Isolation and characterization of bacteria associated with silkworm gut under antibiotic-treated larval feeding / Isolamento e caracterização de bactérias associadas ao trato intestinal do bicho-da-seda sob alimentação larval tratada com antibióticos

Abstract The impact of antibiotics on growth, cocoon production was assessed in addition to isolation and characterization of bacteria associated with silkworm gut of infected larvae. Larval rearing was maintained at recommended conditions of temperature and humidity. Silkworm larvae showing abnormal symptoms were collected from the control group and dissected for gut collection. Bacteria were isolated from the gut content by spreading on agar plates and incubated at 37 °C for 48 hrs. Bacterial identification and phylogenetic analysis were carried out by 16S rRNA gene sequencing. The isolated bacteria were subjected to antimicrobial susceptibility test (disc diffusion methods) by using Penicillin (10 µg/mL), Tetracycline (30 µg/mL), Amoxicillin (25 µg/mL), Ampicillin (10 µg/mL), and Erythromycin (15 µg/mL). All isolated strains showed positive results for the catalase test. We isolated and identified bacterial strains (n = 06) from the gut of healthy and diseased silkworm larvae. Based on the 16S rRNA gene sequence, isolated bacteria showed close relation with Serratia, Bacillus, and Pseudomonas spp. Notably, 83.3% of strains were resistant to Penicillin, Tetracycline, Amoxicillin, Ampicillin, and Erythromycin but 16.6% showed antibiotic susceptibility to the above-mentioned commonly used antibiotics. Silkworm larvae fed on penicillin-treated leaves showed significant improvement in larval weight, larval length, and cocoon production. Significantly higher larval weight (6.88g), larval length (5.84cm), and cocoon weight (1.33g) were recorded for larvae fed on leaves treated with penicillin as compared to other antibiotics. Isolated bacterial strains showed close relation with Serratia spp., Bacillus spp. and Pseudomonas spp.

Resumo O impacto dos antibióticos no crescimento e na produção do casulo foi avaliado, além do isolamento e caracterização das bactérias associadas ao intestino de larvas infectadas do bicho-da-seda. A criação das larvas foi mantida nas condições recomendadas de temperatura e umidade. As larvas do bicho-da-seda com sintomas anormais foram coletadas do grupo controle e dissecadas para coleta do intestino. As bactérias foram isoladas do conteúdo intestinal por espalhamento em placas de ágar e incubadas a 37° C durante 48 horas. A identificação bacteriana e a análise filogenética foram realizadas pelo sequenciamento do gene 16S rRNA. As bactérias isoladas foram submetidas a teste de sensibilidade antimicrobiana (métodos de difusão em disco) com penicilina (10 µg / mL), tetraciclina (30 µg / mL), amoxicilina (25 µg / mL), ampicilina (10 µg / mL) e eritromicina (15 µg / mL). Todas as cepas isoladas apresentaram resultados positivos para o teste da catalase. Isolamos e identificamos cepas bacterianas (n = 06) do intestino de larvas de bicho-da-seda saudáveis e doentes. Com base na sequência do gene 16S rRNA, as bactérias isoladas mostraram estreita relação com Serratia, Bacillus e Pseudomonas spp. Notavelmente, 83,3% das cepas eram resistentes a penicilina, tetraciclina, amoxicilina, ampicilina e eritromicina, mas 16,6% mostraram suscetibilidade aos antibióticos comumente usados mencionados acima. As larvas do bicho-da-seda alimentadas com folhas tratadas com penicilina apresentaram melhora significativa no peso larval, comprimento larval e produção de casulo. Peso larval significativamente maior (6,88g), comprimento larval (5,84cm) e peso do casulo (1,33g) foram registrados para larvas alimentadas com folhas tratadas com penicilina, em comparação com outros antibióticos. Cepas bacterianas isoladas mostraram estreita relação com Serratia spp., Bacillus spp. e Pseudomonas spp.

