load of seven batches of samples was N>1 000 MPN•g⁻¹. Sixteen bacterium strains including Serratia plymouthensis, Cedecea neteri, Escherichia vulneris, Klebsiella oxytoca, Enterobacter amnigenus, E. cloacae, E. sakazakii, Proteus penneri and E. gergoviae were obtained and identified. E. cloacae was the predominant bacterium that was isolated from Salviae Miltiorrhizae Radix et Rhizoma, while E. amnigenus, Yersinia pseudotuberculosis was the typical bacterium of Ophiopogonis Radix and Codonopsis Radix, respectively. All these suggested that the contamination of bile-resistant Gram-negative bacteria was severe for the root decoction pieces in Wuhan city. Microbial species have certain selection specificity for medicinal ingredients, so the type and limit of control bacteria for detection should be formulated according to the pollution type and quantity of bile-resistant Gram-negative bacteria.

Mechanism of Involvement of Intestinal Microbiota in Pathogenesis of Irritable Bowel Syndrome / 胃肠病学

The etiology and pathogenesis of irritable bowel syndrome (IBS) are not fully understood, and intestinal microbiota had been assumed as a possible factor in the pathogenesis of IBS.Increasing evidences have shown that alterations of gut microbiota were found in IBS patients and modulation of intestinal microbiota might be effective in the treatment of IBS.This article reviewed the mechanism of involvement of intestinal microbiota in pathogenesis of IBS by altering mucosal permeability, activating immune reaction, disturbing gastrointestinal motility and affecting brain-gut axis.

The origin of hydrogen peroxide in oral cavity and its role in oral microecology balance / 华西口腔医学杂志

Hydrogen peroxide, an important antimicrobial agent in oral cavity, plays a significant role in the balance of oral microecology. At the early stage of biofilm formation, about 80% of the detected initial colonizers belong to the genus Streptococcus. These oral streptococci use different oxidase to produce hydrogen peroxide. Recent studies showed that the produced hydrogen peroxide plays a critical role in modulating oral microecology. Hydrogen peroxide modulates biofilm development attributed to its growth inhibitory nature. Hydrogen peroxide production is closely associated with extracellular DNA(eDNA) release from microbe and the development of its competent cell which are critical for biofilm development and also serves as source for horizontal gene transfer. Microbe also can reduce the damage to themselves through several detoxification mechanisms. Moreover, hydrogen peroxide is also involved in the regulation of interactions between oral microorganisms and host. Taken together, hydrogen peroxide is an imperative ecological factor that contributes to the microbial equilibrium in the oral cavity. Here we will give a brief review of both the origin and the function in the oral microecology balance of hydrogen peroxide.