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Fermentation is a type of metabolism carried out by organisms in environments without oxygen. Despite being studied for over 185 years, the diversity and complexity of this metabolism are just now becoming clear. Our review starts with the definition of fermentation, which has evolved over the years and which we help further refine. We then examine the range of organisms that carry out fermentation and their traits. Over one-fourth of all prokaryotes are fermentative, use more than 40 substrates, and release more than 50 metabolic end products. These insights come from studies analyzing records of thousands of organisms. Next, our review examines the complexity of fermentation at the biochemical level. We map out pathways of glucose fermentation in unprecedented detail, covering over 120 biochemical reactions. We also review recent studies coupling genomics and enzymology to reveal new pathways and enzymes. Our review concludes with practical applications for agriculture, human health, and industry. All these areas depend on fermentation and could be improved through manipulating fermentative microbes and enzymes. We discuss potential approaches for manipulation, including genetic engineering, electrofermentation, probiotics, and enzyme inhibitors. We hope our review underscores the importance of fermentation research and stimulates the next 185 years of study.

Escalating wildfire frequency and severity, exacerbated by shifting climate patterns, pose significant ecological and economic challenges. Prescribed burns, a common forest management tool, aim to mitigate wildfire risks and protect biodiversity. Nevertheless, understanding the impact of prescribed burns on soil and microbial communities in temperate mixed forests, considering temporal dynamics and slash fuel types, remains crucial. Our study, conducted at the University of Tennessee Forest Resources AgResearch and Education Center in Oak Ridge, TN, employed controlled burns across various treatments, and the findings indicate that low-intensity prescribed burns have none or minimal short-term effects on soil parameters but may alter soil nutrient concentrations, as evidenced by significant changes in porewater acetate, formate, and nitrate concentrations. These burns also induce shifts in microbial community structure and diversity, with Proteobacteria and Acidobacteria increasing significantly post-fire, possibly aiding soil recovery. In contrast, Verrucomicrobia showed a notable decrease over time, and other specific microbial taxa correlated with soil pH, porewater nitrate, ammonium, and phosphate concentrations. Our research contributes to understanding the intricate relationships between prescribed fire, soil dynamics, and microbial responses in temperate mixed forests in the Southern Appalachian Region, which is valuable for informed land management practices in the face of evolving environmental challenges.

The core reason for the nutritional richness and special flavour composition of traditional Chinese fermented soybean products lies in the diversity of microbial structures and their metabolites, which include a variety of potential probiotics. However, relatively little mainstream research has been conducted on these microorganisms, especially in regions with unrelated product dietary habits, limiting the high-value utilisation of the characteristic microbial resources. In order to enhance the efficient use and functional exploitation of microbial resources in Chinese traditional fermented soybean products, this paper investigated and reviewed a variety of products such as soybean paste, soy sauce, douchi, sufu, and fermented soybean milk, and carried out a detailed analysis of the sources, flavour characteristics, and potential functionality of microorganisms therein, which elucidated that the microorganisms in Chinese traditional fermented soybean products have the potential to be used as functional probiotics, with a view to contributing to the probiotic resources exploitation, novel food development, and the development of new food products, as well as the development of new foods. [ABSTRACT FROM AUTHOR]

Introduction: Bacterial spot, caused by diverse xanthomonads classified into four lineages within three species, poses a significant threat to global pepper and tomato production. In Taiwan, tomato bacterial spot xanthomonads phylogenetically related to an atypical Xanthomonas euvesicatoria pv. perforans (Xep) strain NI1 from Nigeria were found. Methods: To investigate the genetic structure of Taiwanese Xep strains and determine the phylogenetic position of the atypical strains, we completed high-quality, gap-free, circularized genomes of seven Taiwanese Xep strains and performed comparative genomic analyses with genomes of X. euvesicatoria pathovars. Average nucleotide identity, core genome analysis, and phylogenomic analysis were conducted. Results: Three sequenced strains were identified as typical Xep , while four clustered with the atypical strain NI1, forming a distinct genomovar within X. euvesicatoria, proposed as X. euvesicatoria genomovar taiwanensis (Xet). This new lineage likely originated in Taiwan and spread to Nigeria through global seed trade. At the genomovar level, chromosomes remained conserved among Taiwanese strains, while plasmids likely contributed to bacterial virulence, avirulence, and field fitness. Gap-free genomes revealed associations between the evolution of type III effectors, horizontal gene transfer events, plasmid diversity, and recombination. Discussion: This study highlights the critical roles of horizontal gene transfer and plasmids in shaping the genetic makeup, evolution, and environmental adaptation of plant pathogenic xanthomonads. The identification of a new genomovar, X. euvesicatoria genomovar taiwanensis , provides insights into the diversity and global spread of bacterial spot pathogens through seed trade. [ABSTRACT FROM AUTHOR]

