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Background: Psoriasis is a chronic skin condition affected by genetic and environmental factors. Changes in the skin microbiome may affect the immune system and skin barrier functions, thereby contributing to the development and progression of psoriasis. The scalp, which is a common site for psoriasis, is often resistant to therapy. Although several studies have investigated the scalp microbiome, analyses focusing on both bacteria and fungi remain scarce. Methods: We examined the scalp microbiomes of 11 patients with psoriasis complicated with scalp lesions and categorized them according to their Psoriasis Area Severity Index (PASI) scores. The bacterial and fungal data were analyzed using QIIME2 pipeline version 2021.04 and the UNITE database version 8.3, respectively. Results: The Shannon indices for mild (2 patients), moderate (4 patients), and severe (5 patients) groups were 0.97, 1.38, and 1.88, respectively. A significant correlation was observed between increased mycobiome diversity and disease severity (p = 4.07 × 10−5, Spearman's correlation: 0.9269). Compared with the mild and moderate groups, the severe group exhibited a higher abundance of Malassezia globosa. Pseudomonas and Staphylococcus were, respectively, more prevalent in the moderate and severe groups than in the mild group. Conclusions: This study highlights the potential role of increased fungal diversity and specific microbial compositions in the severity of scalp psoriasis, suggesting a possible avenue for targeted therapeutic interventions. [ABSTRACT FROM AUTHOR]

Simple Summary: Rodents, as the most abundant group of mammals, offer a unique opportunity to study the relationship between diet and host gut microecology. In this study, we focused on two species of the genus Myospalax in the Eurasian steppes in China: M. psilurus and M. aspalax. These specialized herbivorous rodents have adapted to a subterranean lifestyle and exhibit distinct dietary choices. Our study aimed to investigate how their diet composition is related to their gut microbial communities and whether there are unique indicator species for their gut microecology. Using 16S amplicon technology and macro-barcoding technology, we analyzed the gut bacterial communities and diet composition of the two zokor species. We found that M. psilurus had a higher diversity of gut microbial bacterial communities compared to M. aspalax. The two species also possessed different gut bacterial indicator species, with unique relationships between their diet and gut microbes. Our results provide new insights into the adaptation of zokors to long-term subterranean life and shed light on their cellulose degradation abilities and ecological niches. As the most abundant group of mammals, rodents possess a very rich ecotype, which makes them ideal for studying the relationship between diet and host gut microecology. Zokors are specialized herbivorous rodents adapted to living underground. Unlike more generalized herbivorous rodents, they feed on the underground parts of grassland plants. There are two species of the genus Myospalax in the Eurasian steppes in China: one is Myospalax psilurus, which inhabits meadow grasslands and forest edge areas, and the other is M. aspalax, which inhabits typical grassland areas. How are the dietary choices of the two species adapted to long-term subterranean life, and what is the relationship of this diet with gut microbes? Are there unique indicator genera for their gut microbial communities? Relevant factors, such as the ability of both species to degrade cellulose, are not yet clear. In this study, we analyzed the gut bacterial communities and diet compositions of two species of zokors using 16S amplicon technology combined with macro-barcoding technology. We found that the diversity of gut microbial bacterial communities in M. psilurus was significantly higher than that in M. aspalax, and that the two species of zokors possessed different gut bacterial indicator genera. Differences in the feeding habits of the two species of zokors stem from food composition rather than diversity. Based on the results of Mantel analyses, the gut bacterial community of M. aspalax showed a significant positive correlation with the creeping-rooted type food, and there was a complementary relationship between the axis root-type-food- and the rhizome-type-food-dominated (containing bulb types and tuberous root types) food groups. Functional prediction based on KEGG found that M. psilurus possessed a stronger degradation ability in the same cellulose degradation pathway. Neutral modeling results show that the gut flora of the M. psilurus has a wider ecological niche compared to that of the M. aspalax. This provides a new perspective for understanding how rodents living underground in grassland areas respond to changes in food conditions. [ABSTRACT FROM AUTHOR]

Simple Summary: Recent studies have shown a correlation between piglet diarrhea and the gut microbiota. However, the precise mechanism by which intestinal microorganisms and their metabolites influence diarrhea in weaned piglets remains unclear. This study explored differences in the gut microbiota and associated metabolites between healthy and diarrheic-weaned piglets using macrogenomic and metabolomic analyses. We identified microorganisms that differed markedly between the two groups. We noticed that the number and abundance of Bacteroidaceae bacterium were strongly negatively correlated with diarrhea in weaned piglets, whereas Caudoviricetes exhibited a strong positive correlation. Our screening for markedly different metabolites such as carnosine, pantothenic acid, pyridoxal, methylimidazoleacetic acid, indole-3-acetaldehyde and 5-hydroxyindoleacetic acid, along with the identification of metabolite-related metabolic pathways like tryptophan and vitamin B6 metabolism, identified important pathways associated with gut microbiota dysbiosis caused by post-weaning diarrhea in piglets. Conjoint analysis revealed that a substantial increase in the number and abundance of Caudoviricetes, coupled with a decrease in the number and abundance of Bacteroidaceae bacterium could potentially serve as microbial markers of post-weaning diarrhea. Recent studies have shown a correlation between piglet diarrhea and the gut microbiota. However, the precise mechanism by which intestinal microorganisms and their metabolites influence diarrhea in weaned piglets remains unclear. This study explored differences in the gut microbiota and associated metabolites between healthy and diarrheic-weaned piglets using macrogenomic and metabolomic analyses. The histomorphological results showed that diarrheic piglets had shorter jejunal and ileal villi, some of which were shed, compared to healthy piglets. Substantial differences in gut microbial diversity and metabolites were also observed, with Bacteroidaceae bacterium and Caudoviricetes being the main differential organisms that were strongly correlated with host status. Microbial functions, mainly the metabolism of carbohydrates, glycans, lipids, and amino acids, as well as related enzyme activities, were substantially different. The major differential metabolites were carnosine, pantothenic acid (vitamin B5), pyridoxal, methylimidazoleacetic acid, indole-3-acetaldehyde, and 5-hydroxyindoleacetic acid. These metabolites were enriched in beta-alanine, histidine, tryptophan, and vitamin B6 metabolism, and in the pantothenate and CoA biosynthesis pathways. Combined macrogenomic and metabolomic analyses revealed that carnosine, vitamin B5, and pyridoxal were negatively correlated with Caudoviricetes; methylimidazoleacetic acid, indole-3-acetaldehyde, and 5-hydroxyindoleacetic acid were positively correlated with Caudoviricetes. Whereas carnosine and vitamin B5 were positively correlated with Bacteroidaceae bacterium, 5-hydroxyindoleacetic acid was negatively correlated. The decreased abundance of Bacteroidaceae bacterium and the increased abundance of Caudoviricetes and related metabolites likely contribute to post-weaning diarrhea in piglets. Therefore, the abundance of Bacteroidaceae bacterium and Caudoviricetes can likely serve as potential markers for identifying and preventing diarrhea in post-weaning piglets. [ABSTRACT FROM AUTHOR]

Mianning ham is a traditional meat product in China. In this experiment, solid-phase microextraction–gas chromatography (SPME-GC-MS) and high-throughput sequencing were used to study the effects of adding Penicillium lanosum and adding the mixture of Penicillium lanosum and Staphylococcus equorum on the flavor and microbiology of Mianning ham. The results showed that the addition of the ferments resulted in an increase in the abundance of both the dominant bacterial phylum (Thick-walled Bacteria) and the dominant fungal phylum (Ascomycota). The variety of volatile flavor substances and key flavor substances increased after adding fermentation agents. A free amino acid analysis showed that hams from the Penicillium lanosum and Staphylococcus equorum group had significantly higher umami flavor amino acids than the control group and Penicillium lanosum group. Therefore, inoculation with Penicillium lanosum and Staphylococcus equorum favored the dominant bacteria and flavor of Mianning ham. [ABSTRACT FROM AUTHOR]

Fusarium root rot caused by the Fusarium species complex significantly affects the yield and quality of Angelica sinensis, a valuable medicinal herb. Traditional management primarily relies on chemical fungicides, which have led to pathogen resistance, environmental hazards, and concerns regarding public health and the active components in A. sinensis. This study explores the efficacy of a novel plant-derived biopesticide Shi Chuang Zhi Feng Ning (T1; SCZFN), alongside Bacillus subtilis wettable powder (T2) and a chemical fungicide (T3), in controlling root rot and understanding their impacts on the rhizosphere microbial community and root metabolome. Results of the field experiment demonstrated that treatments T1 and T3 achieved control efficiencies of 73.17% and 75.45%, respectively, significantly outperforming T2 (39.99%) and the control. High-throughput sequencing revealed that all treatments altered the diversity and structure of microbial communities, with T1 and T2 reducing the abundance of taxa linked to root rot, such as Muribaculaceae spp., Humicola spp., Fusarium spp., and Mycochlamys spp. Treatment T1 notably enhanced beneficial bacterial taxa, including Acidobacteria spp., Nitrospira spp., and Pedosphaeraceae spp., involved in carbon cycling and plant growth promotion. Metabolomic analysis identified 39, 105, and 45 differentially expressed metabolites (DEMs) across the treatments, demonstrating T1's potential to modulate the root metabolome effectively. Further, a correlation analysis demonstrated a stronger correlation between distinct microorganisms with significant influence and DEMs of T1 treatment compared to other treatments. These findings underscore biopesticide SCZFN's role in enhancing plant health and disease suppression in A. sinensis, providing insights into its biocontrol mechanisms and supporting the development of sustainable disease management strategies in its cultivation. [ABSTRACT FROM AUTHOR]

