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Microbiology Resource Announcements Sep 2023We sequenced the genomes of recently discovered (CCOS 2000) and of the type strains of closely related (DSM 7262) and (LMG 21716). The three genomes set the basis to...
We sequenced the genomes of recently discovered (CCOS 2000) and of the type strains of closely related (DSM 7262) and (LMG 21716). The three genomes set the basis to unambiguous diagnostic of these honey bee associated bacteria.
PubMed: 37530538
DOI: 10.1128/MRA.00209-23 -
Journal of Genomics 2023Here, we describe the isolation and draft genome sequence of sp. CCS19. sp. CCS19 was isolated from leaf soil collected in Japan and identified based on similarity of...
Here, we describe the isolation and draft genome sequence of sp. CCS19. sp. CCS19 was isolated from leaf soil collected in Japan and identified based on similarity of the 16S rRNA sequence with related type strains. The draft genome sequence of sp. CCS19 consisted of a total of 107 contigs containing 6,816,589 bp, with a GC content of 51.5% and comprising 5,935 predicted coding sequences.
PubMed: 37780743
DOI: 10.7150/jgen.87228 -
Applied and Environmental Microbiology Sep 2023WLY78, a N-fixing bacterium, has great potential use as a biofertilizer in agriculture. Recently, we have revealed that GlnR positively and negatively regulates the...
WLY78, a N-fixing bacterium, has great potential use as a biofertilizer in agriculture. Recently, we have revealed that GlnR positively and negatively regulates the transcription of the (trogen ixation) operon () in WLY78 by binding to two loci of the promoter according to nitrogen availability. However, the regulatory mechanisms of nitrogen metabolism mediated by GlnR in the genus remain unclear. In this study, we have revealed that glutamine synthetase (GS) and GlnR in WLY78 play a key role in the regulation of nitrogen metabolism. GS (encoded by within ) and GS1 (encoded by ) belong to distinct groups: GSI-α and GSI-β. Both GS and GS1 have the enzyme activity to convert NH and glutamate into glutamine, but only GS is involved in the repression by GlnR. GlnR represses transcription of under excess nitrogen, while it activates the expression of under nitrogen limitation. GlnR simultaneously activates and represses the expression of and in response to nitrogen availability. Also, GlnR regulates the expression of and . IMPORTANCE In this study, we have revealed that GlnR uses multiple mechanisms to regulate nitrogen metabolism. GlnR activates or represses or simultaneously activates and inhibits the transcription of nitrogen metabolism genes in response to nitrogen availability. The multiple regulation mechanisms employed by GlnR are very different from GlnR which represses nitrogen metabolism under excess nitrogen. Both GS encoded by within the operon and GS1 encoded by in WLY78 are involved in ammonium assimilation, but only GS is required for regulating GlnR activity. The work not only provides significant insight into understanding the interplay of GlnR and GS in nitrogen metabolism but also provides guidance for improving nitrogen fixation efficiency by modulating nitrogen metabolism.
PubMed: 37668407
DOI: 10.1128/aem.00139-23 -
Frontiers in Microbiology 2023Changes in the soil environment in the root zone will affect the growth, development and resistance of plants. The mechanism underlying the effect of drought and flood...
Changes in the soil environment in the root zone will affect the growth, development and resistance of plants. The mechanism underlying the effect of drought and flood stress on rhizosphere bacterial diversity, soil metabolites and soil enzyme activity is not clear and needs further study. To analyze the dynamic changes in bacteria, metabolites and enzyme activities in the rhizosphere soil of maize under different drought-flood abrupt alternation (DFAA) stresses, the barrel test method was used to set up the 'sporadic light rain' to flooding (referring to trace rainfall to heavy rain) (DFAA1) group, 'continuous drought' to flooding (DFAA2) group and normal irrigation (CK) group from the jointing to the tassel flowering stage of maize. The results showed that Actinobacteria was the most dominant phylum in the two DFAA groups during the drought period and the rewatering period, and Proteobacteria was the most dominant phylum during the flooding period and the harvest period. The alpha diversity index of rhizosphere bacteria in the DFAA2 group during the flooding period was significantly lower than that in other stages, and the relative abundance of Chloroflexi was higher. The correlation analysis between the differential genera and soil metabolites of the two DFAA groups showed that the relative abundance of in the DFAA1 group was higher during the drought period, and it was significantly positively correlated with the bioactive lipid metabolites. The differential bacterium was enriched in the DFAA2 group during the flooding period and were strongly correlated with biogenic amine metabolites. The relative abundances of , and in the DFAA2 group were higher compared with DFAA1 group from rewatering to harvest and were significantly positively correlated with hydrocarbon compounds and steroid hormone metabolites. The acid phosphatase activity of the DFAA1 group was significantly higher than that of the DFAA2 group during the flooding period. The study suggests that there is a yield compensation phenomenon in the conversion of 'continuous drought' to flooding compared with 'sporadic light rain', which is related to the improvement in the flooding tolerance of maize by the dominant bacteria Chloroflexi, bacterium SJA-15 and biogenic amine metabolites. These rhizosphere bacteria and soil metabolites may have the potential function of helping plants adapt to the DFAA environment. The study revealed the response of the maize rhizosphere soil environment to DFAA stress and provided new ideas for exploring the potential mechanism of crop yield compensation under DFAA.
