Pathogens,faecal indicators and human-specific microbial source-tracking markers in sewage

The objective of this review is to assess the current state of knowledge of pathogens, general faecal indicators and human-specific microbial source tracking markers in sewage. Most of the microbes present in sewage are from the microbiota of the human gut, including pathogens. Bacteria and viruses are the most abundant groups of microbes in the human gut microbiota. Most reports on this topic show that raw sewage microbiological profiles reflect the human gut microbiota. Human and animal faeces share many commensal microbes as well as pathogens. Faecal-orally transmitted pathogens constitute a serious public health problem that can be minimized through sanitation. Assessing both the sanitation processes and the contribution of sewage to the faecal contamination of water bodies requires knowledge of the content of pathogens in sewage, microbes indicating general faecal contamination and microbes that are only present in human faecal remains, which are known as the human-specific microbial source-tracking (MST) markers. Detection of pathogens would be the ideal option for managing sanitation and determining the microbiological quality of waters contaminated by sewage; but at present, this is neither practical nor feasible in routine testing. Traditionally, faecal indicator bacteria have been used as surrogate indicators of general faecal residues. However, in many water management circumstances, it becomes necessary to detect both the origin of faecal contamination, for which MST is paramount, and live micro-organisms, for which molecular methods are not suitable. The presence and concentrations of pathogens, general faecal indicators and human-specific MST markers most frequently reported in different areas of the world are summarized in this review.     

Winning and losing with microbes: how microbially mediated fitness differences influence plant diversity

Interactions between plants and soil microbes can strongly influence plant diversity and community dynamics. Soil microbes may promote plant diversity by driving negative frequency‐dependent plant population dynamics, or may favor species exclusion by providing one species an average fitness advantage over others. However, past empirical research has focused overwhelmingly on the consequences of frequency‐dependent feedbacks for plant species coexistence and has generally neglected the consequences of microbially mediated average fitness differences. Here we use theory to develop metrics that quantify microbially mediated plant fitness differences, and show that accounting for these effects can profoundly change our understanding of how microbes influence plant diversity. We show that soil microbes can generate fitness differences that favour plant species exclusion when they disproportionately harm (or favour) one plant species over another, but these fitness differences may also favor coexistence if they trade off with competition for other resources or generate intransitive dominance hierarchies among plants. We also show how the metrics we present can quantify microbially mediated fitness differences in empirical studies, and explore how microbial control over coexistence varies along productivity gradients. In all, our analysis provides a more complete theoretical foundation for understanding how plant–microbe interactions influence plant diversity.     

When and where plant‐soil feedback may promote plant coexistence: a meta‐analysis

Plant‐soil feedback (PSF) theory provides a powerful framework for understanding plant dynamics by integrating growth assays into predictions of whether soil communities stabilise plant–plant interactions. However, we lack a comprehensive view of the likelihood of feedback‐driven coexistence, partly because of a failure to analyse pairwise PSF, the metric directly linked to plant species coexistence. Here, we determine the relative importance of plant evolutionary history, traits, and environmental factors for coexistence through PSF using a meta‐analysis of 1038 pairwise PSF measures. Consistent with eco‐evolutionary predictions, feedback is more likely to mediate coexistence for pairs of plant species (1) associating with similar guilds of mycorrhizal fungi, (2) of increasing phylogenetic distance, and (3) interacting with native microbes. We also found evidence for a primary role of pathogens in feedback‐mediated coexistence. By combining results over several independent studies, our results confirm that PSF may play a key role in plant species coexistence, species invasion, and the phylogenetic diversification of plant communities.     

