Increased pathogenicity and pro-inflammatory capabilities of mucosal-associated invariant T cells involved in Oral Lichen Planus.

BACKGROUND: Mucosal-associated invariant T (MAIT) cells assume pivotal roles in numerous autoimmune inflammatory maladies. However, scant knowledge exists regarding their involvement in the pathological progression of oral lichen planus (OLP). The focus of our study was to explore whether MAIT cells were altered across distinct clinical types of OLP. METHODS: The frequency, phenotype, and partial functions of MAIT cells were performed by flow cytometry, using peripheral blood from 18 adults with non-erosive OLP and 22 adults with erosive OLP compared with 15 healthy adults. We also studied the changes in MAIT cells in 15 OLP patients receiving and 10 not receiving corticosteroids. Surface proteins including CD4, CD8, CD69, CD103, CD38, HLA-DR, Tim-3, Programmed Death Molecule-1 (PD-1), and related factors released by MAIT cells such as Granzyme B (GzB), interferon (IFN)-γ, tumour necrosis factor (TNF)-α, interleukin (IL)-17A, and IL-22 were detected. RESULTS: Within non-erosive OLP patients, MAIT cells manifested an activated phenotype, evident in an elevated frequency of CD69+ CD38+ MAIT cells (p < 0.01). Conversely, erosive OLP patients displayed an activation and depletion phenotype in MAIT cells, typified by elevated CD69 (p < 0.01), CD103 (p < 0.05), and PD-1 expression (p < 0.01). Additionally, MAIT cells exhibited heightened cytokine production, encompassing GzB, IFN-γ, and IL-17A in erosive OLP patients. Notably, the proportion of CD103+ MAIT cells (p < 0.05) and GzB secretion (p < 0.01) by MAIT cells diminished, while the proportion of CD8+ MAIT cells (p < 0.05) rose in OLP patients with corticosteroid therapy. CONCLUSIONS: MAIT cells exhibit increased pathogenicity and pro-inflammatory capabilities in OLP. Corticosteroid therapy influences the expression of certain phenotypes and functions of MAIT cells in the peripheral blood of OLP patients.

Circulating mucosal-associated invariant T cell alterations in adults with recent-onset and long-term oral lichen planus.

BACKGROUND: Mucosal-associated invariant T (MAIT) cells play key roles in many inflammatory diseases. However, their effects on the long-term course of oral lichen planus (OLP) and recent-onset OLP remain unclear. In this study, we aimed to investigate the function of MAIT cells in the different processes of OLP and to explore the immunological background of this disease. METHODS: The frequency, phenotype, cytokine secretion, and clinical relevance of MAIT cells were investigated. MAIT cells were collected from the peripheral blood of 14 adults with recent-onset OLP (7-120 days after disease onset) and 16 adults with long-term course OLP (>2 years after diagnosis) using flow cytometry and compared with 15 healthy blood donors. Statistical analyses were performed using the GraphPad Prism software. RESULTS: MAIT cells from adults with recent-onset OLP exhibited an activated phenotype, as indicated by an increased frequency of CD69+ (p < 0.05) and CD38+MAIT cells (p < 0.01) and elevated production of the proinflammatory cytokine IL-17 A (p < 0.01), compared with healthy adult donors. In adults with long-term OLP, MAIT cells exhibited an activated and exhausted phenotype, characterized by high expression of CD69 (p < 0.01) and PD-1 (p < 0.001) and increased production of granzyme B released (p < 0.01). Compared with recent-onset OLP patients, long-term OLP patients showed a decreased production of CD8+, and CD4-CD8- cells, but an increase in PD-1+ production (p < 0.05). CONCLUSIONS: Circulating MAIT cells exhibited activation in OLP patients across varying disease durations. Given that PD-1 expression is elevated in adults with long-term OLP, it is reasonable to infer that circulating MAIT cells in long-term OLP may exhibit a more exhausted state than those in recent-onset OLP.