PubMed: 38170081
DOI: 10.3389/fmicb.2023.1295376 -
MedRxiv : the Preprint Server For... Sep 2023Neonatal infections due to have increasingly been reported over the last few years. We performed a structured literature review of human infections in infants and...
Neonatal infections due to have increasingly been reported over the last few years. We performed a structured literature review of human infections in infants and adults to compare the epidemiology of infections between these distinct patient populations. Thirty-nine reports describing 176 infections met our inclusion criteria and were included. There were 37 infections occurring in adults caused by 23 species. The clinical presentations of infections were quite variable. In contrast, infections in infants were caused by only 3 species: (112/139, 80%), (2/139, 1%) and (2/139, 1%). All of the infants with infection presented with a sepsis syndrome or meningitis, often complicated by extensive cerebral destruction and hydrocephalus. Outcomes were commonly poor with 17% (24/139) mortality. Cystic encephalomalacia due to brain destruction was common in both Ugandan and American cases and 92/139 (66%) required surgical management of hydrocephalus following their infection. infections are likely underappreciated in infants and effective treatments are urgently needed.
PubMed: 37790370
DOI: 10.1101/2023.09.19.23295794 -
Foods (Basel, Switzerland) Jul 2023To develop a process for low-cost and ecologically friendly coffee fermentation, civet gut bacteria were isolated and screened to be used for fermentation. Among 223...
To develop a process for low-cost and ecologically friendly coffee fermentation, civet gut bacteria were isolated and screened to be used for fermentation. Among 223 isolates from civet feces, two bacteria exhibited strong protease, amylase, lipase, pectinase, and cellulase activities. By analyzing 16S rDNA phylogeny, those bacteria were identified to be JT-PN39 (LP) and JT-A29 (PM), where their potency (pure or mixed bacterial culture) for fermenting 5 L of arabica parchment coffee in 48-72 h was further determined. To characterize the role of bacteria in coffee fermentation, growth and pH were also determined. For mixed starter culture conditions, the growth of PM was not detected after 36 h of fermentation due to the low acid conditions generated by LP. Coffee quality was evaluated using a cupping test, and LP-fermented coffee expressed a higher cupping score, with a main fruity and sour flavor, and a dominant caramel-honey-like aroma. Antioxidant and anti-foodborne pathogenic bacteria activity, including total phenolic compounds of PM and LP fermented coffee extracts, was significantly higher than those of ordinary coffee. In addition, LP-fermented coffee expressed the highest antibacterial and antioxidant activities among the fermented coffee. The toxicity test was examined in the murine macrophage RAW 264.7 cell, and all fermented coffee revealed 80-90% cell variability, which means that the fermentation process does not generate any toxicity. In addition, qualifications of non-volatile and volatile compounds in fermented coffee were examined by LC-MS and GC-MS to discriminate the bacterial role during the process by PCA plot. The flavors of fermented coffee, including volatile and non-volatile compounds, were totally different between the non-fermented and fermented conditions. Moreover, the PCA plot showed slightly different flavors among fermentations with different starter cultures. For both the cupping test and biological activities, this study suggests that LP has potential for health benefits in coffee fermentation.
PubMed: 37569163
DOI: 10.3390/foods12152894 -
Physiology (Bethesda, Md.) Jul 2024Bees are the most important insect pollinators of the crops humans grow, and , the Western honey bee, is the most commonly managed species for this purpose. In addition... (Review)
Review
Bees are the most important insect pollinators of the crops humans grow, and , the Western honey bee, is the most commonly managed species for this purpose. In addition to providing agricultural services, the complex biology of honey bees has been the subject of scientific study since the 18th century, and the intricate behaviors of honey bees and ants, fellow hymenopterans, inspired much sociobiological inquest. Unfortunately, honey bees are constantly exposed to parasites, pathogens, and xenobiotics, all of which pose threats to their health. Despite our curiosity about and dependence on honey bees, defining the molecular mechanisms underlying their interactions with biotic and abiotic stressors has been challenging. The very aspects of their physiology and behavior that make them so important to agriculture also make them challenging to study, relative to canonical model organisms. However, because we rely on so much for pollination, we must continue our efforts to understand what ails them. Here, we review major advancements in our knowledge of honey bee physiology, focusing on immunity and detoxification, and highlight some challenges that remain.