A significant part of our stone heritage is made of limestone. Researchers are increasingly concerned about the risk of biodeterioration of these important objects. In this article, we present an up-to-date review of the microbial diversity of biodeteriorated limestone cultural heritage (CHL). This is based on an extensive bibliographic search of the literature investigating biodiversity using culture-dependent (CD) and culture-independent (CI) techniques. In the case of the former, only articles in which microorganisms were identified using molecular tools that generate DNA sequences were selected, with the aim of providing traceable identification based on the sequences submitted to public databases. The literature search resulted in the selection of 50 articles published between 2004 and 2023. The biodiversity data obtained from the CHL were organized into the following groups: fungi (626 records), bacteria and cyanobacteria (786 and 103 records, respectively), algae (51 records), and archaea (27 records). Within each group, the microbial diversity studied was compared according to results obtained using CD and CI techniques. Of all the articles selected, 12 used both approaches, demonstrating the growing effort to discover the total microbiome of biodeteriorated cultural heritage assets. [ABSTRACT FROM AUTHOR]

Hot springs contain many microorganisms, and a great deal of research has been conducted on the bacteria in hot springs but less on the fungi. Microbial diversity research in hot springs will help to further develop and utilize the microbial resources from hot springs. This is the first study to analyze the fungal diversity and ecological functions in Tangchi hot spring (China). In this paper, the fungal ITS sequences in the water samples of Tangchi hot spring were sequenced by Illumina MiSeq high-throughput sequencing technology and bioinformatically analyzed to explore the fungal diversity and ecological functions in the hot spring. The results revealed that the dominant fungal phylum was Ascomycota, followed by Basidiomycota, Chytridiomycota, and Olpidiomycota, and the dominant fungal genera were Rhizophydium, Aureobasidium, Rhodotorula, and Sclerotinia in Tangchi hot spring. The FUNGuild functional analysis results revealed that the dominant guilds in Tangchi hot spring were plant pathogens followed by the undefined saprotroph and the animal endosymbiont–animal pathogen–endophyte–plant pathogen–undefined saprotroph. This study can fill the gap in people's understanding of fungal resources and offer theoretical support for understanding the fungal diversity and fungal resource development and utilization in Tangchi hot spring. [ABSTRACT FROM AUTHOR]

Although gut dysbiosis is associated with cow's milk allergy (CMA), causality remains uncertain. This study aimed to identify specific bacterial signatures that influence the development and outcome of the disease. We also investigated the effect of hypoallergenic formula (HF) consumption on the gut microbiome of milk-allergic children. 16S rRNA amplicon sequencing was applied to characterize the gut microbiome of 32 milk-allergic children aged 5–12 years and 36 age-matched healthy controls. We showed that the gut microbiome of children with CMA differed significantly from that of healthy children, regardless of whether they consumed cow's milk. Compared to that of healthy cow's milk consumers, it was depleted in Bifidobacterium, Coprococcus catus, Monoglobus, and Lachnospiraceae GCA-900066575, while being enriched in Oscillibacter valericigenes, Negativibacillus massiliensis, and three genera of the Ruminococcaceae family. Of these, only the Ruminococcaceae taxa were also enriched in healthy children not consuming cow's milk. Furthermore, the gut microbiome of children who developed tolerance and had received an HF was similar to that of healthy children, whereas that of children who had not received an HF was significantly different. Our results demonstrate that specific gut microbiome signatures are associated with CMA, which differ from those of dietary milk elimination. Moreover, HF consumption affects the gut microbiome of children who develop tolerance. [ABSTRACT FROM AUTHOR]

Biological denitrification is a generally economically viable and reliable technology for nitrate (NO3−-N) and nitrite (NO2−-N) removal from wastewater. Nitrate/nitrite reduction requires an electron donor, which can be supplied from influent wastewater organic compounds, added as an external carbon source, or by endogenous respiration. Decisions regarding the selection of an external carbon source should take into consideration its cost, sludge generation quantity, the rate and efficiency of denitrification, and chemical storage safety. The expense of waste management and external carbon sources accounts for up to 50% of the overall cost of wastewater treatment. The carbon source characteristics required for biological denitrification affect the microbial community structure, denitrification rate, and intermediate products. This review is based on a bibliometric analysis and a systematic literature review providing information and insight into the topic of the denitrification process using different carbon sources. In this review, the main focus was on discussing alternative carbon sources vs. traditional carbon sources in terms of the carbon source price, C/N ratio, denitrification efficiency and rate, operational parameters, and advantages and disadvantages, as well as the limitations in the denitrification process. Future perspectives may include the operating parameters influencing the stability of the removal performance; the maintenance and improvement of nitrate removal; a study of the diversity of the microbial community; research on the application of new alternative carbon sources in denitrification; and N2O emission detection and minimisation. [ABSTRACT FROM AUTHOR]

Theobroma cacao plantations are of significant economic importance worldwide, primarily for chocolate production. During the harvest and processing of cocoa beans, they are subjected to fermentation either by microorganisms present in the environment (spontaneous fermentation) or the addition of starter cultures, with different strains directly contributing distinct flavor and color characteristics to the beans. In addition to fungi and bacteria, viruses are ubiquitous and can affect the quality of the fermentation process by infecting fermenting organisms, destabilizing microbial diversity, and consequently affecting fermentation quality. Therefore, in this study, we explored publicly available metatranscriptomic libraries of cocoa bean fermentation in Limon Province, Costa Rica, looking for viruses associated with fermenting microorganisms. Libraries were derived from the same sample at different time points: 7, 20, and 68 h of fermentation, corresponding to yeast- and lactic acid bacteria-driven phases. Using a comprehensive pipeline, we identified 68 viral sequences that could be assigned to 62 new viral species and 6 known viruses distributed among at least nine families, with particular abundance of elements from the Lenarviricota phylum. Interestingly, 44 of these sequences were specifically associated with ssRNA phages (Fiersviridae) and mostly fungi-infecting viral families (Botourmiaviridae, Narnaviridae, and Mitoviridae). Of note, viruses from those families show a complex evolutionary relationship, transitioning from infecting bacteria to infecting fungi. We also identified 10 and 3 viruses classified within the Totiviridae and Nodaviridae families, respectively. The quantification of the virus-derived RNAs shows a general pattern of decline, similar to the dynamic profile of some microorganism genera during the fermentation process. Unexpectedly, we identified narnavirus-related elements that showed similarity to segmented viral species. By exploring the molecular characteristics of these viral sequences and applying Hidden Markov Models, we were capable of associating these additional segments with a specific taxon. In summary, our study elucidates the complex virome associated with the microbial consortia engaged in cocoa bean fermentation that could contribute to organism/strain selection, altering metabolite production and, consequently, affecting the sensory characteristics of cocoa beans. [ABSTRACT FROM AUTHOR]

The way of disposing of rock mineral material has a significant impact on subsequent spontaneous vegetation succession, soil properties, and respiration. We compared seven spontaneously vegetated samples from a large (2 km2) borrow pit used to dispose of the byproducts of a hard coal mine with seven plots from four coal mine spoil heap piles. We used BIOLOG EcoPlates to assess the microbial catabolic activity of the substrate. The substrate in the borrow pit was characterized by higher water content and lower temperature compared to the heap pile substrate. The borrow pit had a more diverse plant community structure. Higher Rao's quadratic entropy, functional richness, and functional divergence were also calculated from plant functional traits in borrow pit samples. Although borrow pit samples showed higher total microbial biomass, bacteria/fungi ratio, and gram+/gram− ratio, and heap pile samples showed higher soil enzymatic activity, microbial functional diversity, and catabolic activity, these differences were not significant. Soil respiration from the borrow pit substrate was two folds higher. The borrow pit method of disposing of rock mineral material can be suggested to speed up spontaneous vegetation succession. This research provides new insights into the effects of burying hard coal byproducts in borrow pits and offers guidance for the management of hard coal mining. [ABSTRACT FROM AUTHOR]

Exploring species diversity along elevational gradients is important for understanding the underlying mechanisms. Our study focused on analyzing the species diversity of fungal communities and their subcommunities at different trophic and taxonomic levels across three high mountains of the Korean Peninsula, each situated in a different climatic zone. Using high-throughput sequencing, we aimed to assess fungal diversity patterns and investigate the primary environmental factors influencing fungal diversity. Our results indicate that soil fungal diversity exhibits different elevational distribution patterns on different mountains, highlighting the combined effects of climate, soil properties, and geographic topology. Notably, the total and available phosphorus contents in the soil emerged as key determinants in explaining the differences in diversity attributed to soil properties. Despite the varied responses of fungal diversity to elevational gradients among different trophic guilds and taxonomic levels, their primary environmental determinants remained remarkably consistent. In particular, total and available phosphorus contents showed significant correlations with the diversity of the majority of the trophic guilds and taxonomic levels. Our study reveals the absence of a uniform diversity pattern along elevational gradients, underscoring the general sensitivity of fungi to soil conditions. By enriching our understanding of fungal diversity dynamics, this research enhances our comprehension of the formation and maintenance of elevational fungal diversity and the response of microbial communities in mountain ecosystems to climate change. This study provides valuable insights for future ecological studies of similar biotic communities. [ABSTRACT FROM AUTHOR]