[Microbiome of therapeutic muds used in Tatarstan]. / Mikrobiom lechebnykh gryazei, primenyaemykh v Tatarstane.

Therapeutic muds (peloids), which are widely used for body healing, improve metabolism and have antibacterial, anti-inflammatory and analgesic effects due to enrichment with necessary microelements and biological active substances. However, the microbiological component of these effects is not well studied. OBJECTIVE: To characterize the microbiome of therapeutic muds, used in the Tatarstan Republic, by identifying spectrum of cultivated microorganisms, using molecular analysis of bacterial communities, and by determining their biodiversity and functional potential based on revealed genetic determinants. MATERIAL AND METHODS: The study design of 5 peloids samples (local sapropels and peat deposits of swamp; 3 samples of Crimean sulfide muds) included three main techniques: isolation and taxonomic determination of cultivated microorganisms by time-of-flight mass-spectrometry; molecular analysis of peloids bacterial communities by 16S RNA high-throughput sequencing; identification of functional profiles of communities by their genetic determinant using Global Mapper tool on iVikodak platform. RESULTS: Experimental studies have confirmed the safety of examined peloids, where non-pathogenic cultivated bacteria belonging mainly to Bacillus and Rhodococcus genera were dominant. Metagenomic analysis showed that Firmicutes, Proteobacteria and Actinobacteria were predominant in all samples in different ratios. It has been established, that there is both the internal biodiversity of each sample and difference between them. The functional profile of microbial communities was determined based on the identification of bacterial genes. It has been revealed that all communities have an ability to synthesize antibiotics, as well as to decompose dangerous xenobiotics - polyaromatic hydrocarbons, cyclic compounds, and dioxins. CONCLUSION: Various microbial communities, which were identified in the therapeutic muds, contribute both to the clearance of toxicants in the peloids and to the antibacterial properties of the latter. The obtained priority results create a fundamental basis for the subsequent study of the role of peloids' microbiome of different origin in their healing action.

Phytogen Improves Performance during Spotty Liver Disease by Impeding Bacterial Metabolism and Pathogenicity.

A range of antibiotic alternative products is increasingly studied and manufactured in the current animal agriculture, particularly in the poultry industry. Phytogenic feed additives are known for their remarkable ability to suppress pathogens such as Clostridium spp., Escherichia coli, and Salmonella. Other than enhancing biosecurity, improvements in productivity and performance were also observed. However, clear mechanisms for these improvements were not established. In this study, 20,000 Lohman-Brown layers were provided with phytogenic supplement from 16 to 40 weeks of age, and performance parameters were assessed against the same number of unsupplemented control birds. The performance results showed that the birds with phytogenic supplementation presented consistently reduced mortality, increased rate of lay, and increased average egg weight. Functional analysis through shotgun sequencing of cecal metagenomes confirmed a substantial functional shift in the microbial community, showing that phytogen significantly reduced the range of microbial functions, including the production of essential vitamins, cofactors, energy, and amino acids. Functional data showed that phytogen supplementation induced a phenotypic shift in intestinal bacteria LPS phenotype toward the less pathogenic form. The study corroborates the use of phytogenic products in antibiotic-free poultry production systems. The productivity improvements in the number and weight of eggs produced during Spotty Liver Disease justify further optimizing phytogenic alternatives for use in high-risk open and free-range poultry systems. IMPORTANCE The present study establishes the beneficial effects of the continuous phytogenic supplementation reflected in reduced diarrhea and mortality and higher egg productivity under normal conditions and during a natural outbreak of Spotty Liver Disease. Our data points to the importance of phytogen-driven alteration of microbial pathogenicity and fitness-related functional capabilities revealed on the commercial layer farm. Phytogenic product showed an ability to improve the bird's welfare and sustainability in free-range poultry production systems.

Shifts in diversity and function of bacterial community during manufacture of rushan.