Antioxidants and iron chelators inhibit oxygen radical generation in fungal cultures of plant pathogenic fungi

Eutypa dieback and Esca are serious fungal grapevine trunk diseases (GTDs). Eutypa dieback is caused by Eutypa lata (Elata), and is often associated Phaeoacremonium minimum (Pmin), and Phaeomoniella chlamydospora (Pch) which are also important contributors to Esca disease.Understanding the complex pathogenesis mechanisms used by these causative fungi may potentially lead targeted treatments for GTDs in the future. Elata has been reported as a wood decay “soft rot” fungus and understanding of Elata’s pathogenesis chemistries can aid in controlling GTDs. Recent work that suggests that Pmin and Pch may contribute to pathogenesis by stimulating hydroxyl radical generation via secretion of low molecular weight phenolic metabolites. Building on these findings, we tested a hypothesis that antioxidants and chelators, and biocontrol agents that have been reported to secrete antioxidants and low molecular weight chelators, may inhibit the growth and activity of these fungi. Butylated hydroxy anisole (BHA) and butylated hydroxytoluene (BHT) were tested as antioxidant/chelators. BHA was found to be a highly effective control measure for the three pathogenic fungi tested at concentrations >0.5 mM. The biocontrol species Bacillus subtilis and Hypocrea (Trichoderma) atroviride were also tested, with both H. atroviride and B. subtilis effectively inhibiting growth of the three GTD fungi.     

Bacteriophages: A weapon against mixed-species biofilms in the food processing environment

Mixed-species biofilms represent the most frequent actual lifestyles of microorganisms in food processing environments, and they are usually more resistant to control methods than single-species biofilms. The persistence of biofilms formed by foodborne pathogens is believed to cause serious human diseases. These challenges have encouraged researchers to search for novel, natural methods that are more effective towards mixed-species biofilms. Recently, the use of bacteriophages to control mixed-species biofilms have grown significantly in the food industry as an alternative to conventional methods. This review highlights a comprehensive introduction of mixed-species biofilms formed by foodborne pathogens and their enhanced resistance to anti-biofilm removal strategies. Additionally, several methods for controlling mixed-species biofilms briefly focused on applying bacteriophages in the food industry have also been discussed. This article concludes by suggesting that using bacteriophage, combined with other ‘green’ methods, could effectively control mixed-species biofilms in the food industry.     

The application and research progress of bacteriophages in food safety

The abuse of antibiotics and the emergence of drug-resistant bacteria aggravate the problem of food safety. Finding safe and efficient antibiotic substitutes is an inevitable demand for ensuring the safety of animal-derived food. Bacteriophages are a kind of virus that can infect bacteria, fungi or actinomycetes. They have advantages of simple structure, strong specificity and nontoxic side effects for the human body. Bacteriophages can not only differentiate live cells from dead ones but also detect bacteria in a viable but nonculturable state. These characteristics make bacteriophages more and more widely used in the food industry. This paper describes the concept and characteristics of bacteriophages, and introduces the application of bacteriophages in preharvest production, food processing, storage and sales. Several methods of using bacteriophages to detect foodborne pathogens are listed. Finally, the advantages and limitations of bacteriophages in the food industry are summarized, and the application prospect of bacteriophages in the food industry is discussed.     

