Standardized framework for assessing soil quality at antimony smelting site by considering microbial-induced resilience and heavy metal contamination.

Antimony smelting activities damage the soil and vegetation surroundings while generating economic value. However, no standardized methods are available to diagnose the extent of soil degradation at antimony smelting sites. This study developed a standardized framework for assessing soil quality by considering microbial-induced resilience and heavy metal contamination at Xikuangshan antimony smelting site. The soil resilience index (SRI) and soil contamination index (SCI) were calculated by Minimum Data Set and geo-accumulation model, respectively. After standardized by a multi-criteria quantitative procedure of modified Nemerow's pollution index (NPI), the integrated assessment of soil quality index (SQI), which is the minimum of SRINPI and SCINPI, was achieved. The results showed that Sb and As were the prominent metal(loid) pollutants, and significant correlations between SQI and SRI indicated that the poor soil quality was mainly caused by the low level of soil resilience. The primary limiting factors of SRI were Fungi in high and middle contaminated areas, and Skermanella in low contaminated area, suggesting that the weak soil resilience was caused by low specific microbial abundances. Microbial regulation and phytoremediation are greatly required to improve the soil quality at antimony smelting sites from the perspectives of pollution control and resilience improvement. This study improves our understanding of ecological effects of antimony smelting sites and provides a theoretical basis for ecological restoration and sustainable development of mining areas.

Recent advances in microbial high-value utilization of brewer's spent grain.

Mitigating the adverse impacts of agricultural and industrial by-products on human populations and the environment is essential. It is crucial to continually explore methods to upgrade and reengineer these by-products. Brewer's Spent Grain (BSG), the primary by-product of the beer brewing process, constitutes approximately 85% of these by-products. Its high moisture content and rich nutritional profile make BSG a promising candidate for microbial utilization. Consequently, valorizing high-yield, low-cost BSG through microbial fermentation adds significant value. This paper provides a comprehensive overview of two valorization pathways for BSG via microbial processing, tailored to the desired end products: utilizing fermented BSG as a nutritional supplement in human or animal diets, or cultivating edible fungi using BSG as a substrate. The review also explores the microbial fermentation of BSG to produce valuable metabolites, laying a theoretical foundation for its high-value utilization.

Multiple omics integration analysis reveals the regulatory effect of chitosan oligosaccharide on testicular development.

Infertility is a global health problem affecting millions of people of reproductive age worldwide, with approximately half caused by males. Chitosan oligosaccharide (COS) has strong antioxidant capacity, but its impact on the male reproductive system has not been effectively evaluated. To address this, we integrated RNA-seq, serum metabolomics and intestinal 16 S rDNA analysis to conduct a comprehensive investigation on the male reproductive system. The results showed that COS has potential targets for the treatment of oligospermia, which can promote the expression of meiotic proteins DDX4, DAZL and SYCP1, benefit germ cell proliferation and testicular development, enhance antioxidant capacity, and increase the expression of testicular steroid proteins STAR and CYP11A1. At the same time, COS can activate PI3K-Akt signaling pathway in testis and TM3 cells. Microbiome and metabolomics analysis suggested that COS alters gut microbial community composition and cooperates with serum metabolites to regulate spermatogenesis. Therefore, COS promotes male reproduction by regulating intestinal microorganisms and serum metabolism, activating PI3K-Akt signaling pathway, improving testicular antioxidant capacity and steroid regulation.

Identification of carbon fixation microorganisms and pathways in an aquifer contaminated with long-chain petroleum hydrocarbons.