Rushan is a traditional dairy product consumed by the Bai people in the Yunnan Province of China, and its production still follows the traditional procedure of backslopping. However, how the microbial composition of raw materials and processing shape the microorganisms in rushan have not been systemically reported. In this study, high-throughput sequencing technique was applied to analyze the microbial compositions of raw milk, fresh rushan, curd whey, acid whey, and dry rushan at the phylum, family, genus, and Lactobacillus species levels. The results indicated that Lactobacillus, Lactococcus, and Streptococcus were dominant genera in rushan, whereas Lactobacillus kefiranofaciens and Lactobacillus helveticus were the 2 abundant species at the Lactobacillus species level. The network analysis indicated that raw milk mainly contributed to the microbial diversity of rushan, whereas acid whey made a great contribution to shaping the relative abundance of microbes in rushan and dramatically increased acid-producing genera, such as Lactobacillus and Acetobacter. The variation in microbial composition led to an increase in the relative abundance of pathways related to energy supply, acid production, fatty acid accumulation, cysteine, methionine, and lysine accumulation. The volatile profile of rushan was rich in esters and acids, and the high relative abundance of Lactobacillus might be associated with reduction of amino acid metabolism, degradation of unpleasant flavored xylene, and accumulation of decanoic, dodecanoic, and tetradecanoic acids in the products. The accumulation of medium long-chain fatty acids might result from the relative abundance of FabF, FabZ, and FabI, particularly from Lactobacillus amylolyticus and Lacticaseibacillus paracasei.

FUNCTIONAL CLASSIFICATION OF CHILDREN WITH CEREBRAL PALSY IN KRAPINA-ZAGORJE COUNTY.

The aim was to study functional abilities and to create functional classification of children with cerebral palsy (CP) in Krapina-Zagorje County, based on the classification of gross and fine motor skills and associated impairments. Classification was performed according to the SCPE (Surveillance of Cerebral Palsy in Europe) criteria. We used standardized and complementary functional classification systems for cerebral palsy to create a functional profile. Research included 44 children with CP in the age range of 4 to 18 years. The results showed that the majority of children had bilateral spastic CP (63.6%), followed by unilateral spastic (22.7%) while the representation of dyskinetic CP was 9.09% and ataxic CP 4.55%. Based on the classification of gross and fine motor skills, 43.2% of children had the ability to walk, 11% of children could walk with assistive mobility devices, while 45.4% of children had a low functional level. The study also analyzed the associated impairments where higher classification score of motor impairment correlated with the severity of impairment. The results showed that children with dyskinetic CP and severe motor impairment could have mild cognitive impairment. We systematically present the neuropsychological and functional profile according to the CP type.

Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment.

During the 1960s, small quantities of radioactive materials were codisposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in 3-meter-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess the impact of changing water levels upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically diverse microbial community played in this transition. In particular, aerobes dominated in the first day, followed by an increase of facultative anaerobes/denitrifiers at day 4. Toward the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.IMPORTANCE The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility. Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.

Changes in the Functional Potential of the Gut Microbiome Following Probiotic Supplementation during Helicobacter Pylori Treatment.

BACKGROUND: Probiotic supplementation is utilized to alleviate the side effects associated with antibiotic therapy for Helicobacter pylori infection. Several studies have described the effects of administration of probiotics on the gut microbiota during antibiotic therapy. However, most of these studies have focused on specific bacteria, thereby providing limited information on the functional roles of the altered microbiota. Therefore, we examined the impact of probiotic supplementation on the structure and functional dynamics of the gut microbiota during H. pylori eradication, using whole-metagenomic sequence analysis. METHODS: Subjects were divided into two groups: the antibiotics group, which received only antibiotics, and the probiotics group, which received antibiotics with probiotic supplementation. The structural and functional profiles of gut microbiota was analyzed using metagenomic DNA extracted from the feces during treatment by Illumina MiSeq system. RESULTS: The overall alterations in microbiota, as revealed by whole metagenome sequencing, were similar with results from our previous 16S rRNA gene-based analysis. The proportional shift in functional gene families was greater in the antibiotics group than in the probiotics group. In particular, the proportion of genes related to selenocompound metabolism was reduced in the probiotics group, whereas genes associated with the metabolism of nucleotide sugars were increased. CONCLUSION: The functional alterations of gut microbiota may link to the reduction in intestinal irritation and maintenance of bacterial diversity observed following probiotic supplementation with antibiotic therapy. The potential beneficial roles of altered gut microbiota following probiotic supplementation are expected a reduction in side effects such as intestinal irritation and antibiotics resistance.