Diet shapes the gut microbiome, which in turn influences host phenotype. Accordingly, there is much interest in leveraging diet to modulate gut microbial communities and host biology. However, recent approaches have not fully appreciated that hosts and gut microbes experience diet differently. Whether dietary nutrients reach the gut microbiota, which primarily resides in the colon in humans and other hindgut fermenters, depends on nutrient absorption in the small intestine. That gut microbes utilize the fraction of diet that escapes host-driven digestion creates a paradigm where host nutrient status is decoupled from, and often negatively correlated with, gut microbiota nutrient status. Here, we present a framework based on this concept of decoupled nutrient status (DNS), which can be used to understand distinct host and gut microbial phenotypes that are ultimately mediated by the small intestinal digestibility of the diet. We evaluate our framework against existing research employing diets of varying digestibility and demonstrate convergence of host phenotypes and gut microbial signatures across studies. Further, we highlight that gut microbial signatures predicted by DNS manifest most strongly in humans living industrialized lifestyles and in captive animals that habitually consume diets with high host-driven digestibility. We posit that the evolutionary decoupling of nutritional status between hosts and their gut microbiota has likely been especially pronounced in humans due to our intensified pursuit of calorie-rich, easy-to-digest diets. We conclude by proposing future research directions to better capture diet as it appears to gut microbes, a perspective likely to deliver new understanding of diet-microbiome interactions. [ABSTRACT FROM AUTHOR]

ABSTRACT Objective Method Results Discussion Avoidant/restrictive food intake disorder (ARFID) is an eating disorder characterized by a severely restrictive diet leading to significant physical and/or psychosocial sequelae. Largely owing to the phenotypic heterogeneity, the underlying pathophysiological mechanisms are relatively unknown. Recently, the communication between microorganisms within the gastrointestinal tract and the brain—the so‐called microbiota‐gut‐brain axis—has been implicated in the pathophysiology of eating disorders. This Spotlight review sought to investigate and conceptualize the possible ways that the microbiota‐gut‐brain axis is involved in ARFID to drive future research in this area.By relating core symptoms of ARFID to gut microbiota and its signaling pathways to the brain, we evaluated how the gut microbiota is potentially involved in the pathophysiology of ARFID.We hypothesized that the restricted type and amount of food intake characteristic of ARFID diminishes gut microbial diversity, including beneficial bacteria and their metabolites capable of signaling to the brain, to modulate biopsychological pathways relevant to ARFID: homeostatic signaling, food reward, interoception, sensory sensitivity, disgust, perseveration, fear‐based learning, and mood. Candidate signaling mechanisms include microbial‐induced effects on inflammation, cortisol, and neurotransmitters such as dopamine and serotonin.Through reviewing the extant evidence, we conceptualized a new theoretical framework of ARFID with an emphasis on microbiota‐gut‐brain axis signaling to inform future research. Although more research is necessary to evaluate this theoretical model, the tentative evidence suggests that therapeutics specifically targeting the gut microbiota for the treatment of ARFID symptomatology warrants more investigation. [ABSTRACT FROM AUTHOR]

Background: This meta-analysis explores alterations in the gut microbiota of patients with Multiple Sclerosis (MS) using 16S ribosomal RNA (rRNA) gene sequencing. Methods: Adhering to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, our comprehensive review spanned major databases, including PubMed, Web of Science, Embase, Cochrane, and Ovid, targeting observational studies that implemented 16S rRNA gene sequencing on fecal specimens. The quality of these studies was meticulously evaluated using the Newcastle-Ottawa scale. Results: Our search yielded 26 relevant studies conducted between 2015-2022, encompassing 2885 participants. No significant differences were observed in alpha diversity indices (Shannon, Chao1, Operational Taxonomic Units (OTU), and Simpson) between MS patients and controls in general. Nonetheless, subgroup analyses according to disease activity using the Shannon index highlighted a significant decrease in microbial diversity during MS's active phase. Similarly, an evaluation focusing on MS phenotype revealed diminished diversity in individuals with relapsing-remitting MS (RRMS). Microbial composition analysis revealed no consistent increase in pro-inflammatory Bacteroidetes or decrease in anti-inflammatory Firmicutes within the MS cohort. Conclusion: The gut microbiome's role in MS presents a complex panorama, where alterations in microbial composition might hold greater significance to disease mechanisms than diversity changes. The impact of clinical factors such as disease activity and phenotype are moderately significant, underscoring the need for further research to elucidate these relationships. Prospective research should employ longitudinal methodologies to elucidate the chronological interplay among gut microbiota, disease evolution, and therapeutic strategies. [ABSTRACT FROM AUTHOR]

The objective of this study was to evaluate the effects of different concentrations of hydrogen-rich water (HRW) on in vitro rumen fermentation characteristics and the dynamics of bacterial communities. The experiment included four treatment groups: a control (CON) and hydrogen-rich water (HRW) at 200, 400, and 800 ppb. Each group was analyzed at 12-hour (h) and 48-hour (h) time points with five replicates, totaling 40 samples. The experimental results highlighted the HRW800ppb group as the top production in terms of gas production and CH4 content. In contrast, the HRW200ppb group exhibited significantly lower methane levels at both 12 h and 48 h (P < 0.05). Regarding rumen fermentation, the HRW400ppb group significantly increased the levels of ammonia nitrogen (NH3-N) and microbial crude protein (MCP) at 12 h fermentation, but reduced the dry matter degradation rate (P < 0.05). After 48 h, the HRW400ppb group had highest MCP content (P < 0.05), but no significant differences in NH3-N and dry matter degradation rate compared with the CON group (P > 0.05). Although HRW did not significantly benefit the synthesis of total volatile fatty acids (TVFA) and individual VFA, the HRW800ppb group significantly increased the ratio of acetate to propionate (P < 0.05). Based on CH4 emissions and MCP synthesis, we selected the HRW400ppb group for subsequent bacterial community analysis. Bacterial community analysis showed that at 12 h, compared with the CON group, the Bacterial community analysis revealed that the HRW400ppb group had significant increases in the Simpson index, Firmicutes, Streptococcus, Schwartzia, Prevotellaceae_YAB2003_group, and Oribacterium, and decreases in Prevotella, Ruminobacter, Succinivibrio, unclassified_Succinivibrionaceae, and Prevotellaceae_UCG-003 (P < 0.05). At 48 h, the Prevotellaceae_YAB2003_group and Oribacterium abundances continued to rise significantly, while Rikenellaceae_RC9_gut_group and Succiniclasticum abundances fell in the HRW400ppb group (P < 0.05). Correlation analysis indicated a negative link between CH4 and Streptococcus, and a positive correlation between the abundance of Rikenellaceae_RC9_gut_group and CH4. Collectively, these results indicate that HRW can modulate rumen fermentation and microbial community structure to reduce methane emissions without significantly affecting VFA synthesis, highlighting its potential as drinking water for enhancing ruminant nutrition and mitigating the environmental impact of livestock farming. [ABSTRACT FROM AUTHOR]