Petroleum hydrocarbons (PHCs) can be biodegraded into CO2, and PHC-contaminated aquifers are always deemed as carbon sources. Fortunately, some carbon fixation microorganisms have been found in PHC-contaminated sites. However, most of the studies are related to volatile short-chain PHC, and few studies focus on long-chain PHC-contaminated sites. To reveal the carbon fixation microorganisms in these sites, in the study, a long-chain PHC polluted site in North China was selected. Through hydrochemical and metagenomics analysis, the structure and capacity of carbon fixing microorganisms in the site were revealed. Results showed that there were many kinds of carbon fixed microorganisms that were identified such as Flavobacterium, Pseudomonas. HP/4HB, rTCA, and DC/4HB cycles were dominated carbon fixation pathways. The long-chain PHC were weakly correlated with carbon fixation microorganisms, but it may stimulate the growth of some carbon fixation microorganisms, such as microorganisms involved in rTCA cycle. PRACTITIONER POINTS: The microorganisms with carbon fixation gene exist in the aquifer contaminated by long-chain petroleum hydrocarbon. Microorganisms that have the ability to degrade petroleum also have the ability to carbon fixation. Long-chain petroleum hydrocarbon may promote the growth of carbon fixation microorganisms.

Chemokines Kill Bacteria by Binding Anionic Phospholipids without Triggering Antimicrobial Resistance.

Classically, chemokines coordinate leukocyte trafficking during immune responses; however, many chemokines have also been reported to possess direct antibacterial activity in vitro. Yet, the bacterial killing mechanism of chemokines and the biochemical properties that define which members of the chemokine superfamily are antimicrobial remain poorly understood. Here we report that the antimicrobial activity of chemokines is defined by their ability to bind phosphatidylglycerol and cardiolipin, two anionic phospholipids commonly found in the bacterial plasma membrane. We show that only chemokines able to bind these two phospholipids kill Escherichia coli and Staphylococcus aureus and that they exert rapid bacteriostatic and bactericidal effects against E. coli with a higher potency than the antimicrobial peptide beta-defensin 3. Furthermore, our data support that bacterial membrane cardiolipin facilitates the antimicrobial action of chemokines. Both biochemical and genetic interference with the chemokine-cardiolipin interaction impaired microbial growth arrest, bacterial killing, and membrane disruption by chemokines. Moreover, unlike conventional antibiotics, E. coli failed to develop resistance when placed under increasing antimicrobial chemokine pressure in vitro. Thus, we have identified cardiolipin and phosphatidylglycerol as novel binding partners for chemokines responsible for chemokine antimicrobial action. Our results provide proof of principle for developing chemokines as novel antibiotics resistant to bacterial antimicrobial resistance mechanisms.

Rhizosphere microbial community construction during the latitudinal spread of the invader Chromolaena odorata.

The colonization of alien plants in new habitats is typically facilitated by microorganisms present in the soil environment. However, the diversity and structure of the archaeal, bacterial, and fungal communities in the latitudinal spread of alien plants remain unclear. In this study, the rhizosphere and bulk soil of Chromolaena odorata were collected from five latitudes in Pu' er city, Yunnan Province, followed by amplicon sequencing of the soil archaeal, bacterial, and fungal communities. Alpha and beta diversity results revealed that the richness indices and the structures of the archaeal, bacterial, and fungal communities significantly differed along the latitudinal gradient. Additionally, significant differences were observed in the bacterial Shannon index, as well as in the structures of the bacterial and fungal communities between the rhizosphere and bulk soils. Due to the small spatial scale, trends of latitudinal variation in the archaeal, bacterial, and fungal communities were not pronounced. Total potassium, total phosphorus, available nitrogen, available potassium and total nitrogen were the important driving factors affecting the soil microbial community structure. Compared with those in bulk soil, co-occurrence networks in rhizosphere microbial networks presented lower complexity but greater modularity and positive connections. Among the main functional fungi, arbuscular mycorrhizae and soil saprotrophs were more abundant in the bulk soil. The significant differences in the soil microbes between rhizosphere and bulk soils further underscore the impact of C. odorata invasion on soil environments. The significant differences in the soil microbiota along latitudinal gradients, along with specific driving factors, demonstrate distinct nutrient preferences among archaea, bacteria, and fungi and indicate complex microbial responses to soil nutrient elements following the invasion of C. odorata.

Therapeutic Strategies to Combat Increasing Rates of Multidrug Resistant Pathogens.