Combined use of Mycobacterium tuberculosis-specific CD4 and CD8 T-cell responses is a powerful diagnostic tool of active tuberculosis.

Immune-based assays are promising tools to help to formulate diagnosis of active tuberculosis. A multiparameter flow cytometry assay assessing T-cell responses specific to Mycobacterium tuberculosis and the combination of both CD4 and CD8 T-cell responses accurately discriminated between active tuberculosis and latent infection.

Bacterial wilt affects the structure and assembly of microbial communities along the soil-root continuum.

BACKGROUND: Beneficial root-associated microbiomes play crucial roles in enhancing plant growth and suppressing pathogenic threats, and their application for defending against pathogens has garnered increasing attention. Nonetheless, the dynamics of microbiome assembly and defense mechanisms during pathogen invasion remain largely unknown. In this study, we aimed to investigate the diversity and assembly of microbial communities within four niches (bulk soils, rhizosphere, rhizoplane, and endosphere) under the influence of the bacterial plant pathogen Ralstonia solanacearum. RESULTS: Our results revealed that healthy tobacco plants exhibited more diverse community compositions and more robust co-occurrence networks in root-associated niches compared to diseased tobacco plants. Stochastic processes (dispersal limitation and drift), rather than determinism, dominated the assembly processes, with a higher impact of drift observed in diseased plants than in healthy ones. Furthermore, during the invasion of R. solanacearum, the abundance of Fusarium genera, a known potential pathogen of Fusarium wilt, significantly increased in diseased plants. Moreover, the response strategies of the microbiomes to pathogens in diseased and healthy plants diverged. Diseased microbiomes recruited beneficial microbial taxa, such as Streptomyces and Bacilli, to mount defenses against pathogens, with an increased presence of microbial taxa negatively correlated with the pathogen. Conversely, the potential defense strategies varied across niches in healthy plants, with significant enrichments of functional genes related to biofilm formation in the rhizoplane and antibiotic biosynthesis in the endosphere. CONCLUSION: Our study revealed the varied community composition and assembly mechanism of microbial communities between healthy and diseased tobacco plants along the soil-root continuum, providing new insights into niche-specific defense mechanisms against pathogen invasions. These findings may underscore the potential utilization of different functional prebiotics to enhance plants' ability to fend off pathogens.

Gut microbiome encoded purine and amino acid pathways present prospective biomarkers for predicting metformin therapy efficacy in newly diagnosed T2D patients.