Percentage Incidences of Bacteria in Mahseer (Tor putitora), Silver carp (Hypophthalmichthys molitrix) Fish Collected from Hatcheries and Local Markets of District Malakand and Peshawar of Khyber Pakhtunkhwa, Pakistan / Incidências percentuais de bactérias em Mahseer (Tor putitora), carpa-prateada (Hypophthalmichthys molitrix), peixes coletados em incubatórios e mercados locais do distrito de Malakand e Peshawar de Khyber Pakhtunkhwa, Paquistão

Abstract Fish is the main source of animal protein for human diet. The aim of this study was to find out prevalence of pathogenic bacteria of two selected economically important fish of Pakistan namely Mahseer (Tor putitora) and Silver carp (Hypophthalmichthys molitrix). Live fish samples from hatcheries and dead fish samples from different markets of study area were randomly collected. The fish samples were analyzed for isolation, identification and prevalence of bacteria. The isolated bacteria from study fish were identified through biochemical test and about 10 species of pathogenic bacteria were identified including the pathogenic bacteria to human and fish namely, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus iniae, Serratia spp. Citrobacter spp. Stenotrophomonas spp. Bacillus spp. and Salmonella spp. The bacterial percentage frequency of occurrence in Silver carp and Mahseer fish showed Pseudomonas aeruginosa 21.42%, Staphylococcus epidermidis 17.85%, Escherichia coli 11.90%, Staphylococcus aureus 9.52%, Citrobacter spp. 9.52%, Serratia spp. 8.33%, Streptococcus iniae 7.14%, Stenotrophomonas spp. 5.95%, Bacillus spp. 4.76% and Salmonella spp. 3.57%. The study revealed that Fish samples of Mahseer and Silver carp that were collected from markets have found more isolates (10 bacterial species) than did the fresh fish pond samples (03 bacterial species) of hatcheries. The occurrence of pathogenic bacteria in study fish showed risk factor for public health consumers.

Resumo O peixe é a principal fonte de proteína animal para a alimentação humana. O objetivo deste estudo foi descobrir a prevalência de bactérias patogênicas de dois peixes economicamente importantes selecionados do Paquistão, nomeadamente Mahseer (Tor putitora) e carpa prateada (Hypophthalmichthys molitrix). Amostras de peixes vivos de incubatórios e amostras de peixes mortos de diferentes mercados da área de estudo foram coletadas aleatoriamente. As amostras de peixes foram analisadas quanto ao isolamento, identificação e prevalência de bactérias. As bactérias isoladas dos peixes do estudo foram identificadas através de testes bioquímicos e cerca de 10 espécies de bactérias patogênicas foram identificadas incluindo as bactérias patogênicas para humanos e peixes, nomeadamente, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus iniae, Serratia spp. Citrobacter spp. Stenotrophomonas spp. Bacillus spp. e Salmonella spp. A porcentagem de freqüência de ocorrência bacteriana em carpa prateada e peixes Mahseer mostrou Pseudomonas aeruginosa 21,42%, Staphylococcus epidermidis 17,85%, Escherichia coli 11,90%, Staphylococcus aureus 9,52%, Citrobacter spp. 9,52%, Serratia spp. 8,33%, Streptococcus iniae 7,14%, Stenotrophomonas spp. 5,95%, Bacillus spp. 4,76% e Salmonella spp. 3,57%. O estudo revelou que as amostras de peixes de Mahseer e carpa prateada coletadas nos mercados encontraram mais isolados (10 espécies bacterianas) do que as amostras de peixes frescos (03 espécies bacterianas) de incubatórios. A ocorrência de bactérias patogênicas nos peixes do estudo apresentou fator de risco para consumidores de saúde pública.

Bacterial, short-chain fatty acid and gas profiles of partially hydrolyzed guar gum in vitro fermentation by human fecal microbiota.

Carbohydrates with different structures have metabolic differences in the human body, as well as individual differences. The present study aimed to investigate the effects of bacterial, short-chain fatty acids (SCFAs) and gas profiles of partially hydrolyzed guar gum (PHGG) on the fecal microbiota of 41 Chinese individuals by simulated fermentation in vitro. Results showed that PHGG stimulated the growth of Bifidobacterium and Faecalibacterium, inhibited the growth of Escherichia-Shigella, Klebsiella, and Dorea, and induced the production of fermentation gases (CO2, and H2) and SCFAs (acetic acid, butyric acid). Furthermore, Bifidobacterium was significantly increased in the young female and the old male-originated samples, while Klebsiella was significantly decreased in the old female ones after PHGG intervention, and there were also certain differences in gases and SCFAs among different population samples. These findings indicate that PHGG can modulate gut microbiota and metabolism well, whereas its use varies in different populations.