In this research, the connection between age and microbial diversity in cattle was explored, revealing significant changes in both protist diversity and fungal microbiota composition with age. Using fecal samples from 21 Simmental cattle, microbial communities were analyzed through 18S rRNA gene sequencing. Results indicated significant differences in alpha protist diversity among the three age groups, while fungal composition varied notably with age and was linked to hematological parameters. Despite the stability of fungal alpha diversity, compositional changes suggest the gut as a stable niche for microbial colonization influenced by diet, clinical parameters, and microbial interactions. All cattle were maintained on a consistent diet, tailored to meet the specific nutritional needs of each age group. These findings emphasize the importance of understanding age-related microbial dynamics to enhance livestock management and animal health, contributing to broader ecological and biomedical research. This study was limited by the lack of comprehensive metabolic analyses correlating microbiota changes with specific age-related variations, indicating a need for further research in this area. [ABSTRACT FROM AUTHOR]

Genetic and environmental factors influence the growth and quality of medicinal plants. In recent years, rhizosphere microorganisms have also emerged as significant factors affecting the quality of medicinal plants. This study aimed to identify Schisandra resources with high lignan content and analyze the microbial diversity of the rhizosphere soil. High-performance liquid chromatography was used to measure the lignan content in nine Schisandra fruits. High-throughput sequencing was used to analyze the 16S rDNA sequences of rhizosphere bacteria to identify bacterial species diversity. The total lignan content of the nine Schisandra resources ranged from 9.726 mg/g to 14.031 mg/g, with ZJ27 having the highest content and ZJ25 the lowest. Among the six lignan components, Schisandrol A had the highest content, ranging from 5.133 mg/g to 6.345 mg/g, with a significant difference between ZJ25, ZJ27, and other resources (p < 0.05). Schizandrin C had the lowest content, ranging from 0.062 mg/g to 0.419 mg/g, with more significant differences among the resources. A total of 903,933 sequences were obtained from the rhizosphere soil of the nine Schisandra resources, clustered into 10,437 OTUs at a 97% similarity level. The dominant bacterial phyla were Actinobacteriota, Acidobacteriota, Proteobacteria, Chloroflexi, Gemmatimonadota, and Verrucomicrobiota. The dominant bacterial genera were Candidatus_Udaeobacter, Candidatus_Solibacter, RB41, Bradyrhizobium, Gaiella, and Arthrobacter. ZJ27 is the Schisandra resource with the highest lignan content, and the rhizosphere bacteria of Schisandra are rich in diversity. Schisandra B is negatively correlated with Bryobacter, Candidatus_Solibacter, and unnamed genera of Gaiellales. [ABSTRACT FROM AUTHOR]

Simple Summary: Buffalo milk has a significantly greater fatty acid content, up to 11%, than cow's milk, making buffalo milk more suitable for dairy products such as cheese. Several factors affect the quantity and proportion of milk fatty acids, and among the intrinsic factors, breed is important. However, the role of breed is still not fully understood. It is known that gastrointestinal microbiota serve as a key factor in modulating the content of milk fatty acids, since breed affects the type of gastrointestinal microbiota and consequently the milk fatty acids (FA). Therefore, we used 16S rDNA sequencing to analyze the microbial causes of different milk fatty acids in two breeds of dairy buffaloes. The results showed that the abundance of fatty acids such as C18:3 and C18:2c9t11 in Murrah buffalo milk was associated with the abundance of bacteria such as Acetobacter and Ruminalococcus in the rumen, as well as bacteria such as UCG-005 in the feces. This experiment investigated gastrointestinal microbes' role in milk fatty acid differences between Murrah and Nili-Ravi buffaloes. After 30 days of a basal diet, rumen microbial diversity was similar, but Murrah buffaloes had greater partially unsaturated fatty acids like C18:2c9t11. Rumen bacteria like Acetobacter, Ruminococcus, and Prevotellaceae_YAB2003_group correlated positively with milk fatty acids C22:5n-6 and C18:3 in Murrah. Fecal microbial beta diversity differed, with UCG-005 and Prevolla positively correlated with C18:2c9t11 and C22:5n-6. The greater quantity of milk fatty acids C18:3, C18:2c9t11, and C22:5n-6 in Murrah milk was linked to rumen and fecal microbes. This suggests that gastrointestinal microbes like Acetobacter, Ruminococcus, and UCG_005 regulate milk fatty acid concentrations in buffaloes. [ABSTRACT FROM AUTHOR]

Thiacloprid, a neonicotinoid pesticide, is known to affect the gut microbiome of honeybees, yet studies often focus on immediate alternations during exposure, overlooking long-term microbiological impacts post-exposure. This study investigates the influences of sublethal thiacloprid administered during the larval developmental stage of honeybees on physiological changes and gut microbiota of adult honeybees. We found that thiacloprid exposure increased mortality and sugar intake in emerged honeybees. Using 16S rDNA sequencing, we analyzed intestinal microbial diversity of honeybees at one and six days post-emergence. Our findings reveal a significant but transient disruption in gut microbiota on day 1, with recovery from dysbiosis by day 6. This study emphasizes the importance of evaluating chronic sublethal exposure risks of thiacloprid to protect honeybee health. [ABSTRACT FROM AUTHOR]

Sourdough is one of the oldest technologies employed by humans to leaven bread because of its ability to enhance the flavour and structure of bread using micro-organisms. However, there is a lack of comprehensive information in Botswana regarding the diversity of sourdough starters and the fermentative micro-organisms responsible for spontaneous fermentation. The present study aimed to explore the microbial species diversity of sourdoughs in Botswana and gain insight into the unique microbial communities involved in sourdough production. A total of nine samples were collected from different areas in Botswana. The microbial diversity in sourdoughs was characterized through the sequencing of amplicons of the 16S ribosomal DNA and internal transcribed spacer regions. In silico polymerase chain reaction–restriction fragment length polymorphism and phylogenetics were utilized to determine the genetic diversity among the isolates. The dominant yeast species identified were Saccharomyces cerevisiae, Wickerhamomyces anomamlus, Pichia kudriazverii and kazachstania humilis. Additionally, the presence of Lactiplantibacillus plantarum, Lacticaseibacillus paracasei, Liquorilactobacillus nageli and Bacillus cereus was also detected. It is worth noting that two species of acetic acid bacteria (AAB), namely Acetobacter pasteurianus and A. indonesiensis, were isolated, though in low levels, but the finding is significant in sourdough fermentation. The low occurrence of AAB (acetic acid bacteria) species observed in this study could be an important finding, as these bacteria are considered understudied, yet they are known to contribute significantly to the final product. [ABSTRACT FROM AUTHOR]

Kombucha brewers selling non-alcoholic beverages in the United States must ensure that the ethanol content of their products remains below 0.5% (v/v) throughout all stages of production and shelf life. Producers struggle to comply with this regulation in the absence of expensive dealcoholizing equipment if they wish to sell the unpasteurized or minimally pasteurized products that consumers typically expect. To identify which bacterial and/or fungal species contribute to the high ethanol content of commercial kombucha, we analyzed 47 commercial kombucha samples purchased at supermarkets near Cornell University in Ithaca, NY, USA. We analyzed samples for ethanol content via HPLC, microbial load determination, and next-generation amplicon sequencing of the bacterial and fungal populations of those samples. Two brands were found to contain significantly more than 0.5% ethanol (v/v) in the tested samples (t-test, p < 0.05, greater), and three brands were found to contain significantly different amounts of sugar in the tested samples compared to what was reported on the nutrition label (one higher and two lower, t-test, p < 0.05, two-sided). The microbial communities of the samples most significantly varied due to brand (PERMANOVA, p < 0.05). The main bacterial genera observed in the samples were Komagataeibacter, Acetobacter, Gluconobacter, Oenococcus, Lactobacillus, and Bifidobacterium. The main fungal genera observed in the samples were Saccharomyces, Dekkera, Cyberlindnera, Lachancea, Schizosaccharomyces, and Pichia. We did not identify any bacterial or fungal species associated with differences in ethanol content between samples within brands, suggesting significant strain variation in the bacteria and fungi involved in commercial kombucha fermentation. However, we did find that the relative abundance of Lactobacillales and the lactic acid content of the samples were significantly correlated (Kendall correlation test, p < 0.05). These results build upon recent research elucidating the role of lactic acid bacteria in the commercial fermentation of kombucha. [ABSTRACT FROM AUTHOR]

Xuanwei ham is a traditional fermented meat product in China with a unique production process and excellent-quality reputation at home and abroad. To reveal the microbial community succession of Xuanwei ham at different post-ripening times (W1-4) and its relationship with flavour formation, the microbial community, free amino acids, and volatile flavour compounds (VOCs) were analysed by high-throughput sequencing, liquid chromatography (LC), and gas chromatography–mass spectrometry (GC-MS), respectively. A total of 25 free amino acids were detected, among which W3 contained the fewest, and most were generally lower than in hams in the other three years. Fifty-nine VOCs were detected, among which 17 were esters, and the highest ester content was found in W4. Analysis of the bacterial community composition revealed that the bacterial community composition of ham samples from W3 and other years differed greatly, and at the gate level, the dominant bacterial group of Xuanwei ham from different years was Pseudomonadota. At the genus level, the most abundant genera in W1, W2, and W4 were all dominated by Sarocladium, Klebsiella, and Vibrio, with Klebsiella being the most abundant in W1. The most abundant genus in W3 was Vibrio, and the second most dominant genera were Sarocladium and Gammaretrovirus. In short, this study provides a theoretical basis for the storage, quality, and improvement of Xuanwei ham. [ABSTRACT FROM AUTHOR]