Background: Wood-feeding termites have been employed as sources of novel and highly efficient lignocellulolytic enzymes due to their ability to degrade lignocellulose efficiently. As a higher wood-feeding termite, Globitermes sulphureus (Blattaria: Termitidae) plays a crucial role as a decomposer in regions such as Vietnam, Singapore, Myanmar, and Yunnan, China. However, the diversity of its gut microbiome and carbohydrate-active enzymes (CAZymes) remains unexplored. Here, we analyzed the diversity of hindgut microbial communities and CAZymes in a higher wood-feeding termite, G. sulphureus, and a lower wood-feeding termite, Coptotermes formosanus (Blattaria: Rhinotermitidae). Results: 16S rRNA sequencing revealed that Spirochaetota, Firmicutes, and Fibrobacterota were the dominant microbiota in the hindgut of the two termite species. At the phylum level, the relative abundances of Proteobacteria and Bacteroidota were significantly greater in the hindgut of C. formosanus than in G. sulphureus. At the genus level, the relative abundances of Candidatus_Azobacteroides and Escherichia-Shigella were significantly lower in the hindgut of G. sulphureus than in C. formosanus. Metagenomic analysis revealed that glycoside hydrolases (GHs) with cellulases and hemicellulases functions were not significantly different between G. sulphureus and C. formosanus. Interestingly, the cellulases in G. sulphureus were mainly GH5_2, GH5_4, GH6, GH9, and GH45, while the hemicellulases were mainly GH11, GH8, GH10, GH11, GH26, and GH53. In C. formosanus, the cellulases were mainly GH6 and GH9, and the hemicellulases were mainly GH5_7, GH5_21, GH10, GH12, and GH53. In addition, β-glucosidase, exo-β-1,4-glucanase, and endo-β-1,4-glucanase activities did not differ significantly between the two termite species, while xylanase activity was higher in G. sulphureus than in C. formosanus. The bacteria encoding GHs in G. sulphureus were mainly Firmicutes, Fibrobacterota, and Proteobacteria, whereas Bacteroidota and Spirochaetota were the main bacteria encoding GHs in C. formosanus. Conclusions: Our findings characterized the microbial composition and differences in the hindgut microbiota of G. sulphureus and C. formosanus. Compared to C. formosanus, G. sulphureus is enriched in genes encoding for hemicellulase and debranching enzymes. It also highlights the rich diversity of GHs in the hindgut microbiota of G. sulphureus, including the GH5 subfamily, GH6, and GH48, with the GH6 and GH48 not previously reported in other higher termites. These results strengthen the understanding of the diversity of termite gut microbiota and CAZymes. [ABSTRACT FROM AUTHOR]

BACKGROUND RESULTS CONCLUSION Polyphenolic compounds in millet vinegar are crucial functional substances, but the mechanisms underlying their formation and metabolism remain unclear. Acetic acid fermentation (AAF) represents the most active microbial metabolism stage and is pivotal for forming polyphenolic compounds. This study comprehensively analyzed the role of the microbiome in polyphenolic compound production and metabolism during AAF.Changing patterns were observed in both the microbiome and polyphenolic monomer compounds during AAF of millet vinegar. Lactobacillus harbinensis (0.624–0.454%) was identified as the dominant species in the pre‐AAF stage, exhibiting a significant positive correlation with caffeic acid, kaempferic acid and kaempferolide (P < 0.05). Lactobacillus harbinensis‐mediated polyphenolic compound metabolism was further confirmed through genomic analysis and pure culture fermentation techniques. Lactobacillus harbinensis encodes enzymes such as carbohydrate hydrolases, glycosidases and cellulases, which promote the release and metabolism of polyphenolic compounds from grain hulls.This study confirmed that L. harbinensis, as a core microorganism in millet vinegar fermentation, can significantly augment the content of total phenols and specific polyphenolic compounds. These findings provide valuable insights for optimizing millet vinegar production. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