Microbial interactions and dynamic changes of volatile flavor compounds during the fermentation of traditional kombucha.

This study aims to explore the core microbiota of kombucha and to discover potential correlations between microbiota and volatile flavor compounds. The total acidity and microbial colony numbers changed dramatically in different fermentation periods of kombucha. Microbial analysis based on high throughput sequencing technology showed that the bacteria of Komagataeibacter, Pseudomonas, Burkholderia, Ralstonia, Halomonas, Sphingomonas and fungi of Dekkera, Saccharomyces cerevisiae, Botryotrichum, Monascus, Pichia were the dominant genera. In addition, the correlation coefficients between the bacteria and fungi were different. The volatile flavor compounds of alcohols, acids, esters, aldehydes, ketones, phenolics, and terpenes were identified using headspace solid-phase microextraction combined with gas chromatography coupled with mass spectrometry. Typically, the concentrations of ethanol, acetic acid, and ethyl acetate was 71.59-248.23 µg/L, 97.73-849.00 µg/L, and 44.52-181.59 µg/L, respectively, during fermentation. This study is helpful to understand the dynamic changes of microbial communities and volatile flavor compounds during the fermentation of kombucha.

Off-line two-dimensional LC-tandem MS of menaquinones from thermophilic bacteria.

Thermophilic bacteria of four genera in contrast to the commonly used production strains such as Bacillus subtilis, produce homologs other than menaquinone (MK) with seven isoprene units. The number of isoprene units and the configuration of double bonds are essential factors for their biological activity. The goal was to obtain a strain of bacteria that produces a wide range of MK homologs and only all-trans geometrical isomers, which was the strain G. kaustophilus. Using off-line two-dimensional LC-tandem MS in columns with the RP18 phase and the COSMOSIL cholester phase (separation according to the geometric configuration of double bonds) it was shown that thermophilic bacteria grown at different temperatures produce only all-trans isomers of menaquinones from MK-5 (menaquinone with five isoprenyl units) to MK-15 (fifteen isoprenyl units). Therefore, G. kaustophilus appears to be a biotechnologically important strain produces only trans isomers and additionally homologs from 5 to 15 isoprene units.

Traditional Chinese Medicine: A promising strategy to regulate the imbalance of bacterial flora, impaired intestinal barrier and immune function attributed to ulcerative colitis through intestinal microecology.

ETHNOPHARMACOLOGICAL RELEVANCE: Globally, plant materials are widely used as an additional and alternative therapy for the treating of diverse diseases. Ulcerative colitis (UC) is a chronic, recurrent and nonspecific inflammation of the bowel, referred to as "modern intractable disease" according to the World Health Organization. With the continuous development of theoretical research in Traditional Chinese Medicine (TCM) and the advantages of TCM in terms of low side effects, TCM has shown great progress in the research of treating UC. AIM OF THIS REVIEW: This review aimed to explore the correlation between intestinal microbiota and UC, summarize research advances in TCM for treating UC, and discuss the mechanism of action of TCM remedies in regulating intestinal microbiota and repairing damaged intestinal barrier, which will provide a theoretical basis for future studies to elucidate the mechanism of TCM remedies based on gut microbiota and provide novel ideas for the clinical treatment of UC. METHODS: We have collected and collated relevant articles from different scientific databases in recent years on the use of TCM in treating UC in relation to intestinal microecology. Based on the available studies, the therapeutic effects of TCM are analysed and the correlation between the pathogenesis of UC and intestinal microecology is explored. RESULTS: TCM is used to further protect the intestinal epithelium and tight junctions, regulate immunity and intestinal flora by regulating intestinal microecology, thereby achieving the effect of treating UC. Additionally, TCM remedies can effectively increase the abundance of beneficial bacteria that produce short-chain fatty acids, decrease the abundance of pathogenic bacteria, restore the balance of intestinal microbiota, and indirectly alleviate intestinal mucosal immune barrier dysfunction and promote the repair of damaged colorectal mucosa. CONCLUSION: Intestinal microbiota is closely related to UC pathogenesis. The alleviation of intestinal dysbiosis can be a potential novel therapeutic strategy for UC. TCM remedies can exert protective and therapeutic effects on UC through various mechanisms. Although intestinal microbiota can aid in the identification of different TCM syndromes types, further studies are needed using modern medical technology. This will improve the clinical therapeutic efficacy of TCM remedies in UC and promote the application of precision medicine.