The distinctive taste of Sichuan sauce-flavored sausage comes from an intricate microbial metabolism. The correlation between microbial composition and distinct flavor components has not been researched. The study used headspace solid-phase microextraction action with gas chromatography mass spectrometry to find flavor components and high-throughput sequencing of 16S rRNA to look at the diversity and succession of microbial communities. The correlation network model forecasted the connection between essential bacteria and the development of flavors. The study revealed that the primary flavor compounds in Sichuan sauce-flavored sausages were alcohols, aldehydes, and esters. The closely related microbes were Leuconostoc, Pseudomonas, Psychrobacter, Flavobacterium, and Algoriella. The microbes aided in the production of various flavor compounds, such as 1-octen-3-ol, benzeneacetaldehyde, hexanal, (R,R)-2,3-butanediol, and ethyl caprylate. This work has enhanced our comprehension of the diverse functions that bacteria serve in flavor development during the fermentation of Sichuan sauce-flavored sausage. [ABSTRACT FROM AUTHOR]

Coffee is a critical agricultural commodity and is used to produce premium beverages enjoyed by people worldwide. The microbiome of coffee beans has proven to be an essential tool that improves the flavor profile of coffee by creating aromatic flavor compounds through natural fermentation. This study investigated the natural microbial consortium during the wet process fermentation of coffee onsite in Thailand in order to identify the correlation between microbial diversity and biochemical characteristics including flavor, aroma, and metabolic attributes. Our study found 64 genera of bacteria and 59 genera of yeast/fungi present during the fermentation process. Group of microbes, mainly yeast and lactic acid bacteria, that predominated in the process were significantly correlated with preferable flavor and aroma compounds, including linalyl formate, linalool, cis-isoeugenol, trans-geraniol, and (-)-isopulegol. Some of the detected metabolites were found to be active compounds which could play a role in health. [ABSTRACT FROM AUTHOR]

Desertification and salt stress are major causes of terrestrial ecosystem loss worldwide, and the Gobi, representing a salt-stressed area in inland China, has a major impact on the ecosystems and biodiversity of its surrounding environment. The restoration of the Gobi Desert is an important way to control its expansion, but there are few studies on the evaluation of restoration. In this study, soils under different restoration scenarios, namely, soils in restored areas (R1, R2), semi-restored areas (SR1, SR2), and unrestored control areas (C1, C2), were used to investigate differences in microbial diversity and physicochemical properties. The results showed that the soil was mainly dominated by particles of 4–63 μm (26.45–37.94%) and >63 μm (57.95–72.87%). Across the different restoration levels, the soil pH (7.96–8.43) remained basically unchanged, salinity decreased from 9.23–2.26 to 0.24–0.25, and water content remained constant (10.98–12.27%) except for one restored sample in which it was higher (22.32%). The effective Al, Cu, and Zn in the soil increased, but only slightly. Total organic matter (TOM) decreased from 3.86–5.20% to 1.31–1.47%, and total organic nitrogen (TON) decreased from 0.03–0.06% to 0.01–0.02%, but the difference in total organic carbon (TOC) was not significant. High-throughput testing revealed that the bacterial population of the restored area was dominated by A4b (6.33–9.18%), MND1 (4.94–7.39%), and Vicinamibacteraceae (7.04–7.39%). Regarding archaea, samples from the restored areas were dominated by Marine Group II (76.17–81.49%) and Candidatus Nitrososphaera (6.07–9.75%). PCoA showed that the different restoration levels were the main cause of the differences between the samples. Additionally, salinity was the dominant factor that induced this difference, but it was inhibited by the restoration and targeted enrichment of some of these functional genera. Desert restoration should therefore focus on conserving water rather than adding nutrients. Planting salt- and drought-tolerant vegetation will contribute to the initial restoration of the desert and the restoration of the microbiological content of the soil as it migrates over time, creating a cycle of elements. Restoration stimulates and enhances the microbial diversity of the soil via beneficial microorganisms. [ABSTRACT FROM AUTHOR]

Plant leaves harbor a rich diversity of bacteria and fungi that, through their interactions with host plants, assume an influential role in plant physiological and metabolic processes. The unique phyllosphere environment of different plant species may shape and select distinct phyllosphere microbial communities. While most academic research has focused on the phyllosphere microorganisms within the same plant variety, there is relatively limited research on the phyllosphere microbial communities between different varieties. Populus L. is a typical tree species in temperate monsoon climates, widely distributed in northern China, and it constitutes a crucial component of China's forestry resources. For the purpose of this study, we investigated the community structure and diversity of phyllosphere fungi and bacteria in different poplar varieties under identical growth conditions to elucidate the main factors contributing to differences in phyllosphere microbial communities among these varieties. Our findings revealed variations in nitrogen, phosphorus, starch, and soluble sugar contents among the three poplar species studied. Additionally, there were considerable disparities in both abundance and α diversity index of phyllosphere fungal and bacterial communities among these species. At the phylum level, Ascomycota and Basidiomycota have been identified as the dominant fungal communities; while Proteobacteria and Actinomycetes were dominant bacterial communities. The correlation analysis pointed out that chemical traits in the leaves, in particular the total phosphorus and the quantity of soluble sugar, had a significant correlation with the structure and diversity of the microbial community residing in the phyllosphere. Overall, our results demonstrate that even under identical site conditions, each poplar species harbors its own unique phyllosphere microbial community composition as well as distinct leaf characteristics—highlighting host plant diversity as a crucial factor driving differences in phyllosphere microbial composition. [ABSTRACT FROM AUTHOR]

Seawater intrusion significantly affects the microbial communities within coastal aquifers. Investigating the spatial distribution of groundwater microbial communities in coastal regions is crucial for understanding seawater intrusion. The primary objective of this study is to develop a novel microbial index-based method for detecting seawater intrusion. Groundwater microbial samples were collected and sent to the laboratory in the west coastal area of Longkou City, Shandong Province. By characterizing the microbial community within the whole interval of seawater intrusion into fresh groundwater and discussing the effects of salt-freshwater displacement intensities on groundwater microbial communities, including diversity, structure, and function, using indoor domestication experiments, we reveal the response of microorganisms to the seawater intrusion process under in situ environmental conditions. The results show that the microbial community diversity is highest in environments with a seawater mixing proportion (P(sm)) of 2.5% and lowest in those with a P(sm) of 75%. When considering species abundance and evolutionary processes, the microbial community structure is similar at higher P(sm) levels, while it is similar at lower P(sm) levels based on the presence or absence of species. Tenericutes, Flavobacteriia, Rhodobacterales, Flavobacteriales, Rhodobacteraceae, Flavobacteriaceae, Cohaesibacteraceae, and Cohaesibacter are significantly positively correlated with the P(sm). Strong salt-freshwater displacement enhanced the richness and evenness of the microbial community, whereas weak displacement showed the opposite trend. Strong displacement affects the functional profiles of the microbial community. This study effectively addressed the challenge of obtaining samples in coastal areas and also incorporated salt-freshwater displacement intensities, which can more comprehensively describe the microbial community characteristics within the groundwater of coastal aquifers. [ABSTRACT FROM AUTHOR]

Simple Summary: After piglet weaning, with the exposure to the inherent stress of this productive stage, the intestinal microbiota experiences an imbalance, resulting in a loss of beneficial microbial diversity and the development of potentially pathogenic or opportunistic bacteria. This leads to diarrhea and a decrease in the productivity and parameters of intestinal integrity and health. To address this issue, growth-promoting antibiotics have been used. However, in recent years, the search for nutraceutical compounds that can improve intestinal microbial balance and, thus, reduce antibiotic use has become important. In this regard, the effect of four nutraceutical compounds on piglet intestinal microbiota was evaluated for 30 days post-weaning. Following bioinformatic analyses, we report that essential oil from Lippia origanoides and short-chain fructo-oligosaccharides showed promising effects in reducing weaning-induced intestinal dysbiosis, with a decrease in potentially pathogenic taxa and an increase in bacteria associated with improved productivity and morphometric variables of the intestine, as well as the expression of intestinal barrier proteins. These findings elucidate the mechanisms of microbiota modulation by these compounds, aiming to reduce the use of prophylactic antibiotics and promoting the development of new studies focused on exploring metabolic changes in intestinal microbial communities. Due to the challenge of weaning pigs and the need to reduce the use of antimicrobials in animal feed, there is a growing need to look for nutraceutical alternatives to reduce the adverse effects of the post-weaning period. We evaluate the effect of different feed nutraceutical additives on the microbial communities, gut health biomarkers, and productivity of pigs during the post-weaning period. The study involved 240 piglets weaned on the 21st day of age and randomized to six different diets: D1-BD commercial standard feed, D2-AGP: D1 + 150 ppm zinc bacitracin, D3-MD: D1 + 550 ppm maltodextrin, D4-FOS: D1 + 300 ppm fructo-oligosaccharides, D5-EO: D1 + 70 ppm Lippia origanoides essential oil, and D6-SH: D1 + 750 ppm sodium humate. On day 30 post-weaning, zootechnical parameters were evaluated, and jejunal samples were taken to obtain morphometric variables, expression of barrier and enzymatic proteins, and analysis of microbial communities. Animals fed D4-FOS and D5-EO had the lowest feed conversion ratio and higher expression of barrier and enzymatic proteins compared to D1-BD, D2-AGP, and D3-MD. The use of the additives modified the gut microbial communities of the piglets. In conclusion, fructo-oligosaccharides and Lippia origanoides essential oil were the best alternatives to zinc bacitracin as antibiotic growth promoters. [ABSTRACT FROM AUTHOR]