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Introduction: Understanding the microbial diversity and potential functional dynamics within the rhizocompartments of Dendrobium huoshanense is crucial for unraveling the plant–microbe interactions that influence its medicinal properties. Methods: This study is the first to characterize the microbiome associated with the rhizocompartments of D. huoshanense , including its cultivation medium, rhizosphere, rhizoplane, and root endosphere, using high-throughput sequencing and subsequent bioinformatic analysis. Results: Bacterial phylogenetic diversity was significantly higher in the endosphere than in the rhizosphere, while fungal α-diversity significantly decreased from the cultivation medium to the endosphere. Both bacterial and fungal niche widths decreased from the cultivation medium to the endosphere. β-Diversity analysis revealed distinct spatial patterns in both bacterial and fungal communities across the rhizocompartments, with the most pronounced differences between the cultivation medium and the endosphere. Taxonomically, Proteobacteria and Ascomycota were predominant in the endosphere for bacterial and fungal communities, respectively. Functional predictions showed significant enrichment of pathways related to xenobiotics biodegradation, lipid metabolism, and nitrogen fixation in the endosphere, while functions associated with plant pathogens and saprotrophs were significantly reduced. Discussion: The results indicate a shift from generalist to specialist microbes from the cultivation medium to the endosphere, suggesting that D. huoshanense exerts strong selective pressure for endophytic fungi. Interestingly, a high proportion of fungi with unknown functions were found in the endosphere, highlighting an area for further research regarding the medicinal efficacy of D. huoshanense. Overall, this study provides foundational data for understanding the adaptive evolution of these microbial communities in response to specific microhabitats. [ABSTRACT FROM AUTHOR]

Root-knot nematodes (RKNs) of the genus Meloidogyne are one of the most damaging genera to cultivated woody plants with a worldwide distribution. The knowledge of the soil and rhizosphere microbiota of almonds infested with Meloidogyne could help to establish new sustainable and efficient management strategies. However, the soil microbiota interaction in deciduous woody plants infected with RKNs is scarcely studied. This research was carried out in six commercial almond groves located in southern Spain and infested with different levels of Meloidogyne spp. within each grove. Several parameters were measured: nematode assemblages, levels and biocontrol agents in Meloidogyne 's eggs, levels of specific biocontrol agents in rhizoplane and soil, levels of bacteria and fungi in rhizoplane and soil, fungal and bacterial communities by high-throughput sequencing of internal transcribed spacer (ITS), and 16S rRNA gene in soil and rhizosphere of the susceptible almond hybrid rootstock GF-677 infested with Meloidogyne spp. The studied almond groves showed soil degradation by nematode assemblies and fungi:bacterial ratio. Fungal parasites of Meloidogyne eggs were found in 56.25% of the samples. However, the percentage of parasitized eggs by fungi ranged from 1% to 8%. Three fungal species were isolated from Meloidogyne eggs, specifically Pochonia chlamydosporia , Purpureocillium lilacinum , and Trichoderma asperellum. The diversity and composition of the microbial communities were more affected by the sample type (soil vs rhizosphere) and by the geographical location of the samples than by the Meloidogyne density, which could be explained by the vigorous hybrid rootstock GF-677 and a possible dilution effect. However, the saprotrophic function in the functional guilds of the fungal ASV was increased in the highly infected roots vs the low infected roots. These results indicate that the presence of biocontrol agents in almond fields and the development of new management strategies could increase their populations to control partially RKN infection levels. [ABSTRACT FROM AUTHOR]

Pine Wilt Disease (PWD) is a devastating pine tree disease characterized by rapid onset, high mortality rate, quick spread, and difficulty in control. Plant microbiome plays a significant role in the development of PWD. However, the endophytic microbial communities of Pinus koraiensis infected by pine wood nematode (PWN) Bursaphelenchus xylophilus remain largely unexplored. In this study, we analyzed the structural changes of endophytic communities of P. koraiensis after infection by the PWN using high-throughput sequencing technology. The results showed that the community structure underwent significant changes as the degree of PWN infection intensified. The diversity and abundance of endophytic fungi in P. koraiensis increased, while those of endophytic bacteria in P. koraiensis decreased during the infection process. Meanwhile, the abundance of some dominant microorganisms has also changed, including species such as Graphilbum and Pseudoalteromonas. Functional prediction analysis showed that the functional composition of endophytic fungi in P. koraiensis was significantly different across the development of PWD, while the composition of endophytic bacteria remained essentially similar. The results indicated that PWN infection had a significant impact on the structure, diversity, abundance, and functional gene composition of endophytic microbial communities in P. koraiensis , and most of the main endophytic microbial groups tended to coordinate with each other. This work provides a better understanding of the changes in endophytic community structure and function caused by PWD infection of P. koraiensis , which may benefit the exploration of potential endophytes for PWN biocontrol. [ABSTRACT FROM AUTHOR]