The emergence of antimicrobic-resistant infectious pathogens and the consequent rising in the incidence and prevalence of demises caused by or associated to infections which are not sensitive to drug treatments is one of today's major global health challenges. Antimicrobial resistance (AMR) can bring to therapeutic failure, infection's persistence and risk of serious illness, in particular in vulnerable populations such as the elderly, patients with neoplastic diseases or the immunocompromised. It is assessed that AMR will induce until 10 million deaths per year by 2050, becoming the leading cause of disease-related deaths. The World Health Organisation (WHO) and the United Nations General Assembly urgently call for new measures to combat the phenomenon. Research and development of new antimicrobial agents has decreased due to market failure. However, promising results are coming from new alternative therapeutic strategies such as monoclonal antibodies, microbiome modulators, nanomaterial-based therapeutics, vaccines, and phages. This narrative review aimed to analyse the benefits and weaknesses of alternative therapeutic strategies to antibiotics which treat multidrug-resistant bacterial infections.

Impact of elevated CO2 on soil microbiota: A meta-analytical review of carbon and nitrogen metabolism.

In the face of 21st-century challenges driven by population growth and resource depletion, understanding the intricacies of climate change is crucial for environmental sustainability. This review systematically explores the interaction between rising atmospheric CO2 concentrations and soil microbial populations, with possible feedback effects on climate change and terrestrial carbon (C) cycling through a meta-analytical approach. Furthermore, it investigates the enzymatic activities related to carbon acquisition, gene expression patterns governing carbon and nitrogen metabolism, and metagenomic and meta-transcriptomic dynamics in response to elevated CO2 levels. The study reveals that elevated CO2 levels substantially influence soil microbial communities, increasing microbial biomass C and respiration rate by 15 % and upregulating genes involved in carbon and nitrogen metabolism by 12 %. Despite a 14 % increase in C-acquiring enzyme activity, there is a 5 % decrease in N-acquiring enzyme activity, indicating complex microbial responses to CO2 changes. Additionally, fungal marker ratios increase by 14 % compared to bacterial markers, indicating potential ecosystem changes. However, the current inadequacy of data on metagenomic and meta-transcriptomic processes underscores the need for further research. Understanding soil microbial feedback mechanisms is crucial for elucidating the role of rising CO2 levels in carbon sequestration and climate regulation. Consequently, future research should prioritize a comprehensive elucidation of soil microbial carbon cycling, greenhouse gas emission dynamics, and their underlying drivers.

From raw milk cheese to the gut: investigating the colonization strategies of Bifidobacterium mongoliense.

The microbial ecology of raw milk cheeses is determined by bacteria originating from milk and milk-producing animals. Recently, it has been shown that members of the Bifidobacterium mongoliense species may become transmitted along the Parmigiano Reggiano cheese production chain and ultimately may colonize the consumer intestine. However, there is a lack of knowledge regarding the molecular mechanisms that mediate the interaction between B. mongoliense and the human gut. Based on 128 raw milk cheeses collected from different Italian regions, we isolated and characterized 10 B. mongoliense strains. Comparative genomics allowed us to unveil the presence of enzymes required for the degradation of sialylated host-glycans in B. mongoliense, corroborating the appreciable growth on de Man-Rogosa-Sharpe (MRS) medium supplemented with 3'-sialyllactose (3'-SL) or 6'-sialyllactose (6'-SL). The B. mongoliense BMONG18 was chosen, due to its superior ability to utilize 3'-SL and mucin as representative strain, to investigate its behavior when co-inoculated with other bifidobacterial species. Conversely, members of other bifidobacterial species did not appear to benefit from the presence of BMONG18, highlighting a competitive scenario for nutrient acquisition. Transcriptomic data of BMONG18 reveal no significant differences in gene expression when cultivated in a gut simulating medium (GSM), regardless of whether cheese was included or not. Furthermore, BMONG18 was shown to exhibit high adhesion capabilities to HT29-MTX human cells, in line with its colonization ability of a human host.IMPORTANCEFermented foods are nourishments produced through controlled microbial growth that play an essential role in worldwide human nutrition. Research interest in fermented foods has increased since the 80s, driven by growing awareness of their potential health benefits beyond mere nutritional content. Bifidobacterium mongoliense, previously identified throughout the production process of Parmigiano Reggiano cheese, was found to be capable of establishing itself in the intestines of its consumers. Our study underscores molecular mechanisms through which this bifidobacterial species, derived from food, interacts with the host and other gut microbiota members.