Metformin is widely used for treating type 2 diabetes mellitus (T2D). However, the efficacy of metformin monotherapy is highly variable within the human population. Understanding the potential indirect or synergistic effects of metformin on gut microbiota composition and encoded functions could potentially offer new insights into predicting treatment efficacy and designing more personalized treatments in the future. We combined targeted metabolomics and metagenomic profiling of gut microbiomes in newly diagnosed T2D patients before and after metformin therapy to identify potential pre-treatment biomarkers and functional signatures for metformin efficacy and induced changes in metformin therapy responders. Our sequencing data were largely corroborated by our metabolic profiling and identified that pre-treatment enrichment of gut microbial functions encoding purine degradation and glutamate biosynthesis was associated with good therapy response. Furthermore, we identified changes in glutamine-associated amino acid (arginine, ornithine, putrescine) metabolism that characterize differences in metformin efficacy before and after the therapy. Moreover, metformin Responders' microbiota displayed a shifted balance between bacterial lipidA synthesis and degradation as well as alterations in glutamate-dependent metabolism of N-acetyl-galactosamine and its derivatives (e.g. CMP-pseudaminate) which suggest potential modulation of bacterial cell walls and human gut barrier, thus mediating changes in microbiome composition. Together, our data suggest that glutamine and associated amino acid metabolism as well as purine degradation products may potentially condition metformin activity via its multiple effects on microbiome functional composition and therefore serve as important biomarkers for predicting metformin efficacy.

Afforestation changed the fungal functional community of paddy fields and dry farmlands differently.

Afforestation currently makes a great contribution to carbon uptake in terrestrial ecosystems, while dramatically affects soil ecosystem functions too. Little is known, however, about the changes in soil fungal functional groups and their interactions following afforestation. Here, based on high-throughput sequencing and FUNGuild annotation, we investigated the functional characteristics of soil fungi as well as environmental factors in a watershed where paddy field and dry farmland were changed to eucalyptus plantation. The results showed that afforestation on paddy field resulted in greater changes in diversity, community structure and taxon interactions of fungal functional groups than afforestation on dry farmland. The most complex and distinctive community structure was found in eucalyptus plantation, as well as the greatest taxon interactions, and the lowest alpha-diversity of functional guilds of symbiotrophic fungi because of the dominant ectomycorrhizal fungi. Paddy field exhibited the highest proportion of saprotrophic fungi, but the lowest taxonomic diversity of saprotrophic and pathotrophic fungi. The taxonomic diversity of undefined saprotrophic fungi shaped the differences in community structure and network complexity between eucalyptus plantation and cropland. Limited cooperation within dominant fungi was the main reason for the establishment of a loose co-occurrence network in paddy field. From croplands to artificial forests, reduced soil pH boosted the taxonomic diversity of fungal functional groups. All of these findings suggested that afforestation may lead to an increase in the taxonomic diversity of soil fungal functional groups, which would further intensify the taxon interactions.

Identification and characterization of molecular entities differentially expressed in bacteria genome upon treatment with glyphosate shock.

Antimetabolites developed from enzymes in the shikimate pathway are appealing targets. There are, however, certain unidentified molecular entities that show bacterial sensitivity to glyphosate shock. This study aims to identify the expression pattern of such entities following treatment with glyphosate shock and to characterize them structurally and functionally. Understanding such entities' catalytic structure and modulatory role guides the design and development of novel antibiotics. This study's functional profiling of 16S rRNA sequencing data and transcriptome analysis of glyphosate-exposedE. coli revealed that two genes were upregulated and twenty-eight were downregulated after glyphosate shock. We discovered the differential expression of some processes based on functional gene analysis, such as global and overview maps (4.2195 on average), carbohydrate metabolism (0.6858 on average), amino acid metabolism (0.5032 on average), and co-factor and vitamin metabolism (0.5032 on average) (0.2876 on average). After examining the two data sets, we discovered that some unidentified proteins were strongly expressed after glyphosate treatment. After examining the two datasets, we discovered a protein with no unique features expressed when treated with glyphosate. The Ecs2020 model looks to be the most stable in structural modeling investigations, while the catalytic residues sought in drug development are anticipated. Furthermore, biological processes and cellular component enrichment analysis revealed that the differentially expressed genes were strongly related to the trehalose manufacturing process and represented the cell membrane's outer membrane component. To estimate the functional gene content of soil sample metagenomics based on 16S rRNA, predictive functional analysis was done with R using the Tax4Fun2 package. On the other hand, transcriptome analysis was carried out using the R tool GEO2R. The results could be a good starting point for making new antibiotic medicines.