Soil microorganisms are key indicators of soil health, and it is crucial to investigate the structure and interactions of soil microbial communities among three different provenances of Pennisetum alopecuroides under varying nitrogen fertilizer and temperature levels in Northwest China. This study aims to provide theoretical support for the sustainable use of artificial grassland in this region. Employing a two-factor pot-control experiment with three nitrogen fertilizer treatments and three temperature treatments, a total of all treatments was utilized to examine the composition and abundance of soil microbial communities associated with Pennisetum alopecuroides using high-throughput sequencing, PCR technology, and molecular ecological network analysis. The results revealed that Proteobacteria was the dominant bacterial phylum while Ascomycota was the dominant fungal phylum in the soil samples from three provenances of Pennisetum. Specifically, Proteobacteria exhibited higher abundance in the N3T2 treatment compared to other treatments under N3T2 (25–30°C, 3 g/pot) treatment conditions in Shaanxi and Gansu provinces; similarly, Proteobacteria was more abundant in the N1T2 (25–30°C, 1 g/pot) treatment in Inner Mongolia under N1T2. Moreover, Ascomycota displayed higher abundance than other treatments in both Inner Mongolia and Gansu provinces. Additionally, Pennisetum Ascomycota demonstrated greater prevalence under (25–30°C, 3 g/pot) treatment compared to other treatments; furthermore, Shaanxi's Pennisetum Ascomycota exhibited increased prevalence under N3T1 (18–23°C, 3 g/pot) treatment compared to other treatments. The richness and diversity of soil microbial communities were significantly influenced by nitrogen fertilizer and temperature changes, leading to notable alterations in their structure. Molecular ecological network analyses revealed strong collaborative relationships among microbial species in Shaanxi Pennisetum and Inner Mongolia Pennisetum under high nitrogen and high temperature treatments, while competitive relationships were observed among microbial species in Gansu Pennisetum under similar conditions. Redundancy analysis indicated that soil pH, total potassium, and total phosphorus were the primary environmental factors influencing microorganisms. In summary, this study offers a theoretical foundation for assessing the sustainable utilization of Pennisetum artificial grasslands in Northwest China by investigating the shifts in soil microbial communities and the driving factors under varying nitrogen fertilizer and temperature levels. [ABSTRACT FROM AUTHOR]

In the first days of life, the newborns' intestinal microbiota develops simultaneously with the intestinal gut barrier and follows intestinal immunity. The mode of delivery shows significant impact on microbial development and, thus, the initiation of the tryptophan catabolism pathway. Further antibiotics (ATB) treatment of mothers before or during delivery affects the microbial and tryptophan metabolite composition of stool of the caesarean- and vaginal-delivered newborns. The determination of microbiome and levels of tryptophan microbial metabolites in meconium and stool can characterize intestinal colonization of a newborn. From 134 samples from the Central European Longitudinal Studies of Parents and Children: The Next Generation (CELSPAC: TNG) cohort study, 16S rRNA gene sequencing was performed, and microbial tryptophan metabolites were quantified using ultra-high-performance liquid chromatography with triple-quadrupole mass spectrometry. Microbial diversity and concentrations of tryptophan metabolites were significantly higher in stool compared to meconium. Treatment of mothers with ATB before or during delivery affects metabolite composition and microbial diversity in stool of vaginal- and caesarean-delivered newborns. Correlation of microbial and metabolite composition shows significant positive correlations of indol-3-lactic acid, N-acetyl-tryptophan and indol-3-acetic acid with Bifidobacterium, Bacteroides and Peptoclostridium. The positive effect of vaginal delivery on newborns' microbiome development is degraded when mother is treated with ATB before or during delivery. Key points: • Antibiotic treatment diminishes the positive effects of vaginal delivery. • Antibiotic treatment affects metabolite and microbial composition in newborns. • Bifidobacterium and Peptoclostridium could be the producer of indole-lactic acid. [ABSTRACT FROM AUTHOR]

Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy‐specific liver disease and the second most frequent cause of jaundice in pregnancy, but the etiology of it is poorly understood. By collecting blood and fecal samples from 12 healthy pregnant women (CON group) and 32 ICP patients (ICP group) in China, we performed 16s rRNA gene sequencing and analyzed microbial diversity. The results showed a decrease in species richness of the ICP group compared to that in the CON group, with a significant difference in species diversity between the two groups. Differential analysis revealed the following biomarkers: s__unclassified__Megamonas, g__Megamonas, f__Selenomonadaceae, c__Bacilli, and o__Lactobacillales. Importantly, we found a decrease in species richness of Selenomonadaceae at the family level and decreased bacilli at the class level in ICP patients. Correlation network analysis and functional gene prediction were performed accordingly. Our data provided new information linking microbiota and ICP, and are possibly helpful for further exploration of the disease. [ABSTRACT FROM AUTHOR]

Global mountain ecosystems have garnered significant attention due to their rich biodiversity and crucial ecological functions; however, there is a dearth of research on the variations in soil active organic carbon across altitudinal gradients and their impacts on microbial communities. In this study, soil samples at an altitude of 3,800 m to 4,400 m were collected from Sejira Mountain in the southeast Tibet, and soil active organic carbon components, soil microbial community diversity, composition and structure distribution and their relationships were systematically analyzed. The results revealed a non-linear relationship between the elevation and the contents of soil organic carbon (SOC) and easily oxidized organic carbon (ROC), with an initial increase followed by a subsequent decrease, reaching their peak at an altitude of 4,200 m. The Shannon diversity of bacteria exhibited a significant decrease with increasing altitude, whereas no significant change was observed in the diversity of fungi. The bacterial community primarily comprised Acidobacteria, Proteobacteria, Chloroflexi, and Actinobacteriota. Among them, the relative abundance of Proteobacteria exhibited a negative correlation with increasing altitude, whereas Actinobacteriota demonstrated a positive correlation with elevation. The fungal communities primarily consisted of Basidiomycota, Ascomycota, and Mortierellomycota, with Ascomycota prevailing at lower altitudes and Basidiomycota dominating at higher altitudes. The diversity and composition of bacterial communities were primarily influenced by altitude, SOC, ROC, and POC (particulate organic carbon). Soil carbon-to-nitrogen ratio (C/N), dissolved organic carbon (DOC), and available phosphorus (AP) emerged as key factors influencing fungal community diversity, while POC played a pivotal role in shaping the composition and structure of the fungal community. In conclusion, we believe that soil active organic carbon components had a greater impact on the bacterial community in the primary forest ecosystem in southeast Tibet with the elevation gradient increasing, which provided a theoretical basis for further understanding of the relationship between the microbial community and soil carbon cycle in the plateau mountain ecosystem under the background of climate change. [ABSTRACT FROM AUTHOR]