Characterisation of the Novel Filamentous Phage PMBT54 Infecting the Milk Spoilage Bacteria Pseudomonas carnis and Pseudomonas lactis.

Filamentous bacteriophages are lysogenic and pseudo-lysogenic viruses that do not lyse their host but are often continuously secreted from the infected cell. They belong to the order Tubulavirales, which encompasses three families, with the Inoviridae being the largest. While the number of identified inoviral sequences has greatly increased in recent years due to metagenomic studies, morphological and physiological characterisation is still restricted to only a few members of the filamentous phages. Here, we describe the novel filamentous phage PMBT54, which infects the spoilage-relevant Pseudomonas species P. carnis and P. lactis. Its genome is 7320 bp in size, has a mol% GC content of 48.37, and codes for 13 open-reading frames, two of which are located on the (-) strand. The virion exhibits a typical filamentous morphology and is secreted from the host cell at various lengths. The phage was shown to promote biofilm formation in both host strains and, therefore, has potential implications for milk spoilage, as biofilms are a major concern in the dairy industry.

In situ fabrication of Ag decorated porous ZnO photocatalyst via inorganic-organic hybrid transformation for degradation of organic pollutant and bacterial inactivation.

In this study, in situ silver (Ag) - porous ZnO photocatalysts were synthesized via solvothermal and post-annealing treatment. The formation of the porous ZnO structure due to the removal of organic moieties from the inorganic-organic hybrids Ag-ZnS(en)0.5 during the annealing process. The optimal Ag-ZnO photocatalyst showed excellent photocatalytic degradation activity, with 95.5% orange II dye and 97.2% bisphenol A (BPA) degradation under visible light conditions. Additionally, the photocatalytic inactivation of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) led to a 97% inactivation rate after 2 h under dark conditions. Trapping experiments suggest that the superoxide anion (O2-) radicals are the main active species to degrade the organic dye. The improved photocatalytic dye degradation activity and inactivation of bacteria were attributed to the synergistic effect of Ag and porous ZnO structure, increased surface area, and efficiently separated the photoexcited charge carriers. This work could provide an effective strategy for the synthesis of porous structures toward organic pollutant degradation and bacterial inactivation in wastewater.

Lipoxygenase in a Giant Sulfur Bacterium: An Evolutionary Solution for Size and Complexity?

Discovery of Thiomargarita magnifica - an exceptionally large giant sulfur bacterium - urges us to pay additional attention to the giant sulfur bacteria and to revisit our recent bioinformatic finding of lipoxygenases in the representatives of the genus Beggiatoa. These close relatives of Thiomargarita magnifica meet the similar size requirements by forming multicellular structures. We hypothesize that their lipoxygenases are a part of the oxylipin signaling system that provides high level of cell-to-cell signaling complexity which, in turn, enables them to reach large sizes.

Winogradskyella vincentii sp. nov. and Winogradskyella alexanderae sp. nov., two novel bacteria isolated from intertidal sediment.

Two novel Gram-stain-negative, facultative anaerobic, chemoheterotrophic, non-motile and rod-shaped strains were isolated from intertidal sediment sampled at Xiaoshi Island, Weihai, PR China. Full sequence analysis of the 16S rRNA genes showed that the two strains were closely related to members of the genus Winogradskyella and the phylogenetic similarities to their closest relative, Winogradskyella aquimaris, were 96.7 and 95.8 %, respectively. The DNA G+C contents of strains 2Y89T and D23T were 33.3 and 35.1 mol%, respectively. The respiratory quinone detected in both strains was MK-6. The major fatty acids detected in strain 2Y89T were iso-C15 : 0 and iso-C15 : 1G, and in strain D23T they were iso-C15 : 1G, iso-C15 : 0 and iso-C17 : 03-OH. The principal polar lipids of strain 2Y89T mainly included phosphatidylethanolamine, aminoglycolipids, unidentified aminolipids, unidentified glycolipids and unidentified lipids; strain D23T was the same as strain 2Y89T except that it did not contain aminoglycolipids. Based on the phenotypic, chemical taxonomic, genotypic and phylogenetic features established in this study, we suggest that the new strains represent two novel species of the genus Winogradskyella, for which the names Winogradskyella vincentii sp. nov. (type strain 2Y89T=MCCC 1H00477T=KCTC 92034T) and Winogradskyella alexanderae sp. nov. (type strain D23T=MCCC 1H00462T=KCTC 92023T) are proposed.