Novel object recognition test as an alternative approach to assessing the pharmacological profile of sigma-1 receptor ligands.

BACKGROUND: Although the terms "agonist" and "antagonist" have been used to classify sigma-1 receptor (σ1R) ligands, an unambiguous definition of the functional activity is often hard. In order to determine the pharmacological profile of σ1R ligands, the most common method is to assess their potency to alleviate opioid analgesia. It has been well established that σ1R agonists reduce opioid analgesic activity, while σ1R antagonists have been demonstrated to enhance opioid analgesia in different pain models. METHODS: In the present study, we evaluated the pharmacological profile of selected σ1R ligands using a novel object recognition (NOR) test, to see if any differences in cognitive functions between σ1R agonists and antagonists could be observed. We used the highly selective PRE-084 and S1RA as reference σ1R agonist and antagonist, respectively. Furthermore, compound KSK100 selected from our ligand library was also included in this study. KSK100 was previously characterized as a dual-targeting histamine H3/σ1R antagonist with antinociceptive and antiallodynic activity in vivo. Donepezil (acetylcholinesterase inhibitor and σ1R agonist) was used as a positive control drug. RESULTS: Both tested σ1R agonists (donepezil and PRE-084) improved learning in the NOR test, which was not observed with the σ1R antagonists S1RA and KSK100. CONCLUSIONS: The nonlinear dose-response effect of PRE-084 in this assay does not justify its use for routine assessment of the functional activity of σ1R ligands.

Time-dependent effects of microplastics on soil bacteriome.

Microplastic threats to biodiversity, health and ecological safety are adding to concern worldwide, but the real impacts on the functioning of organisms and ecosystems are obscure owing to their inert characteristics. Here we investigated the long-lasting ecological effects of six prevalent microplastic types: polyethylene (PE), polypropylene (PP), polyamide (PA), polystyrene (PS), polyethylene terephthalate (PET), and polyvinyl chloride (PVC) on soil bacteria at a 2 % (w/w) level. Due to the inertia and lack of available nitrogen of these microplastics, their effects on bacteriome tended to converge after one year and were strongly different from their short-term effects. The soil volumes around microplastics were very specific, in which the microplastic-adapted bacteria (e.g., some genera in Actinobacteria) were enriched but the phyla Bacteroidetes and Gemmatimonadetes declined, resulting in higher microbial nitrogen requirements and reduced organic carbon mineralization. The reshaped bacteriome was specialized in the genetic potential of xenobiotic and lipid metabolism as well as related oxidation, esterification, and hydrolysis processes, but excessive oxidative damage resulted in severe weakness in community genetic information processing. According to model predictions, microplastic effects are indirectly derived from nutrients and oxidative stress, and the effects on bacterial functions are stronger than on structure, posing a heavy risk to soil ecosystems.

Natural fermentation quality, bacteria, and functional profiles of three cuttings of alfalfa silage in a year in Inner Mongolia, China.

Alfalfa is harvested two or three times a year in central and western Inner Mongolia, China. However, the variations in bacterial communities as affected by wilting and ensiling, and the ensiling characteristics of alfalfa among the different cuttings, are not fully understood. To enable a more complete evaluation, alfalfa was harvested three times a year. At each time of cutting, alfalfa was harvested at early bloom, wilted for 6 h, and then ensiled in polyethylene bags for 60 days. The bacterial communities and nutritional components of fresh alfalfa(F), wilted alfalfa(W) and ensiled alfalfa(S), and the fermentation quality and functional profile of bacterial communities of the three cuttings alfalfa silage, were then analyzed. Functional characteristics of silage bacterial communities were evaluated according to the Kyoto Encyclopedia of Genes and Genomes. The results showed that all nutritional components, fermentation quality, bacterial communities, carbohydrate, amino acid metabolism and key enzymes of bacterial communities were influenced by cutting time. The species richness of F increased from the first cutting to the third cutting; it was not changed by wilting, but was decreased by ensiling. At phylum level, Proteobacteria were more predominant than other bacteria, followed by Firmicutes (0.063-21.39%) in F and W in the first and second cuttings. Firmicutes (96.66-99.79%) were more predominant than other bacteria, followed by Proteobacteria (0.13-3.19%) in S in the first and second cuttings. Proteobacteria, however, predominated over all other bacteria in F, W, or S in the third cutting. The third-cutting silage showed the highest levels of dry matter, pH and butyric acid (p < 0.05). Higher levels of pH and butyric acid were positively correlated with the most predominant genus in silage, and with Rosenbergiella and Pantoea. The third-cutting silage had the lowest fermentation quality as Proteobacteria were more predominant. This suggested that, compared with the first and second cutting, the third cutting is more likely to result in poorly preserved silage in the region studied.