This study analysed basidiomycetous yeasts isolated from the phylloplane of crops and spontaneous plants in Italian agroecosystems. A total of 25 species belonging to 17 genera were recognized by analysing 83 isolates from vineyards and orchards, that are not treated with synthetic fungicides, and adjacent natural areas. Rhodotorula graminis and Filobasidium magnum were the most frequent species but 13 others were represented by a single isolate (e.g., Buckleyzyma salicina, Pseudozyma prolifica, and Moniliella megachiliensis). Preliminary analysis of (GTG)5-PCR fingerprinting revealed high genetic intraspecific heterogeneity. All isolates were characterized by their production of extracellular hydrolytic enzymes and their sensitivity to six commercial fungicides used in Italy. The isolates displayed great variability in these phenotypic traits, which play an important role in the survival of yeast populations in agroecosystems. Most of them exhibited lipolytic, proteolytic, β-glucosidase and pectinolytic activities, but only three (F. magnum, Kwoniella mangroviensis and Ps. prolifica) also had cellulolytic and amylolytic activity. Most isolates were sensitive to four fungicides, and one R. graminis isolate was resistant to all six. This heterogeneity was not related to the geographical origin of the isolates. The lack of selective factors (i.e. pesticide treatments) in the sampling fields and the presence of adjacent natural areas may have favored the maintenance of an elevated level of strain diversity. This study provides new information on phylloplane basidiomycetous yeasts in agroecosystems and opens the way to further investigations into the impact of agricultural practices on the microbial diversity of these natural habitats. [ABSTRACT FROM AUTHOR]

Anthocyanins, key quality components of tea, act as an important bridge between plants and the environment due to their function on protecting plants from biotic and abiotic irritants. This study aimed to assess the interactions between anthocyanins metabolism and the environment. Purple (P) and green (G) leaves with different anthocyanin contents were inoculated with tea plant anthracnose. High-throughput metabolomics and 16S microbial diversity sequencing methods were used to screen the anthocyanin fractions of tea plant leaves responsive to anthracnose. The interconnections between metabolites and the resistance of phyllosphere microorganisms to fungal pathogens were then analyzed. The results showed that leaves with high anthocyanin content (0.14% of diseased area ratio) were less impacted by anthracnose infestation than leaves with low anthocyanin (3.12%). The cyanidin content decreased after infection in purple leaves (PR) and increased in green leaves (GR). The relative abundance of Cyanobacteria was suppressed by the significant enrichment of Proteobacteria after anthracnose infection in green leaves. However, there were no significant differences between these two groups of microorganisms in purple leaves. Collinear network analysis revealed a strong correlation between Cyanobacteria and Dihydrosorbinol and between Proteobacteria and cyanidin metabolites. Among them, OTU456 (Bosea) was identified as the key taxonomic group of bacterial communities in the green-infected leaf network. In summary, the anthracnose resistance benefits from cyanidin mediated by proteobacteria in tea plants. These results deepen our understanding of the regulation of secondary metabolism in tea plants and the formation of plant resistance. [ABSTRACT FROM AUTHOR]

Acne vulgaris is a widespread dermatological condition that significantly affects the quality of life of adolescents and adults. Traditionally, acne pathogenesis has been linked to factors such as excess sebum production, follicular hyperkeratinization, and the presence of Cutibacterium acnes (C. acnes). However, recent studies have highlighted the role of the skin microbiome, shifting focus from individual pathogens to microbial community dynamics. This review critically evaluates existing research on the skin microbiome and its relationship to acne, focusing on microbial diversity, C. acnes strain variability, and emerging therapies targeting the microbiome. While certain studies associate C. acnes with acne severity, others show this bacterium's presence in healthy skin, suggesting that strain-specific differences and overall microbial balance play crucial roles. Emerging therapeutic approaches, such as probiotics and bacteriophage therapy, aim to restore microbial equilibrium or selectively target pathogenic strains without disturbing the broader microbiome. However, the lack of standardized methodologies, limited longitudinal studies, and the narrow focus on bacterial communities are major limitations in current research. Future research should explore the broader skin microbiome, including fungi and viruses, use consistent methodologies, and focus on longitudinal studies to better understand microbial fluctuations over time. Addressing these gaps will enable the development of more effective microbiome-based treatments for acne. In conclusion, while microbiome-targeted therapies hold promise, further investigation is needed to validate their efficacy and safety, paving the way for innovative, personalized acne management strategies. [ABSTRACT FROM AUTHOR]