角膜激光共聚焦显微镜在单眼感染性角膜炎疾病诊断中的应用

摘要 目的：探讨角膜激光共聚焦显微镜在单眼感染性角膜炎疾病诊断中的应用价值。方法：回顾性研究2020年6月到2021年6月选择在本院诊治的单眼感染性角膜炎疾病患者62例,所有患者都给予角膜激光共聚焦显微镜检查,记录影像学特征并判断诊断价值（以病原学诊断为金标准）。结果：真菌性角膜炎在角膜激光共焦显微镜下的病变区纵横交错的高反射的真菌菌丝或高反光细长颗粒状的孢子,细菌性角膜炎的病变处会聚集活化的树突状细胞及大量的炎症细胞,病毒性角膜炎的基底膜下神经纤维密度、神经主干的分支数减少,棘阿米巴性角膜炎的包囊表现为圆形高反光厚壁结构。角膜激光共聚焦显微镜判断为病毒性角膜炎17例,诊断病毒性角膜炎的敏感性与特异性为94.4 %和100.0 %;角膜激光共聚焦显微镜判断为棘阿米巴性角膜炎4例,诊断棘阿米巴性角膜炎的敏感性与特异性为94.4 %和100.0 %;角膜激光共聚焦显微镜判断为细菌性角膜炎21例,诊断细菌性角膜炎的敏感性与特异性为95.5 %和97.5 %;角膜激光共聚焦显微镜判断为真菌性角膜炎20例,诊断真菌性角膜炎的敏感性与特异性为94.4 %和93.2 %。ROC曲线分析显示角膜激光共聚焦显微镜诊断细菌性角膜炎、真菌性角膜炎、病毒性角膜炎、棘阿米巴性角膜炎的曲线下面积分别为0.525、0.579、0.777、0.731。结论：角膜激光共聚焦显微镜在单眼感染性角膜炎疾病诊断中的应用能较好的区分细菌性角膜炎、真菌性角膜炎、病毒性角膜炎、棘阿米巴性角膜炎,具有良好的诊断敏感性与特异性。     

Viral metagenomics reveals diverse viruses in the fecal samples of children with diarrhea

Diarrhea is the third leading cause of death in developing countries in children under the age of five. About half a million children die of diarrhea every year, most of which in developing countries. Viruses are the main pathogen of diarrhea. In China, the fecal virome of children with diarrhea has been rarely studied. Using an unbiased viral metagenomics approach, we analyzed the fecal virome in children with diarrhea. Many DNA or RNA viruses associated with diarrhea identified in those fecal samples were mainly from six families of Adenoviridae, Astroviridae, Caliciviridae, Parvoviridae, Picornaviridae, and Reoviridae. Among them, the family of Caliciviridae accounts for the largest proportion of 78.42%, following with Adenoviridae (8.94%) and Picornaviridae (8.36%). In addition to those diarrhea-related viruses that have already been confirmed to cause human diarrhea, the viruses not associated with diarrhea were also identified including anellovirus and picobirnavirus. This study increased our understanding of diarrheic children fecal virome and provided valuable information for the prevention and treatment of viral diarrhea in this area.     

Genome annotation and antimicrobial properties of Bacillus toyonensis VU‐DES13, isolated from the Folsomia candida gut

Antibiotic resistance necessitates the search for new bioactive compounds with novel mechanisms of action. Natural products derived from bacteria and fungi are widely used in the field of medicine and new environments can be explored as sources of antimicrobials. Bacteria associated with springtails have shown high inhibitory activity against pathogens. Here, we characterized a bacterial strain with high potential for antimicrobial activity, isolated from the gut of the springtail Folsomia candida Willem (Collembola: Isotomidae). The strain was characterized using the ‘analytical profile index’ and the ‘minimal inhibitory concentration’ assay to test for antibiotic resistance. Agar overlay and agar disk diffusion assays were used to test the inhibitory activity of the strain and its extract against a variety of pathogens, and reporter assays were used to investigate the mode of action. High‐performance liquid chromatography was used to analyze and fractionate the extract of bacterial culture, followed by additional assays on the fractions. The genome of the strain was screened for presence of antibiotic resistance genes and secondary metabolite gene clusters. The isolate was identified as Bacillus toyonensis Jiménez et al., but it displayed differences in metabolic profile when compared to the type species. The isolate was highly resistant to penicillin and inhibited the growth of a variety of pathogenic microorganisms. Genome analysis revealed an enrichment of resistance genes for β‐lactam antibiotics compared to the type isolate. Also, secondary metabolite clusters involved in the production of siderophores, bacteriocins, and nonribosomal peptide synthetases were identified. In conclusion, a unique Bacillus strain was isolated from the gut of F. candida, for which we provide evidence of inhibitory activity against an array of pathogens. This, coupled with high resistance to penicillin as substantiated by the presence of resistance genes, points to the potential of B. toyonensis VU‐DES13 to provide a new source of antimicrobial compounds.