Topics: Animals; Bees; Pesticides; Host-Pathogen Interactions
PubMed: 38411571
DOI: 10.1152/physiol.00033.2023 -
JDS Communications Mar 2024Bacterial endospores, or simply spores, are formed by a diverse group of members within the phylum and include notable genera such as , , and . Spores are distributed... (Review)
Review
Bacterial endospores, or simply spores, are formed by a diverse group of members within the phylum and include notable genera such as , , and . Spores are distributed ubiquitously in natural environments, with soil being an important primary reservoir for these microbes. As such, spores are present throughout the dairy farm environment, and transmission into raw milk occurs through several pathways that coalesce at the point of milk harvest. Despite the very low spore concentrations typically found in bulk tank raw milk, the impact of spores on dairy product quality, safety, and product conformance is widely documented. Processed dairy products affected by the presence of sporeforming bacteria include milk, cheese, dairy powders, ice cream mix, and more. Although raw milk is a major source of spores leading to quality, safety, and conformance issues in dairy products, the impact of other sources should not be discounted and may include ingredients (e.g., cocoa powder), contamination originating from biofilms in processing equipment, and even cross-contamination from the processing environment itself. Addressing spore contamination in the dairy system is complicated by this widespread distribution and by the diversity of these organisms, and successful source tracking often requires discriminatory molecular subtyping tools. Here, we review the key sources of sporeforming bacteria in the dairy system, the factors leading to the transmission of this diverse group of microbes into processed dairy products, and methods employed to enumerate and track spore contaminants.
PubMed: 38482119
DOI: 10.3168/jdsc.2023-0428 -
Foods (Basel, Switzerland) Sep 2023Tea is the most popular and widely consumed beverage worldwide, especially black tea. Summer tea has a bitter and astringent taste and low aroma compared to spring tea...
Tea is the most popular and widely consumed beverage worldwide, especially black tea. Summer tea has a bitter and astringent taste and low aroma compared to spring tea due to the higher content of polyphenols and lower content of amino acids. Microbial fermentation is routinely used to improve the flavor of various foods. This study analyzed the relationship between the quality of black tea, metabolic characteristics, and microbial communities after microbial stuck fermentation in summer black tea. Stuck fermentation decreased the bitterness, astringency sourness, and freshness, and increased the sweetness, mellowness, and smoothness of summer black tea. The aroma also changed from sweet and floral to fungal, with a significant improvement in overall quality. Metabolomics analysis revealed significant changes in 551 non-volatile and 345 volatile metabolites after fermentation. The contents of compounds with bitter and astringent taste were decreased. Sweet flavor saccharides and aromatic lipids, and acetophenone and isophorone that impart fungal aroma showed a marked increase. These changes are the result of microbial activities, especially the secretion of extracellular enzymes. , , and contribute to the reduction of bitterness and astringency in summer black teas after stuck fermentation, and Paenibacillus and contribute positively to sweetness. In addition, Aspergillus was associated with the formation of fungal aroma. In summary, our research will provide a suitable method for the improvement of tea quality and utilization of summer tea, as well as provide a reference for innovation and improvement in the food industry.
PubMed: 37761123
DOI: 10.3390/foods12183414 -
Frontiers in Microbiology 2024Legumes are renowned for their distinctive biological characteristic of forming symbiotic associations with soil bacteria, mostly belonging to the familiy, leading to... (Review)
Review
Legumes are renowned for their distinctive biological characteristic of forming symbiotic associations with soil bacteria, mostly belonging to the familiy, leading to the establishment of symbiotic root nodules. Within these nodules, rhizobia play a pivotal role in converting atmospheric nitrogen into a plant-assimilable form. However, it has been discerned that root nodules of legumes are not exclusively inhabited by rhizobia; non-rhizobial endophytic bacteria also reside within them, yet their functions remain incompletely elucidated. This comprehensive review synthesizes available data, revealing that and are the most prevalent genera of nodule endophytic bacteria, succeeded by , , , , and . To date, the bibliographic data available show that followed by and are the main hosts for nodule endophytic bacteria. Clustering analysis consistently supports the prevalence of and as the most abundant nodule endophytic bacteria, alongside , , and . Although non-rhizobial populations within nodules do not induce nodule formation, their presence is associated with various plant growth-promoting properties (PGPs). These properties are known to mediate important mechanisms such as phytostimulation, biofertilization, biocontrol, and stress tolerance, emphasizing the multifaceted roles of nodule endophytes. Importantly, interactions between non-rhizobia and rhizobia within nodules may exert influence on their leguminous host plants. This is particularly shown by co-inoculation of legumes with both types of bacteria, in which synergistic effects on plant growth, yield, and nodulation are often measured. Moreover these effects are pronounced under both stress and non-stress conditions, surpassing the impact of single inoculations with rhizobia alone.
PubMed: 38812696
DOI: 10.3389/fmicb.2024.1386742