The variation in the soil microbial community composition over time was assessed at monthly time steps for 1 year in three neighboring Mollisols spanning a drainage gradient. This was done to distinguish between natural oscillations in the community composition versus lasting adaptations to environmental factors such as soil water availability. To isolate soil water availability as a controlling factor, we selected three soils sharing the same soil order (fine‐silty, superactive Argixerolls/Argialbolls); slope (0%–1%); temperature regime (mesic); moisture regime (xeric); and land use history (continuous grassland for the past 10 years) but differing in drainage class (well‐drained vs. moderately well‐drained vs. poorly drained). Changes in microbial diversity were quantified by monitoring the bacterial community at monthly intervals for 1 year. Within individual soils, α‐diversity varied little with season and drainage classes. Despite the three soils experiencing the same climate regime and vegetation/land use, they exhibited distinct community composition and turnover, which we attribute to differences in moisture availability across drainage and seasons. We posit that a seasonal recurring drop in soil redox potential induced by seasonal water saturation in the poorly drained soil is the most probable cause setting the microbial community of that soil apart from those in the better drained soils. Our investigation suggests that not all indicators of microbial diversity share the same sensitivity to seasonal and drainage‐related soil moisture variations. Core Ideas: Seasonal moisture fluctuations have a small effect on bacterial phylogenetic diversity.Phylogenetic diversity may increase with improved drainage.Impacts of seasonal saturation on the microbial community persist year‐round.Responsiveness to seasonal moisture fluctuations can influence the viability of microbial abundance as a bioindicator. [ABSTRACT FROM AUTHOR]

The aims of this research were to evaluate how prolonged feeding of a high-concentrate diet affects the ruminal degradation kinetics of fiber and starch, and to evaluate the effects of the high-concentrate diet on apparent total-tract nutrient digestibility in dairy cows. We also investigated the dysbiotic effects and the remodeling of the hindgut microbiome with prolonged high-concentrate feeding. Nine Holstein cows were used in 2 experimental periods; in each period, cows were first fed a 100% forage diet for 1 wk, followed by stepwise adaptation during one week to a high-concentrate (HC) diet (65% concentrate), which was then fed for 4 consecutive weeks. The kinetics of in situ ruminal degradability of grass silage (DM and NDF), corn grain and wheat grain (DM and starch), as well as the apparent total-tract nutrient digestibility were evaluated in the forage feeding and in wk 4 on the HC diet. Whereas the hindgut microbiome and fermentation profile were evaluated on a weekly basis. Regarding the in situ ruminal degradability due to grain type, the rate of degradation of the potentially degradable fraction and the effective rumen degradability of wheat grain were greater compared with corn grain. The in situ ruminal degradability of NDF decreased with the HC diet. However, the apparent total-tract digestibility of CP, fat, starch, NDF, ADF, and NFC increased with the HC diet compared with forage feeding. In addition, the HC diet increased the concentration of short-chain fatty acids in the hindgut, lowering fecal pH by 0.6 units, which correlated positively with microbial α diversity. This resulted in lower α diversity with the HC diet; however, α diversity (number of amplicon sequence variants) showed recovery in wk 3 and 4 on HC; in addition, microbial β diversity did not change from wk 2 onward on the HC diet. Two microbial enterotypes were identified: one for the forage diet with abundance of Akkermansia and Anaerosporobacter , and another enterotype for the HC diet with enrichment in Bifidobacterium and Butyrivibrio. Overall, results show that major microbial shifts and hindgut dysbiosis occurred in wk 1 on the HC diet. However, the hindgut microbial diversity of cows adapted after 3 wk of consuming the starch-rich ration. Thus, feeding the HC diet impaired fiber degradation in the rumen, but increased apparent total-tract nutrient digestibility. Likely, the forage diet contained less digestible NDF than the HC diet due to greater inclusion of forages with lower NDF digestibility and lower inclusion of more digestible nonforage NDF. Results also suggest that the adaptation of the hindgut microbial diversity of cows observed 3 weeks after the diet transition likely contributed to enhance total-tract nutrient digestibility. The list of standard abbreviations for JDS is available at adsa.org/jds-abbreviations-24. Nonstandard abbreviations are available in the Notes. [ABSTRACT FROM AUTHOR]

Background: The airway microbiome in severe asthma has not been characterised at species‐level by metagenomic sequencing, nor have the relationships between specific species and mucosal immune responses in 'type‐2 low', neutrophilic asthma been defined. We performed an integrated species‐level metagenomic data with inflammatory mediators to characterise prevalence of dominant potentially pathogenic organisms and host immune responses. Methods: Sputum and nasal lavage samples were analysed using long‐read metagenomic sequencing with Nanopore and qPCR in two cross‐sectional adult severe asthma cohorts, Wessex (n = 66) and Oxford (n = 30). We integrated species‐level data with clinical parameters and 39 selected airway proteins measured by immunoassay and O‐link. Results: The sputum microbiome in health and mild asthma displayed comparable microbial diversity. By contrast, 23% (19/81) of severe asthma microbiomes were dominated by a single respiratory pathogen, namely H. influenzae (n = 10), M. catarrhalis (n = 4), S. pneumoniae (n = 4) and P. aeruginosa (n = 1). Neutrophilic asthma was associated with H. influenzae, M. catarrhalis, S. pneumoniae and T. whipplei with elevated type‐1 cytokines and proteases; eosinophilic asthma with higher M. catarrhalis, but lower H. influenzae, and S. pneumoniae abundance. H. influenzae load correlated with Eosinophil Cationic Protein, elastase and IL‐10. R. mucilaginosa associated positively with IL‐6 and negatively with FGF. Bayesian network analysis also revealed close and distinct relationships of H. influenzae and M. catarrhalis with type‐1 airway inflammation. The microbiomes and cytokine milieu were distinct between upper and lower airways. Conclusions: This species‐level integrated analysis reveals central, but distinct associations between potentially pathogenic bacteria and airways inflammation in severe asthma. [ABSTRACT FROM AUTHOR]