Inactivation of chlorine-resistant bacteria (CRB) via various disinfection methods: Resistance mechanism and relation with carbon source metabolism.

With the widespread use of chlorine disinfection, chlorine-resistant bacteria (CRB) in water treatment systems have gained public attention. Bacterial chlorine resistance has been found positively correlated with extracellular polymeric substance (EPS) secretion. In this study, we selected the most suitable CRB controlling method against eight bacterial strains with different chlorine resistance among chloramine, ozone, and ultraviolet (UV) disinfection, analyzed the resistance mechanisms, clarified the contribution of EPS to disinfection resistance, and explored the role of carbon source metabolism capacity. Among all the disinfectants, UV disinfection showed the highest disinfection capacity by achieving the highest average and median log inactivation rates for the tested strains. For Bacillus cereus CR19, the strain with the highest chlorine resistance, 40 mJ/cm2 UV showed a 1.90 log inactivation, which was much higher than that of 2 mg-Cl2/L chlorine (0.67 log), 2 mg-Cl2/L chloramine (1.68 log), and 2 mg/L ozone (0.19 log). Meanwhile, the UV resistance of the bacteria did not correlate with EPS secretion. These characteristics render UV irradiation the best CRB controlling disinfection method. Chloramine was found to have a generally high inactivation efficiency for bacteria with high chlorine-resistance, but a low inactivation efficiency for low chlorine-resistant ones. Although EPS consumed up to 56.7% of chloramine which an intact bacterial cell consumed, EPS secretion could not explain chloramine resistance. Thus, chloramine is an acceptable CRB control method. Similar to chlorine, ozone generally selected high EPS-secreting bacteria, with EPS consuming up to 100% ozone. Therefore, ozone is not an appropriate method for controlling CRB with high EPS secretion. EPS played an important role in all types of disinfection resistance, and can be considered the main mechanism for bacterial chlorine and ozone disinfection resistance. However, as EPS was not the main resistance mechanism in UV and chloramine disinfection, CRB with high EPS secretion were inactivated more effectively. Furthermore, carbon source metabolism was found related to the multiple resistance of bacteria. Those with low carbon source metabolism capacity tended to have higher multiple resistance, especially to chlorine, ozone, and UV light. Distinctively, among the tested gram-negative bacteria, in contrast to other disinfectants, chloramine resistance was negatively correlated with EPS secretion and positively correlated with carbon source metabolism capacity, suggesting a special disinfection mechanism.

Combining different bacteria in vaccine formulations enhances the chance for antiviral cross-reactive immunity: a detailed in silico analysis for influenza A virus.

Bacteria are well known to provide heterologous immunity against viral infections through various mechanisms including the induction of innate trained immunity and adaptive cross-reactive immunity. Cross-reactive immunity from bacteria to viruses is responsible for long-term protection and yet its role has been downplayed due the difficulty of determining antigen-specific responses. Here, we carried out a systematic evaluation of the potential cross-reactive immunity from selected bacteria known to induce heterologous immunity against various viruses causing recurrent respiratory infections. The bacteria selected in this work were Bacillus Calmette Guerin and those included in the poly-bacterial preparation MV130: Streptococcus pneumoniae, Staphylococcus aureus, Staphylococcus epidermidis, Klebisella pneumoniae, Branhamella catarrhalis and Haemophilus influenzae. The virus included influenza A and B viruses, human rhinovirus A, B and C, respiratory syncytial virus A and B and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Through BLAST searches, we first identified the shared peptidome space (identity ≥ 80%, in at least 8 residues) between bacteria and viruses, and subsequently predicted T and B cell epitopes within shared peptides. Interestingly, the potential epitope spaces shared between bacteria in MV130 and viruses are non-overlapping. Hence, combining diverse bacteria can enhance cross-reactive immunity. We next analyzed in detail the cross-reactive T and B cell epitopes between MV130 and influenza A virus. We found that MV130 contains numerous cross-reactive T cell epitopes with high population protection coverage and potentially neutralizing B cell epitopes recognizing hemagglutinin and matrix protein 2. These results contribute to explain the immune enhancing properties of MV130 observed in the clinic against respiratory viral infections.