Probiotics and prebiotics have gained attention for their potential health benefits. However, their efficacy hinges on probiotic survival through the harsh gastrointestinal environment. Microencapsulation techniques provide a solution, with resistant starch (RS)-based techniques showing promise in maintaining probiotic viability. Specifically, RS-encapsulated probiotics significantly improved probiotic survival in gastric acid, bile salts, and simulated intestinal conditions. This study investigated the effects of a resistant-starch-encapsulated probiotic cocktail (RS-Pro) in the context of 5-fluorouracil (5-FU) chemotherapy, which frequently induces microbiota dysbiosis and intestinal mucositis. Female BALB/c mice were divided into three groups: a 5-FU group, a 5-FU+Pro group receiving free probiotics, and a 5-FU+RS-Pro group receiving RS-encapsulated probiotics. After 28 days of treatment, analyses were conducted on fecal microbiota, intestinal histology, peripheral blood cell counts, and body and organ weights. It was revealed by 16S rRNA MiSeq sequencing that 5-FU treatment disrupted gut microbiota composition, reduced microbial diversity, and caused dysbiosis. RS-Pro treatment restored microbial diversity and increased the population of beneficial bacteria, such as Muribaculaceae, which play roles in carbohydrate and polyphenol metabolism. Furthermore, 5-FU administration induced moderate intestinal mucositis, characterized by reduced cellularity and shortened villi. However, RS-Pro treatment attenuated 5-FU-induced intestinal damage, preserving villus length. Mild leukopenia observed in the 5-FU-treated mice was partially alleviated in 5-FU+Pro and 5-FU+RS-Pro groups. These findings suggest that RS-Pro may serve as an adjunct to chemotherapy, potentially reducing adverse effects and improving therapeutic outcomes in future clinical applications. [ABSTRACT FROM AUTHOR]

We have investigated the changes in the microbial communities on the surface of trout eggs and the skin of adult trout in relation to the presence of Saprolegnia parasitica. This pathogen causes saprolegniosis, a disease responsible for significant losses in salmonid farms and hatcheries. It is known from other disease systems that the host-associated microbiome plays a crucial role in the defence against pathogens, but if the pathogen predominates, this can lead to dysbiosis. However, analyses of the effects of S. parasitica on the diversity, composition, and function of microbial communities on fish skin and eggs are scarce. Thus, we have collected skin swabs from injured and healthy trout (N = 12), which differed in S. parasitica load, from three different fish farms in Croatia (Kostanjevac, Radovan, and Solin), while trout egg samples (N = 12) were infected with S. parasitica in the laboratory. Illumina sequencing of the V4 region of the 16S rRNA marker gene showed that infection with S. parasitica reduced the microbial diversity on the surface of the eggs, as evidenced by decreased Pielou's evenness and Shannon's indices. We further determined whether the bacterial genera with a relative abundance of >5.0% in the egg/skin samples were present at significantly different abundances in relation to the presence of S. parasitica. The results have shown that some genera, such as Pseudomonas and Flavobacterium, decreased significantly in the presence of the pathogen on the egg surface. On the other hand, some bacterial taxa, such as Acinetobacter and Janthinobacterium, as well as Aeromonas, were more abundant on the diseased eggs and the injured trout skin, respectively. Finally, beta diversity analyses (weighted UniFrac, unweighted UniFrac, Bray–Curtis) have shown that the sampling location (i.e., fish farm), along with S. parasitica infection status, also has a significant influence on the microbial communities' composition on the trout skin and eggs, demonstrating the strong influence of the environment on the shaping of the host surface microbiome. Overall, we have shown that the presence of S. parasitica was associated with changes in the diversity and structure of the trout skin/egg microbiome. The results obtained could support the development of new strategies for the management of saprolegniosis in aquaculture. [ABSTRACT FROM AUTHOR]

The gut microbiota plays an important role in host nutrient absorption, immune function, and behavioral patterns. Much research on the gut microbiota of wildlife has focused on feces samples, so the microbial composition along the gastrointestinal tract of wildlife is not well reported. To address this gap, we performed high-throughput sequencing of 16s rRNA genes and ITs rRNA genes in the gastrointestinal contents of a wild adult male Chinese muntjac (Muntiacus reevesi) to comparatively analyze the microbial diversity of different gastrointestinal regions. The results showed that the dominant bacterial phyla were Firmicutes (66.19%) and Bacteroidetes (22.7%), while the dominant fungal phyla were Ascomycetes (72.81%). The highest bacterial diversity was found in the stomach, and the highest fungal diversity was found in the cecum. The microbial communities of the large intestine and small intestine were of similar structures, which were distinct from that of the stomach. These results would facilitate the continued exploration of the microbial composition and functional diversity of the gastrointestinal tract of wild Chinese muntjacs and provide a scientific basis for microbial resource conservation of more wildlife. [ABSTRACT FROM AUTHOR]

This study aimed to elucidate responses of the bacterial structure and diversity of the rhizosphere in flowering broomcorn millet after rehydration following drought stress. In this study, the broomcorn millet varieties 'Hequ red millet' (A1) and 'Yanshu No.10′ (A2), known for their different drought tolerance levels, were selected as experimental materials. The plants were subjected to rehydration after drought stress at the flowering stage, while normal watering (A1CK and A2CK) served as the control. Soil samples were collected at 10 days (A11, A21, A1CK1, and A2CK1) and 20 days (A12, A22, A1CK2, and A2CK2) after rehydration. High-throughput sequencing technology was employed to investigate the variations in bacterial community structure, diversity, and metabolic functions in the rhizosphere of the broomcorn millet at different time points following rehydration. The findings indicated that the operational taxonomic units (OTUs) of bacteria in the rhizosphere of broomcorn millet were notably influenced by the duration of treatment, with a significant decrease in OTUs observed after 20 days of rehydration. However, bacterial Alpha diversity was not significantly impacted by rehydration following drought stress. The bacterial community in the rhizosphere of broomcorn millet was mainly composed of Actinobacteria and Proteobacteria. After rewatering for 10 to 20 days after drought stress, the abundance of Sphingomonas and Aeromicrobium in the rhizosphere soil of the two varieties of broomcorn millet decreased gradually. Compared with Yanshu No.10, the abundance of Pseudarthrobacter in the rhizosphere of Hequ red millet gradually increased. A Beta diversity analysis revealed variations in the dissimilarities of the bacterial community which corresponded to different rehydration durations. The relative abundance of bacterial metabolic functions in the rhizosphere of broomcorn millet was lower after 20 days of rehydration, compared to measurements after 10 days of rehydration. This observation might be attributed to the exchange of materials between broomcorn millet and microorganisms during the initial rehydration stage to repair the effects of drought, as well as to the enrichment of numerous microorganisms to sustain the stability of the community structure. This study helps to comprehend the alterations to the bacterial structure and diversity in the rhizosphere of broomcorn millet following drought stress and rehydration. It sheds light on the growth status of broomcorn millet and its rhizosphere microorganisms under real environmental influences, thereby enhancing research on the drought tolerance mechanisms of broomcorn millet. [ABSTRACT FROM AUTHOR]

Apical periodontitis is an inflammatory disease triggered by oral pathogens invading necrotic root canals. The aim of this study was to evaluate the coronal and root canal bacterial community profiles in primary endodontic infections with different periapical (PAI) indices in comparison to oral mucosa controls. A total of 31 patients with primary apical periodontitis, 14 with PAI-1 and 17 with PAI-3 were recruited. Microbial specimens from mucosa (control samples) and endodontic necrotic tissues were collected in each patient. Microbiota composition was studied through 16S ribosomal RNA gene amplicon sequencing analysis. Overall, 2953 taxa from 168 different genera of 451 various microbial species were retrieved in the controls and PAI-1 and PAI-3 groups. Firmicutes is the predominant phylum in the oral controls (34.5%) and PAI-1 (44.4%) groups, while Bacteroidetes is predominant in PAI-3 (38.6%). The Proteobacteria (21.5%) and Fusobacteria (12.5%) relative abundance is higher in oral controls while that of Synergistetes is higher in the PAI-1 (3.5%) and PAI-3 (2.5%) groups, being almost absent in controls (less than 0.1%). Most of the increased bacterial species found in the PAI groups were strict anaerobes. A diminished microbial diversity was found in apical periodontitis with higher PAI. These samples were also characterized by an increase in bacteria belonging to phyla and genera with an increased anaerobic character. [ABSTRACT FROM AUTHOR]