Unraveling the core microorganisms and metabolic pathways related to off-flavor compounds formation during Jiang-flavor Baijiu fermentation.

Off-flavor is one of the most frequent and serious causes for the aroma deterioration in Jiang-flavor Baijiu. However, the key compounds and their formation mechanism responsible for off-flavor are still unclear. This study identified 271 volatile compounds from 1 normal and 5 types of off-flavor fermented grains (putrid, rancidity, mud, musty, and burnt) by headspace solid-phase microextraction combined with gas chromatography-mass spectrometry. Using VIP and OAV analysis, 47 key flavor compounds including indole, phenol, isoamyl alcohol, diacetyl, acetic acid, isobutyric acid, and isovaleric acid were found to distinguish normal and off-flavor fermented grains. Furthermore, 40 microbial genera (mainly Monascus, Enterococcus, Dyadobacter, Ottowia, Pseudoxanthomonas, Stenotrophomonas, Pseudomonas, and Xanthomonas) were significantly (p < 0.05, Pearson correlation) related to these 47 compounds. Finally, metabolic pathways for off-flavor compounds formation were constructed. This study provides comprehensive information on the off-flavor compounds and their potential formation mechanism during Jiang-flavor Baijiu fermentation.

An Analysis of the Contaminants on Otoscopes of Otolaryngology Residents: An Observational Study.

The study was conducted to learn if the otoscope, a noncritical medical device, used by ENT residents harbor pathogenic organism. This study was conducted in a medical teaching hospital in India. Total of 38 otoscopes of ENT residents were examined after taking samples using sterile cotton swabs from otoscope speculum and otoscope head and both bacterial and fungal culture were studied. The study showed that 11 otoscope heads (28.94%) and 11 otoscope speculums (28.94%) out of the 38 otoscopes studied showed bacterial growth. Most commonly isolated bacteria were skin commensals followed by Klebsiella species. Fungal growth was seen in 3 out of 38 otoscope Speculums (7.89%). All 3 fungi isolated during the study belonged to Aspergillus species. Training residents regarding hygiene of medical equipments is necessary. Residents must be periodically assessed regarding their practice in handling medical equipments. Supplementary Information: The online version contains supplementary material available at 10.1007/s12070-024-04695-8.

Global citrus root microbiota unravels assembly cues and core members.

Introduction: Citrus is one of the most important fruit crops worldwide, and the root-associated microbiota can have a profound impact on tree health and growth. Methods: In a collaborative effort, the International Citrus Microbiome Consortium investigated the global citrus root microbiota with samples collected from nine citrus-producing countries across six continents. We analyzed 16S rDNA and ITS2 amplicon sequencing data to identify predominant prokaryotic and fungal taxa in citrus root samples. Comparative analyses were conducted between root-associated microbial communities and those from the corresponding rhizosphere and bulk soil samples. Additionally, genotype-based group-wise comparisons were performed to assess the impact of citrus genotype on root microbiota composition. Results: Ten predominant prokaryotic phyla, containing nine bacterial phyla including Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes and one archaeal phylum (Thaumarchaeota), and multiple fungal phyla including Ascomycota and Basidiomycota were identified in the citrus root samples. Compared with the microbial communities from the corresponding rhizosphere and bulk soil samples from the same trees, the prokaryotic and fungal communities in the roots exhibited lower diversity and complexity but greater modularity compared to those in the rhizosphere. In total, 30 root-enriched and 150 root-depleted genera in bacterial community were identified, whereas 21 fungal genera were enriched, and 147 fungal genera were depleted in the root niche compared with the rhizosphere. The citrus genotype significantly affected the root prokaryotic and fungal communities. In addition, we have identified the core root prokaryotic genera comprising Acidibacter, Allorhizobium, Bradyrhizobium, Chitinophaga, Cupriavidus, Devosia, Dongia, Niastella, Pseudomonas, Sphingobium, Steroidobacter and Streptomyces, and the core fungal genera including Acrocalymma, Cladosporium, Fusarium, Gibberella, Mortierella, Neocosmospora and Volutella. The potential functions of these core genera of root microbiota were predicted. Conclusion: Overall, this study provides new insights into the assembly of microbial communities and identifies core members of citrus root microbiota across a wide geographic range. The findings offer valuable information for manipulating root microbiota to enhance plant growth and health.