Hydrodynamic Treadmill Reveals Reduced Rising Speeds of Oil Droplets Deformed by Marine Bacteria.

In marine environments, microscopic droplets of oil can be transported over large distances in the water column. Bacterial growth on the droplets' surface can deform the oil-water interface to generate complex shapes and significantly enlarge droplets. Understanding the fate of spilled oil droplets requires bridging these length scales and determining how microscale processes affect the large-scale transport of oil. Here, we describe an experimental setup, the hydrodynamic treadmill, developed to keep rising oil droplets stationary in the lab frame for continuous and direct observation. Oil droplets with radii 10 < R < 100 µm were colonized and deformed by bacteria over several days before their effective rising speeds were measured. The rising speeds of deformed droplets were significantly slower than those of droplets without bacteria. This decrease in rising speed is understood by an increase in drag force and a decrease in buoyancy as a result of bio-aggregate formation at the droplet surface. Additionally, we found sinking bio-aggregate particles of oil and bacterial biofilms and quantified their composition using fluorescence microscopy. Our experiments can be adapted to further study the interactions between oil droplets and marine organisms and could significantly improve our understanding of the transport of hydrocarbons and complex aggregates.

Enhanced ammonia nitrogen and phenol removal by immobilized bacteria through composite mycelium pellet-driven quinone redox cycle.

The composite mycelium pellet (CMP) was coupled with Pseudomonas sp. Y1 (CMP-Y1) to remove phenol and ammonia nitrogen (NH4+-N). The CMP was formed by the self-assembly of fungal mycelium with sponge iron (SIO), gallic acid (GA), and oxalic acid. The results showed that CMP with abundant pore size and successful internal loading of sponge iron containing iron nanoparticles. CMP could induce GA redox cycle to form Fenton-like reaction and thus achieve efficient phenol removal (93.32%, 24 h). Meanwhile, the removal efficiencies of phenol, NH4+-N, and chemical oxygen demand (COD) using CMP-Y1 at 12 h were 93.71, 92.40, and 89.00%, respectively. The increase in the electron transfer activity of strain Y1 by the addition of CMP could facilitate the nitrogen removal processes. In addition, high-throughput sequencing results indicated the abundance of antioxidant and repair genes was increased, which might be a strategy of strain Y1 to cope with oxidative stress. This strategy provided the possibility for the practical application of the combination of advanced oxidation and biological treatment, and offered new insights into the symbiotic system of fungi and bacteria.

Quorum sensing bacteria in microplastics epiphytic biofilms and their biological characteristics which potentially impact marine ecosystem.

Microplastics (MPs) have been shown to be a new type of pollutant in the oceans, with complex biofilms attached to their surfaces. Bacteria with quorum sensing (QS) systems are important participants in biofilms. Such bacteria can secrete and detect signal molecules. When a signal molecule reaches its threshold level, bacteria with QS systems can perform several biological functions, such as biofilm formation and antibiotic metabolite production. However, the ecological effects of QS bacteria in biofilm as MPs distribute globally with ocean currents are not to be elucidate yet. In this study, polypropylene and polyvinyl chloride were selected for on-site enrichment to acquire microplastics with biofilms. Eight culturable QS bacteria in the resulting biofilm were isolated by using biosensor assays, and their biodiversity was analyzed. The profiles of the N-acyl-homoserine lactones (AHLs) produced by these bacteria were analyzed by using thin-layer chromatography (TLC)-bioautography and gas chromatography and mass spectrometry (GC-MS). Biofilm-forming properties and several biological characteristics, such as bacteriostasis, algal inhibition, and dimethylsulfoniopropionate (DMSP) degradation, were explored along with QS quenching. Results showed that QS bacteria were mainly affiliated with class Alphaproteobacteria, particularly Rhodobacteraceae, followed by class Gammaproteobacteria. TLC-bioautography and GC-MS analyses revealed that seven AHLs, namely, C6-HSL, C8-HSL, 3-oxo-C6-HSL, 3-oxo-C8-HSL, 3-oxo-C10-HSL, and two unidentified AHLs were produced. The QS system equipped bacteria with strong biofilm-forming capacity and may contribute to the keystone roles of Rhodobacteraceae. In addition, QS bacteria may exacerbate the adverse environmental effects of MPs, such as inducing the misfeeding of planktons on MPs. This study elucidated the diversity of QS bacteria in MP-associated biofilms and provided a new perspective of the effect of key membrane-forming bacteria on the marine ecological environment.