Dynamics of Phyllosphere Microbiota and Chemical Parameters at Various Growth Stages and Their Contribution to Anaerobic Fermentation of Pennisetum giganteum.

This work evaluated the dynamic changes of phyllosphere microbiota and chemical parameters at various growth stages of Pennisetum giganteum and their effects on the bacterial community, cooccurrence networks, and functional properties during anaerobic fermentation. P. giganteum was collected at two growth stages (early vegetative stage [PA] and late vegetative stage [PB]) and was naturally fermented (NPA and NPB) for 1, 3, 7, 15, 30, and 60 days, respectively. At each time point, NPA or NPB was randomly sampled for the analysis of chemical composition, fermentation parameter, and microbial number. In addition, the fresh, 3-day, and 60-day NPA and NPB were subjected to high-throughput sequencing and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional prediction analyses. Growth stage obviously affected the phyllosphere microbiota and chemical parameters of P. giganteum. After 60 days of fermentation, NPB had a higher lactic acid concentration and ratio of lactic acid to acetic acid but a lower pH value and ammonia nitrogen concentration than NPA. Weissella and Enterobacter were dominant in 3-day NPA and Weissella was dominant in 3-day NPB, while Lactobacillus was the most abundant genus in both 60-day NPA and NPB. The complexity of bacterial cooccurrence networks in the phyllosphere decreased with P. giganteum growth. The ensiling process further decreased the complexity of bacterial networks, with the simplest bacterial correlation structures in NPB. There were great differences in the KEGG functional profiles of PA and PB. Ensiling promoted the metabolism of lipid, cofactors, vitamins, energy, and amino acids but suppressed the metabolism of carbohydrates and nucleotides. Storage time had a greater influence than growth stage on bacterial community diversity, cooccurrence networks, and functional profiles of P. giganteum silage. Differences in bacterial diversity and functionality of P. giganteum silage caused by growth stage appear to be offset by long-term storage. IMPORTANCE The phyllosphere microbiota consists of various and complex microbes, including bacteria with crucial relevance to the quality and safety of fermented food and feed. It initially derives from soil and becomes specific to its host after interaction with plants and climate. Bacteria associated with the phyllosphere are highly abundant and diverse, but we know little about their succession. Here, the phyllospheric microbiota structure was analyzed within the growth of P. giganteum. We also evaluated the effects of phyllosphere microbiota and chemical parameter changes on the anaerobic fermentation of P. giganteum. We observed remarkable differences in bacterial diversity, cooccurrence, and functionality of P. giganteum at various growth stages and storage times. The obtained results are important for understanding the fermentation mechanism and may contribute to high-efficient production without additional cost.

Sustainable utilization of residual grass: effect of anaerobic storage days on chemical composition, fermentation performance, microbial community, and functional profiles of Pennisetum giganteum.