The increasing use of chemicals requires a better understanding of their presence and dynamics in the environment, as well as their impact on ecosystems. The aim of this study was to validate the first steps of an innovative multi-omics approach based on metabolomics and 16S metabarcoding data for analyses of the fate and impact of contaminants in Mediterranean lagoons. Semi-targeted analytical procedures for water and sediment matrices were implemented to assess chemical contamination of the lagoon: forty-six compounds were detected, 28 of which could be quantified in water (between 0.09 and 47.4 ng/L) and sediment (between 0.008 and 26.3 ng/g) samples using the UHPLC-MS/MS instrument. In addition, a non-targeted approach (UHPLC-HRMS) using four different sample preparation protocols based on solid/liquid extractions or an automated pressurized fluid extraction system (EDGE®) was carried out to determine the protocol with the best metabolome coverage, efficiency and reproducibility. Solid/liquid extraction using the solvent mixture acetonitrile/methanol (50/50) was evaluated as the best protocol. Microbial diversity in lagoon sediment was also measured after DNA extraction using five commercial extraction kits. Our study showed that the DNeasy PowerSoil Pro Qiagen kit (Promega, USA) was the most suitable for assessing microbial diversity in fresh sediment. [ABSTRACT FROM AUTHOR]

TGase-7S gels prepared after different HIU pretreatment times were used to intervene in healthy mice to analyze their effects on growth characteristics and intestinal morphology, and 16S rRNA high-throughput sequencing was applied to fecal samples to investigate the effects of the gel on the structure and diversity of intestinal flora in mice. The results showed that the intestinal tissues of mice in different treatment groups showed better integrity, and the intake of gel increased the length of small intestinal villi in mice, among which the 30-gel group had the highest value of villi length (599.27 ± 44.28) μm (p < 0.05) and showed the neatest and tightest arrangement, indicating that the intake of gel did not have adverse effects on the intestinal tract. The effect of gel ingestion on the diversity of the intestinal microbial community structure was more significant, positively promoting the growth of beneficial bacteria such as Desferriobacterium, Synechococcus, and Bifidobacterium. In addition, the ingestion of the gel improved the intestinal health of mice by altering the physiological functions of the intestinal flora and modulating their participation in various metabolic pathways. The above findings provide some theoretical value for the safety of 7S gel in food applications. [ABSTRACT FROM AUTHOR]

Commercially produced cyanobacteria preparations sold under the name spirulina are widely consumed, due to their traditional use as a nutrient-rich foodstuff and subsequent marketing as a superfood. Despite their popularity, the microbial composition of ponds used to cultivate these bacteria is understudied. A total of 19 pond samples were obtained from small-scale spirulina farms and subjected to metagenome and/or virome sequencing, and the results were analysed. A remarkable level of prokaryotic and viral diversity was found to be present in the ponds, with Limnospira sp. and Arthrospira sp. sometimes being notably scarce. A detailed breakdown of prokaryotic and viral components of 15 samples is presented. Twenty putative Limnospira sp.-infecting bacteriophage contigs were identified, though no correlation between the performance of these cultures and the presence of phages was found. The high diversity of these samples prevented the identification of clear trends in sample performance over time, between ponds or when comparing successful and failed fermentations. [ABSTRACT FROM AUTHOR]

Simple Summary: Flies inhabit mushrooms or consume them incidentally throughout their lifecycle. In wild conditions, these flies are part of the recycling process and are not considered pests. However, in commercial mushroom houses, these flies can become problematic, as compost pests, through physical damage of mushroom production through consumption, or as vectors of pathogens or nematodes. Here, we describe the bacterial associates of two fly pest species of Pennsylvania mushroom houses. Mushroom cultivation vastly improves the yield of mushrooms under optimized, controlled conditions, but may be susceptible to opportunistic colonization by pest species that can establish themselves, as well as the pathogens and pests they may transmit. Here, we describe our investigation into the bacterial communities of adult Lycoriella ingenua (Diptera: Sciaridae) and Megaselia halterata (Diptera: Phoridae) collected from button mushroom (Agaricus bisporus) production houses in Pennsylvania. We collected adult flies and sequenced the hypervariable v4 region of the bacterial 16S rRNA using the Illumina MiSeq. The most abundant bacterial genus detected in both species was Wolbachia, but phylogenetic analysis revealed that the infections are from different clades. Future studies include the characterization of Wolbachia infections on fly behavior and biology, comparison of microbial diversity of fly species colonizing wild mushrooms, and other microbiota that may contribute to the success of certain pest fly species. [ABSTRACT FROM AUTHOR]

Aquifers are rich in microbial diversity. However, there is a lack of information about sessile communities in these environments because of the difficulty in sampling fresh in situ rock surfaces. Thus, this study's objective was to better understand the sessile community in a fractured aquifer. Additionally, the impact of the rock mineral composition on microbial community composition during colonization was explored. Using a system of bioreactors, we recreated the environmental conditions of a 1.5 m deep aquifer in Covey Hill (QC, Canada) using groundwater samples collected from the site. We carried out 16S/18S rRNA amplicon sequencing of the water and sessile communities after 24 days of incubation. Our data showed that many microbial taxa overlapped between the sessile and planktonic communities, indicating colonization of the solid surfaces. Quartz and feldspar had a significant impact on bacterial community structure. Sessile communities were dominated by Gaillonella, Alkanindiges, unclassified Acetobacteraceae, Apoikiales, Glissomonadida, and Synurales. We could not detect any Archaea in the sessile community. The sessile communities contained bacterial genera involved in iron cycling and adapted to acidic and low-carbon-concentration environments. Eukaryotic predators dominated the sessile community. [ABSTRACT FROM AUTHOR]

To determine the influence of pig type (Landrace, Wujin, or Tibetan fragrant) on the quality of Xuanwei ham, we measured the ham pH, color, fat content, and moisture content; used an E-nose (a device intended to detect odors or flavors); and analyzed flavoring substances using headspace solid-phase microextraction–gas chromatography, free amino acids using high-performance liquid chromatography, and microbial diversity using high-throughput sequencing. The ham types differed from each other in these attributes. The moisture and fat contents of Landrace pig ham were significantly lower than those of the other pig types, the brightness values of the Tibetan fragrant pig ham were significantly lower than those of the other pig types, and the redness values of the Landrace and Wujin pig hams were significantly higher than those of the Tibetan fragrant pig ham. The essential amino acid contents, e-wind odor response values, and volatile flavor substances of Wujin pig hams were significantly higher than those of the Tibetan fragrant pig ham, and the relative aldehyde contents of Wujin pig ham were significantly higher than those of the other pig types. The dominant microbial phyla in each ham type were assessed based on the species commonness, composition, and diversity and included taxa such as Actinobacteria and Ascomycetes and thick-walled bacteria such as Orphanomyces, Grass Spirochaetes, and Pseudoalteromonas. The microbial diversity and richness were the greatest in the Wujin pig ham. Of the three pigs, we conclude that the Wujin pig produces the best Xuanwei ham. [ABSTRACT FROM AUTHOR]

Despite the current appreciation of pulque as a probiotic fermented beverage, pulque has been also regarded as a poor-quality product, particularly due to the lack of sanitary control during its elaboration. To address this problem, a semi-continuous fermentation system was established, emulating the artisanal production process. Microfiltration-sterilized aguamiel was employed as the substrate, whereas a good-quality pulque was used as the fermentation inoculum. During the fermentation, the physicochemical, microbiological (lactic acid and Leuconostoc-type bacteria and yeasts) and sensory characteristics of the must were monitored. The isolated microorganisms were identified by molecular biology and MALDI-MS techniques. The sterilization of aguamiel by microfiltration did not negatively affect its physicochemical attributes. After 6–8 days of operation of the semi-continuous bioreactor, the fermentation reached a quasi-stationary state considering most of the parameters monitored during the experiment. The final fermentation product presented similar physicochemical, microbial and sensory properties to those of the pulque inoculum. The genera identified were Leuconostoc, Lentilactobacillus, Lactobacillus, Liquorilactobacillus, Fructilactobacillus and Saccharomyces. The strains Lentilactobacillus diolivorans and Liquorilactobacillus capillatus and uvarum have not been previously isolated from pulque. In conclusion, the fermentation system developed in this work was effective to standardize the quality of pulque while preserving the positive attributes of the artisanal process, thus harnessing the probiotic properties of pulque. [ABSTRACT FROM AUTHOR]

Chinese sour bamboo shoot is a traditionally, spontaneous fermented food that is particularly popular due to its complex and distinctive flavor. The volatile compounds of sour bamboo shoot originate mainly from the raw materials and the microbial fermentation. To reveal the correlation between microorganisms and flavor, third-generation sequencing and Gas Chromatography-Ion Mobility Spectrometry were applied to analyze the dynamics of microbial communities at the species level and volatile compounds during sour bamboo shoot fermentation. The abundance of Lactobacillus acetotolerans and Lactobacillus fermentum increased during the fermentation, while Lactobacillus amyloliquefaciens decreased at first but then began to rise. At the end of fermentation, Lactobacillus amyloliquefaciens and Lactobacillus acetotolerans became the predominant species. A total of sixty-seven volatile compounds, which included twenty-three esters, nineteen alcohols, eight ketones, six aldehydes, six aromatic hydrocarbons, four acids and one ether, were identified. These compounds constituted the primary flavor of sour bamboo, which created a complex flavor of sour bamboo shoot. Among them, the contents of acetic acid, propionic acid, and isoamyl alcohol gradually increased during the fermentation process, and they became the main volatile compounds. Furthermore, the correlation between microorganisms and volatile compounds was investigated through two-way Orthogonal Partial Least Squares (O2PLS), which revealed a positive correlation between Lactobacillus amylolyticus and ethyl propanoate. Additionally, the abundance of Lactobacillus acetotolerans and Lactobacillus fermentum was found to be positively correlated with 2-heptenal. These findings provide a theoretical basis for understanding the formation mechanism of sour bamboo shoot flavor and the standardized production of high-quality sour bamboo shoots. [ABSTRACT FROM AUTHOR]