Plant growth-promoting bacteria modulate gene expression and induce antioxidant tolerance to alleviate synergistic toxicity from combined microplastic and Cd pollution in sorghum.

Microplastics (MPs) can act as carriers for environmental pollutants; therefore, MPs combined with heavy metal pollution are attracting increasing attention from researchers. In this study, the potential of the plant growth-promoting bacterium Bacillus sp. SL-413 to mitigate the stress caused by exposure to both MPs and cadmium (Cd) in sorghum plants was investigated. The effects of inoculation on sorghum biomass were investigated using hydroponic experiments, and evaluation of Cd accumulation and enzyme activity changes and transcriptomics approaches were used to analyze its effect on sorghum gene expression. The results showed that combined polyethylene (PE) and Cd pollution reduced the length and the fresh and dry weights of sorghum plants and thus exerted a synergistic toxic effect. However, inoculation with the strains alleviated the stress caused by the combined pollution and significantly increased the biomass. Inoculation increased the dry weights of the aboveground and belowground parts by 11.5-44.6% and 14.9-38.4%, respectively. Plant physiological measurements indicated that inoculation reduced the reactive oxygen species (ROS) content of sorghum by 10.5-27.2% and thereby alleviated oxidative stress. Transcriptome sequencing showed that exposure to combined Cd+MP contamination induced downregulation of gene expression, particularly that of genes related to amino sugar and nucleotide sugar metabolism, starch and sucrose metabolism, and plant hormone signal transduction, in sorghum. However, inoculation with Bacillus sp. SL-413 resulted in an increase in the proportion of upregulated genes involved in signal transduction, antioxidant defense, cell wall biology, and other metabolic pathways, which included the phenylpropanoid biosynthesis, photosynthesis, flavonoid biosynthesis, and MAPK signaling pathways. The upregulation of these genes promoted the tolerance of sorghum under combined Cd+MP pollution stress and alleviated the stress induced by these conditions. This study provides the first demonstration that plant growth-promoting bacteria can alleviate the stress caused by combined pollution with MPs and Cd by regulating plant gene expression. These findings provide a reference for the combined plant-microbial remediation of MPs and Cd.

The influence of dietary patterns on skin bacterial diversity, composition, and co-occurrence relationships at forearm and neck sites of healthy Korean adults.

AIMS: Diet and nutrition are important aspects of skin physiology and health. However, the influence of diet on the bacterial flora of different skin sites is not well understood. Therefore, we investigated the relationship between dietary patterns (DPs) and skin bacterial flora on the forearm (a dry site) and the neck (a sebaceous site) of healthy Korean adults. METHODS AND RESULTS: In metagenomics analysis, Shannon and Simpson indices were higher on the forearm than on the neck and were negatively correlated with the two dominant species, Cutibacterium acnes and Staphylococcus epidermidis, on two skin sites. In addition, the Simpson index of the forearm was positively associated with DP1 (characterized by a high intake of vegetables, mushrooms, meat, fish and shellfish, seaweed, and fat and oil), while that on the neck was negatively associated with DP2 (characterized by a high intake of fast food). A high intake of DP1 was associated with a lower abundance of dominant species, including C. acnes, and higher degrees of the co-occurrence network, whereas a high intake of DP2 was associated with the opposite pattern. CONCLUSIONS: Specific diets may impact both skin bacterial diversity and composition, as well as the co-occurrence of bacteria, which may vary across different skin sites.