Investigating microbial and environmental drivers of nitrification in alkaline forest soil.

Ammonia oxidation is a key step in the biogeochemical cycling of nitrogen, and soils are important ecosystems for nitrogen flux globally. Approximately 25% of the world's soils are alkaline. While nitrification has been studied more extensively in agricultural alkaline soils, less is known about natural, unfertilized alkaline soils. In this study, microorganisms responsible for ammonia oxidation and several environmental factors (season, temperature, ammonia concentration, and moisture content) known to affect nitrification were studied in an alkaline forest soil with a pH ranging from 8.36 to 8.77. Ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea, and comammox were present, and AOB belonging to genera Nitrosospira and Nitrosomonas, originally comprising <0.01% of the total bacterial community, responded rapidly to ammonia addition to the soil. No significant difference was observed in nitrification rates between seasons, but there was a significant difference between in situ field nitrification rates and rates in laboratory microcosms. Surprisingly, nitrification took place under many of the tested conditions, but there was no detectable increase in the abundance of any recognizable group of ammonia oxidizers. This study raises questions about the role of low-abundance microorganisms in microbial processes and of situations where zero or very low microbial growth coincides with metabolic activity. In addition, this study provides insights into nitrification in unfertilized alkaline soil and supports previous studies, which found that AOB play an important role in alkaline soils supplemented with ammonia, including agricultural ecosystems.

The use of droplet-based microfluidic technologies for accelerated selection of Yarrowia lipolytica and Phaffia rhodozyma yeast mutants.

Microorganisms are widely used for the industrial production of various valuable products, such as pharmaceuticals, food and beverages, biofuels, enzymes, amino acids, vaccines, etc. Research is constantly carried out to improve their properties, mainly to increase their productivity and efficiency and reduce the cost of the processes. The selection of microorganisms with improved qualities takes a lot of time and resources (both human and material); therefore, this process itself needs optimization. In the last two decades, microfluidics technology appeared in bioengineering, which allows for manipulating small particles (from tens of microns to nanometre scale) in the flow of liquid in microchannels. The technology is based on small-volume objects (microdroplets from nano to femtolitres), which are manipulated using a microchip. The chip is made of an optically transparent inert to liquid medium material and contains a series of channels of small size (<1 mm) of certain geometry. Based on the physical and chemical properties of microparticles (like size, weight, optical density, dielectric constant, etc.), they are separated using microsensors. The idea of accelerated selection of microorganisms is the application of microfluidic technologies to separate mutants with improved qualities after mutagenesis. This article discusses the possible application and practical implementation of microfluidic separation of mutants, including yeasts like Yarrowia lipolytica and Phaffia rhodozyma after chemical mutagenesis will be discussed.

Are Nurses Aware of Their Contribution to the Antibiotic Stewardship Programme? A Mixed-Method Study from Qatar.