Amazake is a traditional, sweet, non-alcoholic Japanese beverage typically produced through koji fermentation by the fungus Aspergillus oryzae. However, alternative microorganisms such as Bacillus amyloliquefaciens offer potential advantages and novel possibilities for producing similar fermented beverages. This study aimed to replicate the ancestral beverage of amazake by replacing A. oryzae (W-20) with B. amyloliquefaciens (NCIMB 12077) and comparing their fermentation processes and resulting products. Our results show that the production of amazake with B. amyloliquefaciens (ABA) is not only possible but also results in a beverage that is otherwise distinct from traditional amazake (AAO). Saccharification was achievable in ABA at higher temperatures than in AAO, albeit with lower reducing sugar and enzymatic activity values. Amino acids and organic acids were more abundant in AAO, with cysteine being uniquely present in AAO and shikimic acid only being present in ABA. The volatile aroma compound profiles differed between the two beverages, with AAO exhibiting a greater abundance of aldehydes, and ABA a greater abundance of ketones and alcohols. Interestingly, despite these compositional differences, the two beverages showed similar consumer panel acceptance rates. An analysis of their microbial communities revealed pronounced differences between the amazakes, as well as temporal changes in ABA but not in AAO. This study provides promising insights into harnessing the potential of B. amyloliquefaciens as the primary microorganism in the fermentation process of amazake-like beverages, marking an important advancement in the field of fermented low-alcohol beverage production, with possible applications in other fermented foods. [ABSTRACT FROM AUTHOR]

The sea bottom acts as a key natural archive where the memory of long-term timescale environmental changes is recorded. This study discusses some ecological and chemical features of fjord sediments that were explored during the AREX cruise carried out in the Svalbard archipelago in the summer of 2021. The activity rates of the enzymes leucine aminopeptidase (LAP), beta-glucosidase (GLU), and alkaline phosphatase (AP) and community-level physiological profiles (CLPPs) were studied with the aim of determining the functional diversity of the benthic microbial community, while bacterial isolates were screened for their susceptibility to antibiotics in order to explore the role of these extreme environments as potential reservoirs of antibiotic resistance. Enzyme activity rates were obtained using fluorogenic substrates, and CLPPs were obtained using Biolog Ecoplates; antibiotic susceptibility assays were performed through the standard disk diffusion method. Spatial trends observed in the functional profiles of the microbial community suggested variability in the microbial community's composition, presumably related to the patchy distribution of organic substrates. Complex carbon sources, carbohydrates, and amino acids were the organic polymers preferentially metabolized by the microbial community. Multi-resistance to enrofloxacin and tetracycline was detected in all of the examined samples, stressing the role of sediments as a potential reservoir of chemical wastes ascribable to antibiotic residuals. This study provides new insights on the health status of fjord sediments of West Spitsbergen, applying a dual ecological and biochemical approach. Microbial communities in the fjord sediments showed globally a good functional diversity, suggesting their versatility to rapidly react to changing conditions. The lack of significant diversification among the three studied areas suggests that microbial variables alone cannot be suitable descriptors of sediment health, and that additional measures (i.e., physical–chemical characteristics) should be taken to better define environmental status. [ABSTRACT FROM AUTHOR]

In recent years, the invasion of Phyllostachys edulis has intensified. This study selected Phyllostachys edulis, Phyllostachys edulis–Quercus acutissima mixed and Quercus acutissima forest areas and analyzed the changes in soil bulk density, porosity, water-holding capacity, pH, soil organic carbon (SOC), soil readily oxidized organic carbon (ROC), soluble organic carbon (DOC) and microbial biomass carbon (SMBC). Then, we obtained the Chao index, Shannon index and Simpson index and analyzed the relationship between microbial α diversity, β diversity and community composition, abundance and structure and between microbial community changes and environmental factors. The results showed that soil with the invasion of Phyllostachys edulis, soil pH, water content, capillary water capacity and total porosity of surface soil increased significantly by 4.35%, 18.71%, 16.37% and 14.56%, respectively, compared with the Quercus acutissima forest, while soil bulk density, organic carbon, microbial biomass carbon and soluble organic carbon decreased significantly by 7.27%, 18.43%, 61.12% and 61.90%. Soil readily oxidized organic carbon decreased at first and then increased. The soil community richness and diversity of the Phyllostachys edulis forest were significantly greater than those of the other two stands. Soil pH and organic carbon content were the main factors affecting the changes in the soil microbial community. Therefore, the invasion of Phyllostachys edulis improved soil water retention, while soil pH had the greatest effect on the microbial community, followed by soil bulk density and organic carbon, and water content had the smallest effect. [ABSTRACT FROM AUTHOR]

Pinus thunbergii and Euonymus japonicus are two species commonly found in arid and semi-arid areas; however, their responses in terms of physiological traits and soil properties under drought and cadmium (Cd) stress are not clear. In this study, we carried out single and combined stress treatments consisting of drought and Cd on saplings of P. thunbergii and E. japonicus and investigated the responses in terms of the physiological traits and soil properties of both species. For both species, under single Cd stress, Cd was observed in both the xylem and phloem, while the root Cd2+ flow rate fluctuated at different levels of Cd stress. Under both single and combined stress, as the stress level increased, the abscisic acid (ABA) content of the leaves and roots increased significantly, while the indole-3-acetic acid (IAA) content of the leaves and roots decreased significantly. Moreover, the non-structural carbohydrate (NSC) content of the leaves, stems, and roots, as well as the leaf chlorophyll content, decreased significantly. Under drought stress, the xylem water potential and hydraulic conductivity significantly decreased, which was exacerbated by Cd stress; this led to a more significant decrease in water potential and hydraulic conductivity under the combined stresses. Meanwhile, no significant changes in the conduit lumen diameter and double-wall thickness were observed, except for the double cell wall thickness of the P. thunbergii tracheid, which increased. In addition, both the single stresses and the combined stress of drought and Cd induced significant changes in the soil properties of the two species, i.e., the ammonium nitrogen, nitrate nitrogen, and effective phosphorus of the soil increased significantly, and the increase in content was more significant under combined stress. The diversity of the soil microbial community of P. thunbergii saplings significantly increased, while no change was found in its microbial community abundance under the single stresses and combined stress; however, the diversity and abundance of the soil microbial community in E. japonicus saplings showed the opposite pattern, which indicates that the effect of Cd on soil microorganisms is more significant than the effect of drought. The activity of sucrase and catalase in P. thunbergii soil fluctuated under the single stress and combined stress when compared, and the activity of sucrase in the soil of the E. japonicus species decreased. However, its catalase activity increased significantly under the single drought and Cd stress and combined stress when compared. We found that the combined stresses exacerbated the effects of the single stress in both species. Our study provides more detailed information on the responses in terms of the physiological traits and soil properties of the two species under single and combined stress consisting of drought and Cd. [ABSTRACT FROM AUTHOR]

Prebiotics, a subset of biostimulants, have garnered attention for their potential to enhance soil conditions and promote plant growth, offering a promising alternative to conventional agricultural inputs. This study explores how two commercial prebiotics, K1® and NUTRIGEO L® (SPK and SPN), impact soil functions compared to a control (SP). The experiment involved agricultural soil amended with organic wheat straws and cultivated with Zea mays L. Previous research demonstrated substantial effects of these prebiotics on plant biomass, soil parameters, and microbial community ten weeks after application. The present study delves deeper, focusing on soil microbial abundance, enzyme activities, and metabolic diversity. Analysis revealed that SPN notably increased the fungi-to-bacteria ratio, and both prebiotics elevated the activity of several key enzymes. SPN enhanced α-glucosidase and β-galactosidase activities, while SPK increased arylsulfatase, phosphatase, alkaline phosphatase, and urease activities. Enzymatic indexes confirmed the positive impact on soil functional diversity and fertility. Additionally, prebiotic treatments showed distinct metabolic profiles, with SPK degrading eleven carbon sources more rapidly across five groups and SPN accelerating the decomposition rate of four carbon sources from three groups. These findings highlight the ability of prebiotics to shape microbial communities and enhance soil fertility by modulating their functional activity and diversity. [ABSTRACT FROM AUTHOR]