Claveliimonas bilis gen. nov., sp. nov., deoxycholic acid-producing bacteria isolated from human faeces, and reclassification of Sellimonas monacensis Zenner et al. 2021 as Claveliimonas monacensis comb. nov.

Obligately anaerobic, Gram-stain-positive, bacilli, strains 12BBH14T, 9CFEGH4 and 10CPCBH12, were isolated from faecal samples of healthy Japanese people. Strain 12BBH14T showed the highest 16S rRNA gene sequence similarity to Sellimonas monacensis Cla-CZ-80T (97.5 %) and 'Lachnoclostridium phocaeense' Marseille-P3177T (97.2 %). Strain 12BBH14T was also closely related to Eubacterium sp. c-25 with 99.7 % 16S rRNA gene sequence similarity. The 16S rRNA gene sequence analysis showed that strains 12BBH14T, 9CFEGH4 and 10CPCBH12 formed a monophyletic cluster with Eubacterium sp. c-25. Near this monophyletic cluster, S. monacensis Cla-CZ-80T and 'L. phocaeense' Marseille-P3177T formed a cluster and did not form a cluster with other Sellimonas species. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains 12BBH14T, 9CFEGH4, 10CPCBH12 and Eubacterium sp. c-25 were higher than the cut-off values of species demarcation (>88 % dDDH and >98 % ANI), indicating that these four strains are the same species. On the other hand, the dDDH and ANI values of these strains were lower than the cut-off values of species demarcation against other strains (<29 % dDDH and <76 % ANI). Moreover, the average amino acid identity values among these strains were higher than the genus boundary. These results indicate that the isolates should be considered to belong to a new genus of the family Lachnospiraceae. Based on the collected data, strains 12BBH14T, 9CFEGH4 and 10CPCBH12 represent a novel species of a novel genus, for which the name Claveliimonas bilis gen. nov., sp. nov. is proposed. The type strain of C. bilis is 12BBH14T (=JCM 35899T=DSM 115701T). Eubacterium sp. c-25 belongs to C. bilis. In addition, S. monacensis is transferred to the genus Claveliimonas as Claveliimonas monacensis comb. nov.

Replication cycle timing determines phage sensitivity to a cytidine deaminase toxin/antitoxin bacterial defense system.

Toxin-antitoxin (TA) systems are ubiquitous two-gene loci that bacteria use to regulate cellular processes such as phage defense. Here, we demonstrate the mechanism by which a novel type III TA system, avcID, is activated and confers resistance to phage infection. The toxin of the system (AvcD) is a deoxycytidylate deaminase that converts deoxycytidines (dC) to dexoyuridines (dU), while the RNA antitoxin (AvcI) inhibits AvcD activity. We have shown that AvcD deaminated dC nucleotides upon phage infection, but the molecular mechanism that activated AvcD was unknown. Here we show that the activation of AvcD arises from phage-induced inhibition of host transcription, leading to degradation of the labile AvcI. AvcD activation and nucleotide depletion not only decreases phage replication but also increases the formation of defective phage virions. Surprisingly, infection of phages such as T7 that are not inhibited by AvcID also lead to AvcI RNA antitoxin degradation and AvcD activation, suggesting that depletion of AvcI is not sufficient to confer protection against some phage. Rather, our results support that phage with a longer replication cycle like T5 are sensitive to AvcID-mediated protection while those with a shorter replication cycle like T7 are resistant.

Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum.

Bacterial remineralization of algal organic matter fuels algal growth but is rarely quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others. Here, we quantified bacterial incorporation of algal-derived complex dissolved organic carbon and nitrogen and algal incorporation of remineralized carbon and nitrogen in fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum at the single-cell level using isotope tracing and nanoSIMS. We found unexpected strain-to-strain and cell-to-cell variability in net carbon and nitrogen incorporation, including non-ubiquitous complex organic nitrogen utilization and remineralization. We used these data to identify three distinct functional guilds of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional guilds were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics, highlighting the need for direct activity-based measurements in ecological studies of microbial metabolic interactions.