The seasonal surplus and putrefactive property of moist forages inevitably increase the pressure on environmental protection and residual grass disposal. In the current work, the anaerobic fermentation approach was adopted to assist the sustainable recycling of leftover Pennisetum giganteum (LP), and its chemical composition, fermentation performance, bacterial community and functional profiles during anaerobic fermentation were studied. Fresh LP was spontaneously fermented for up to 60 d. At the end of anaerobic fermentation, fermented LP (FLP) displayed homolactic fermentation with low pH value, ethanol, and ammonia nitrogen concentrations but high lactic acid concentration. Weissella was dominant in 3-day FLP, yet Lactobacillus was the overwhelming genus (92.6%) in 60-day FLP. The anaerobic fermentation process promoted (P < 0.05) the metabolism of carbohydrate and nucleotide while suppressing (P < 0.05) that of lipid, cofactors, vitamins, energy, and amino acid. The results showed that the residual grass with LP as an example could be successfully fermented even if no additives were added, without signs of clostridial and fungal contamination.

Microbial Diversity and Functional Potential of Keem: A Traditional Starter Culture for Alcoholic Beverage-Application of Next-Generation Amplicon and Shotgun Metagenome Sequences.

"Pakhoi" is an ethnic drink of the Tons valley, Uttarakhand, India produced by fermenting jaggery and barley with the help of a starter culture called "keem". In the present study, we investigated the microbial diversity and associated functional potential of "keem" using shotgun metagenome sequencing and amplicon sequencing. We also compared the taxonomic data obtained using these two sequencing techniques. The results showed that shotgun sequencing revealed a higher resolution of taxonomic profiling as compared to the amplicon sequencing. Furthermore, it was found that the genera detected by shotgun sequencing were valuable for facilitating the fermentation process. Additionally, to understand the functional profiling of the genera, different databases were used for annotation, resulting in a total of 13 metabolic pathways. The five most abundant KEGG functions were genetic information processing, metabolism, translation, cofactor and vitamin metabolism and xenobiotic degradation. In contrast, the top five COG were in order of highest frequency sequences belonging to transcription, followed by general function prediction, carbohydrate transport metabolism, amino acid transport and metabolism and translation and biogenesis. Gene ontology revealed many pathways, biochemical processes and molecular functions associated with the organisms forming the starter culture. Overall, the present study can help to understand the microbial diversity and its role in fermentation of traditional alcoholic beverages using "Keem".

Effect of deposit chemistry on microbial community structure and activity: Implications for under-deposit microbial corrosion.

Introduction: The deposition of solid particles carried by production fluids from oil and gas companies in horizontal surfaces of different assets has shown to cause severe localised corrosion. Sand, one of the most common deposits in the energy sector pipelines, is frequently mixed with crude, oil, asphaltenes, corrosion inhibitors, and other organic compounds. For this reason, they might favour the metabolic activity of native microbial communities. This study aimed to determine the impact of sand-deposit chemical composition on the microbial community structure and functional attributes of a multispecies consortium recovered from an oilfield and the resulting risk of under-deposit microbial corrosion of carbon steel. Methods: Sand deposits recovered from an oil pipeline were used in their raw form and compared against the same deposits exposed to heat treatment to remove organic compounds. A four-week immersion test in a bioreactor filled with synthetic produced water and a two-centimeter layer of sand was set up to assess corrosion and microbial community changes. Results: The raw untreated deposit from the field containing hydrocarbons and treatment chemicals resulted in a more diverse microbial community than its treated counterpart. Moreover, biofilms developed in the raw sand deposit exhibited higher metabolic rates, with functional profile analysis indicating a predominance of genes associated with xenobiotics degradation. Uniform and localized corrosion were more severe in the raw sand deposit compared to the treated sand. Discussion: The complex chemical composition of the untreated sand might have represented an additional source of energy and nutrients to the microbial consortium, favoring the development of different microbial genera and species. The higher corrosion rate obtained under the untreated sand suggests that MIC occurred due to syntrophic relationships between sulphate reducers or thiosulphate reducers and fermenters identified in the consortium.