The antibiotic stewardship programme (ASP) is a new concept initiated by WHO, but nurses are not yet ready to adopt the program. The training and empowerment of nurses are the best strategies for enhancing their knowledge and engagement in ASP. This mixed-method study was used to assess perceived roles and barriers of nurses' involvement in ASP. An online survey was conducted among 420 clinical nurses to identify their role, and 23 individual interviews were performed among nurses and infection control practitioners to explore the barriers and recommendations to overcome the identified barriers. The majority of the nurses agreed with the sixteen identified roles in ASP, of which 'antibiotic dosing and de-escalation' (82.61%), 'IV to PO conversion of antibiotic, outpatient antibiotic therapy' (85.23%), and 'outpatient management, long-term care, readmission' of the patients (81.19%) had the lowest agreement from the participants. The major themes generated through the qualitative interviews were a lack of knowledge about ASP, poor communication between multidisciplinary teams, lack of opportunity and multidisciplinary engagement, lack of formal education and training about ASP, lack of ASP competency and defined roles in policy, role conflict or power/position, availability of resources, and lack of protected time. Nurses play an integral role in the successful implementation of antibiotic stewardship programs. The empowerment of nurses will help them to adopt the unique role in ASP. Nurses can significantly contribute to antibiotic stewardship efforts and improve patient outcomes through addressing these challenges.

Screening of polyurethane-degrading microbes using a quenching fluorescence probe by microfluidic droplet sorting.

Excessive use of polyurethane (PU) polymers has led contributed to serious environmental pollution. The plastic recycling technology using microorganisms and enzymes as catalysts offers a promising green and low-carbon approach for managing plastic waste. However, current methods for screening PU-degrading strains suffer from drawbacks such as being time-consuming and inefficient. Herein, we present a novel approach for screening PU-degrading microorganisms using a quenching fluorescent probe along with the fluorescence-activated droplet sorting (FADS). The FPAP could specifically recognize the 4,4'-methylenedianiline (MDA) derivates released from PU degradation, with fluorescence quenching as a response. Based on the approach, we successfully screen two PU-degrading strains (Burkholderia sp. W38 and Bacillus sp. C1). After 20 d of cultivation, strain W38 and C1 could degrade 41.58% and 31.45% of polyester-PU film, respectively. Additionally, three metabolites were identified during the degradation of PU monomer (2,4-toluene diamine, 2,4-TDA) and a proposed degradation pathway was established. Consequently, the fluorescence probe integrated with microfluidic droplet systems, demonstrates potential for the development of innovative PU-biocatalysts. Furthermore, the identification of the 2,4-TDA degradation pathway provides valuable insights that can propel advancements in the field of PU biodegradation.

Thermal and structural changes of a starch flexible film and cellulosic semi-rigid tray during the biodegradation process under controlled composting conditions.

Biopolymers used to mitigate the environmental impact needed establish biodegradation percentage. The thermal and structural changes of two plastic materials, a flexible film based on cassava starch - Poly(lactic acid) (PLA) and a semi-rigid cassava flour-stay cellulose fique fiber, were evaluated biodegradation under ISO 4855-1 standard. The tests were carried out for four weeks at constant temperature and flow of 58 °C ±â€¯2 °C and 250 mL/h, using a mature compost as inoculum. The percentages of CO2, thermal, morphological, and structural changes, variation of degradation temperatures, glass transition temperatures (Tg), Melting temperatures (Tm) and enthalpies of fusion (Hm), were properly evaluated as indicators of the materials biodegradation of two materials. Scanning electron microscopy (SEM), showed the microorganisms colonization on the materials surface, evidencing the appearance of cracks and microbial population. The flexible film showed a biodegradation percentage of 98.24 %, the semi-rigid tray 89.06 %, and the microcrystalline cellulose, 81.37 %.

Isolation of native microorganisms from Shengli lignite and study on their ability to dissolve lignite.

To more greenly and efficiently utilize the abundant lignite resources and explore the microbial degradation and transformation potential of lignite for its environmentally friendly and resourceful utilization, Shengli lignite from the Hulunbuir region of Inner Mongolia, China, was selected as the research subject. Through the dilution plating method and streaking method, 31 native microorganisms were successfully isolated from the Shengli lignite, including 16 bacteria and 15 fungi. After microbial coal dissolution experiments, it was found that certain microorganisms have a significant dissolving effect on lignite, with some bacterial and fungal strains showing strong dissolution capabilities. In particular, the bacterium SH10 Lysinibacillus fusiformis and the fungus L1W Paecilomyces lilacinus demonstrated the best coal-dissolving abilities, with dissolution rates both reaching 60%. The products of microbial dissolution of lignite were analyzed using gas chromatography-mass spectrometry (GC-MS) technology, identifying a variety of small molecular organic compounds, including alkanes, alcohols, esters, and phenols. The results of this study provide a new perspective on the biodegradation of lignite and lay the foundation for the development of new lignite treatment and utilization technologies.