Microbial communities are known to play an important role in maintaining ecological balance and can be used as an indicator for assessing environmental pollution. Numerous studies have revealed that air pollution can alter the structure of microbial communities, which may increase health risks. Nevertheless, the relationships between microbial communities and particulate matter (PM) caused by air pollution in terms of health risk assessment are not well understood. This study aimed to validate the influences of PM chemical compositions on microbial communities and assess the associated health risks. Our results, based on similarity analysis, revealed that the stability structure of the microbial communities had a similarity greater than 73%. In addition, the altered richness and diversity of microbial communities were significantly associated with PM chemical compositions. Volatile organic compounds (VOCs) and polycyclic aromatic hydrocarbons (PAHs) exerted a positive influence on microbial communities in different environmental variables. Additionally, a stronger linear correlation was observed between hydroxyl radicals (·OH) and the richness of microbial communities. All estimated health risks from PM chemical compositions, calculated under different environmental variables, significantly exceeded the acceptable level by a factor of more than 49. Cr and 1,2-Dibromoethane displayed dual adverse effects of non-carcinogenic and carcinogenic risks. Overall, the study provides insights into the fundamental mechanisms of the variability in microbial communities driven by PM, which may support the crucial role of PM chemical compositions in the risk of microorganisms in the atmospheric environment. [ABSTRACT FROM AUTHOR]

Processes driving nutrient retention in stormwater green infrastructure (SGI) are not well quantified in water-limited biomes. We examined the role of plant diversity and physiochemistry as drivers of microbial community physiology and soil N dynamics post precipitation pulses in a semi-arid region experiencing drought. We conducted our study in bioswales receiving experimental water additions and a montane meadow intercepting natural rainfall. Pulses of water generally elevated soil moisture and pH, stimulated ecoenzyme activity (EEA), and increased the concentration of organic matter, proteins, and N pools in both bioswale and meadow soils. Microbial community growth was static, and N assimilation into biomass was limited across pulse events. Unvegetated plots had greater soil moisture than vegetated plots at the bioswale site, yet we detected no clear effect of plant diversity on microbial C:N ratios, EEAs, organic matter content, and N pools. Differences in soil N concentrations in bioswales and the meadow were most directly correlated to changes in organic matter content mediated by ecoenzyme expression and the balance of C, N, and P resources available to microbial communities. Our results add to growing evidence that SGI ecological function is largely comparable to neighboring natural vegetated systems, particularly when soil media and water availability are similar. [ABSTRACT FROM AUTHOR]

For deep underground coal mining ecosystems, research on microbial communities and geochemical characteristics of sediments in different functional zones is lacking, resulting in the knowledge of zone-level mine water pollution prevention and control being narrow. In this study, we surveyed the geochemical distinctions and microbial communities of five typical functional zones in a representative North China coalfield, Xinjulong coal mine. The data indicated that the geochemical compounds and microbial communities of sediments showed distinguishing features in each zone. The microbial community richness and diversity were ranked as follows: surface water > rock roadways > sumps > coal roadways ≥ goafs. Canonical Correlation Analysis (CCA), Spearman correlation and co-occurrence network analysis demonstrated that microbial communities were sensitive and closely related to hydrochemical processes. The microbial community distribution in the underground mine was closely related not only to nutrient elements (i.e., C, S, P and N), but also to redox-sensitive substances (i.e., Fe and As). When it comes to mine water pollution prevention and control, the central zones are goafs. With the increase in goaf closure time, total nitrogen (TN), total organic carbon (TOC) and total sulfur (TS) decreased, but As, Fe and total phosphorus (TP) gradually increased, and the characteristic pollutant SO42− concentration in water samples decreased. Additionally, the sulfate-reducing bacteria (SRB) had relatively higher proportions in goafs, suggesting goafs were able to purify themselves. In practical engineering, in situ nitrogen injection technology used to expel oxygen and create an anaerobic environment can be implemented to enhance SRB reducing sulfate in goafs. Meanwhile, because coal mine pollution discharge generally only discharges mine water and leaves sediment underground, the pollutants can be transferred to the sediment by strengthening the relevant reactions including the heavy metal solidification and stabilization function of bacteria. [ABSTRACT FROM AUTHOR]

Lactarius hatsudake Tanaka is a mycorrhizal edible mushroom with an appealing taste and rich nutrition. It is also a significant food and has medicinal value. In this study, the plantation of L. hatsudake during the harvest period was taken as the research object, and this article explores which bacteria in the soil contribute to the production and growth of L. hatsudake. The soil of the control (CK) and the soil of the mushroom-producing area [including the soil of the base of the mushroom (JT) and the mycorrhizal root soil (JG)] was collected in the plantation. The three sites' bacterial community structure and soil diversity were analyzed using high-throughput sequencing technology, and a molecular ecological network was built. Soil bacteria in the L. hatsudake plantation had 28 tribes, 74 classes, 161 orders, 264 families, 498 genera, and 546 species. The dominant phyla were Proteobacteria and Acidobacteria, and the dominant genera were Burkholderia_Caballeronia_Paraburkholderia, Acidothermus, Bradyrhizobium, Candidatus_Xiphinematobacter, and Granulicella. The α-diversity of soil bacteria in JT was significantly lower than that in JG and CK, and the β-diversity in JT samples was significantly different from that in JG and CK samples. The size and complexity of the constructed network were smaller in JT samples than in JG and CK samples, and the stability was higher in JT samples than in JG and CK samples. The positive correlation between species in JT samples was dominant. The potential mycorrhizal helper bacteria (MHB) species of L. hatsudake was determined using correlation and differential group analysis. The results support future research on mycorrhizal synthesis, plantation management, and the function of microorganisms in the soil rhizosphere of L. hatsudake. [ABSTRACT FROM AUTHOR]

Magnaporthe oryzae is one of the most important fungal pathogens of rice. Chitin and avirulent strains can induce two layers of immunity response, pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI), in rice with cognate R genes. However, little is known about the assembly of the rice microbiome induced by PTI and ETI in rice. In this study, we investigate the impact of continuous treatment of the avirulent M. oryzae strain with AvrPi9 and chitin on the bacterial endophytic community of rice varieties harboring resistant gene Pi9 and their antagonistic activity against rice blast fungus. Analysis of the 16S rRNA showed a significant increase in the diversity and microbial co-occurrence network complexity and the number of beneficial taxa—Bacillus, Pseudomonas, Microbacterium, and Stenotrophomonas spp.—following the chitin and avirulent strain treatments. The antifungal assay with bacterial endophytes recovered from the leaves showed few bacteria with antagonistic potential in rice treated with avirulent strains, suggesting that the sequential treatment of the avirulent strain decreased the antagonistic bacteria against M. oryzae. Moreover, we identified Bacillus safensis Ch_66 and Bacillus altitudinis Nc_68 with overall antagonistic activities in vivo and in vitro. Our findings provide a novel insight into rice microbiome assembly in response to different innate immunity reactions. [ABSTRACT FROM AUTHOR]

Patients with colorectal cancer (CRC) have a high prevalence of iron deficiency anemia (IDA), and the gut microbiota is closely related to iron metabolism. We performed metagenomic and metabolomic analyses of stool samples from 558 eligible samples, including IDA CRC patients (IDA, n = 69), non-anemia CRC patients (Non-Anemia, n = 245), and healthy controls (CTRL, n = 244), to explore the dynamically altered gut microbes and their metabolites. Compared with the CTRL group, fecal bacteria in both the IDA group and the Non-Anemia group showed a decrease in alpha diversity and changes in microbial communities. Flavonifractor plautii (F. plautii) increases progressively from CTRL to Non-Anemia to IDA, accompanied by decreased trimethoxyflavanone and a downregulated KO gene, megDIII. In the Non-Anemia group, Parabacteroides showed a specifically elevated abundance positively correlated with enriched 1,25-dihydroxyvitamin D3. The intricate correlations among gut microbiota, metabolites, and KO genes were uncovered and highlighted, implicating an aberrant iron metabolism vulnerable to chronic inflammation during the deterioration of the anemic condition. Furthermore, the amount of F. plautii in feces achieved independent and effective prediction performance for the poor outcome of CRC. Perturbed host-microbe interplays represent a novel prospect for explaining the pathogenesis of CRC-associated IDA. The fecal microbial features also reflect the associations between IDA and elevated CRC recurrence risk. [ABSTRACT FROM AUTHOR]

Seawater intrusion has a significant impact on the irrigation quality of agricultural water, thereby posing a threat to plant growth and development. We hypothesized that the rhizosphere of tea plants harbors beneficial microorganisms, which may improve the tolerance of tea plants to seawater stress. This study utilized 16s and ITS techniques to analyze microbial community shifts in the tea plant rhizosphere and non-rhizosphere under seawater stress conditions. The findings suggest that seawater stress leads to a reduction in microbial diversity, although the rhizosphere microbial diversity in stressed soils showed a relatively higher level. Moreover, the rhizosphere of the tea plant under seawater stress exhibited an enrichment of plant growth-promoting rhizobacteria alongside a higher presence of pathogenic fungi. Network analysis revealed that seawater stress resulted in the construction of a more complex and stable rhizosphere microbial network compared to normal conditions. Predictions of bacterial potential functions highlighted a greater diversity of functional groups, enhancing resource utilization efficiency. In general, the rhizosphere microorganisms of tea plants are jointly selected by seawater and the host. The microorganisms closely related to the rhizosphere of tea plants are retained and, at the same time, attract beneficial microorganisms that may alleviate stress. These findings provide new insights into plant responses to saline stress and have significant implications for leveraging vegetation to enhance the resilience of coastal saline soils and contribute to economic progress. [ABSTRACT FROM AUTHOR]