EFSA statement on the requirements for whole genome sequence analysis of microorganisms intentionally used in the food chain.

Microorganisms, genetically modified or not, may be used in the food chain either as active agents, biomasses or as production organisms of substances of interest. The placement of such microorganisms or their derived substances/products in the European market may be subject to a premarket authorisation process. The authorisation process requires a risk assessment in order to establish the safety and/or the efficacy of the microorganism(s) when used in the food chain as such, as biomasses or as production strains. This includes a full molecular characterisation of the microorganism(s) under assessment. For certain regulated products, the use of whole genome sequence (WGS) data of the microorganism is established as a requirement for the risk assessment. In this regard, data obtained from WGS analysis can provide information on the unambiguous taxonomic identification of the strains, on the presence of genes of concern (e.g. those encoding virulence factors, resistance to antimicrobials of clinical relevance for humans and animals, production of harmful metabolites or of clinically relevant antimicrobials) and on the characterisation of genetic modification(s) (where relevant). This document provides recommendations to applicants on how to describe and report the results of WGS analyses in the context of an application for market authorisation of a regulated product. Indications are given on how to perform genome sequencing and the quality criteria/thresholds that should be reached, as well as the data and relevant information that need to be reported, if required. This updated document replaces the EFSA 2021 Statement and reflects the current knowledge in technologies and methodologies to be used to generate and analyse WGS data for the risk assessment of microorganisms.

Exploration of bacterial lipopolysaccharide-related genes signature based on T cells for predicting prognosis in colorectal cancer.

PURPOSE: The intratumoral microorganisms participates in the progression and immunotherapy of colorectal cancer (CRC). However, due to technical limitations, the impact of microorganisms on CRC has not been fully understood. Therefore, we conducted a systematic analysis of relationship between bacterial lipopolysaccharide (LPS)-associated genes and immune cells to explore new biomarkers for predicting the prognosis of CRC. METHODS: The single-cell RNA sequencing data and the Comparative Toxicogenomics Database were used to screen T cells-associated LPS-related genes (TALRGs). Then, we established and validated the TALRGs risk signature in The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) cohort and GSE39582 cohort. Besides, we compared the differences in tumor-infiltrating immune cell types, immunotherapeutic response, somatic mutation profiles, and tumor mutation burden (TMB) between high-risk group and low-risk group. In addition, the immunotherapeutic cohort (Imvigor210) treated with an anti-PD-L1 agent was performed to explore the potential value of the TALRGs signature on immunotherapy. RESULTS: Five prognostic TALRGs were identified and selected to build the prognostic model. The high-risk group had poor prognosis in both TCGA-COAD cohort (P < 0.0001) and GSE39582 cohort (P = 0.00019). The areas under the curves (AUCs) of TALRGs signature were calculated (TCGA-COAD cohort: 0.624 at 1 years, 0.639 at 3 years, 0.648 at 5 years; anti-PD-L1 cohort was 0.59). The high-risk group had advanced pathological stages and higher TMN stages in both TCGA-COAD cohort and GSE39582 cohort. The high-risk group had the higher infiltration of immunosuppressive cells, the expressions of immune checkpoint molecules, the IC50 values of chemotherapy drugs, and TP53 mutation rate (P < 0.05). In addition, patients with high TMB had worse prognosis (P < 0.05). Furthermore, the Imvigor210 also showed patients with high-risk scores had poor prognosis (platinum-treated cohort: P = 0.0032; non-platinum-treated cohort: P = 0.00017). CONCLUSIONS: Microorganisms are closely related to the tumor microenvironment to influence the progression and immune response of CRC via stimulating T cells through LPS-related genes. The TALRGs signature contributed to predict the prognosis and immunotherapy of CRC, and became new therapeutic targets and biomarkers of CRC.