Sida rhombifolia (S. rhombifolia) is a widely used herbal plant for humans because of its antioxidant and antibacterial effects, but its potential use as a feed additive for livestock has not been investigated. Twenty 350 days‐old Anyi tile‐like grey chickens were randomly divided into a control group (fed basal diet) and a treatment group (fed basal diet + 3% of S. rhombifolia), and these chickens were feed for 31 days. Dietary S. rhombifolia remarkably enhanced plasma antioxidants, including the significantly increased total antioxidant capability (p < 0.01), catalase (p = 0.04), and superoxide dismutase (p < 0.01) in the treatment group. Furthermore, dietary S. rhombifolia also modulated chicken cecal microbiota, including an increased microbial diversity (Shannon, p = 0.03; Chao1, p = 0.03) in the treatment group. Regarding taxonomic analysis, 34 microbial taxa showed significant differences between the two groups. Meanwhile, the dominant phylum Actinobacteriota (p = 0.04), and dominant genera Desulfovibrio (p = 0.04) and Olsenella (p = 0.02) were significantly increased after treatment, whereas the pathogenic genus Escherichia‐Shigella (p = 0.04) was significantly decreased after feeding S. rhombifolia. The results indicating that S. rhombifolia has potential for use as a natural plant feed additive for chickens. [ABSTRACT FROM AUTHOR]

Purpose: The urinary tract is colonized by microbial communities that impact urinary health. Previous studies have suggested that the bacterial composition of the male urinary microbiota is related to STIs. This study assessed the bacterial composition of the urinary microbiome in South African MSM with and without C. trachomatis. Methods: This study used urine samples from MSM attending care at the King Edward VIII hospital and the Aurum Institute in Durban, South Africa. A total of 200 samples were tested for C. trachomatis infection using the Applied Biosystems™ TaqMan® Assays. Urinary microbiomes of 23 samples were characterized using 16 S rRNA (V3 and V4) gene sequencing on the Illumina MiSeq platform. Results: Bacterial taxonomic analysis showed a high abundance of Streptococcus, Corynebacterium, and Staphylococcus in all the sequenced samples. Moreover, Prevotella and Lactobacillus were detected in urine samples of MSM. Alpha diversity metrics showed a slight increase in microbial diversity in C. trachomatis positive samples; however, this was not significant (ANOVA, P > 0.05). Principal coordinates analysis (PCoA) showed that the microbiome of C. trachomatis infected MSM was not clearly different from those uninfected. Distinct bacterial communities were not detected between positive and negative samples (PERMANOVA F1,22= 1.0284, R2 = 0.047%, P = 0.385). Conclusion: Most microbiome studies on MSM to date have focused on the gut microenvironment. Few studies, however, have provided data regarding the normal composition of the male urethral microbiomes or if these microbiomes are associated with male STIs. This study adds to the growing body of knowledge highlighting the urinary microbiome in MSM. [ABSTRACT FROM AUTHOR]

Background: Roux-en-Y (RYGB) and one anastomosis gastric bypass (OAGB) represent two of the most used bariatric/metabolic surgery (BMS) procedures. Gut microbiota (GM) shift after bypass surgeries, currently understated, may be a possible key driver for the short- and long-term outcomes. Methods: Prospective, multicenter study enrolling patients with severe obesity, randomized between OAGB or RYGB. Fecal and blood samples were collected, pre- (T0) and 24 months postoperatively (T1). GM was determined by V3-V4 16S rRNA regions sequencing and home-made bioinformatic pipeline based on Qiime2 plugin and R packages. Objects: To compare OAGB vs RYGB microbiota profile at T1 and its impact on metabolic and nutritional status. Results: 54 patients completed the study, 27 for each procedure. An overall significant variation was detected in anthropometric and serum nutritional parameters at T1, with a significant, similar decrease in overall microbial alpha and beta diversity observed in both groups. An increase in relative abundances of Actinobacteria and Proteobacteria and a reduction of Bacteroidetes, no significant changes in Firmicutes and Verrucomicrobia, with an increase of the Firmicutes/Bacteroidetes ratio were observed. Conclusions: BMS promotes a dramatic change in GM composition. This is the first multicenter, RCT evaluating the impact of OAGB vs Roux-en-Y bypass on GM profile. The bypass technique per se did not impact differently on GM or other examined metabolic parameters. The emergence of slightly different GM profile postoperatively may be related to clinical conditions or may influence medium or long-term outcomes and as such GM profile may represent a biomarker for bariatric surgery's outcomes. [ABSTRACT FROM AUTHOR]

Tailocins, phage tail-like bacteriocins, are bacterial protein complexes that kill neighboring bacteria, thereby suppressing competitors. The specificity of tailocins depends on their tail fibers, which bind to the target cell's outer membrane, especially binding to specific lipopolysaccharide (LPS) components in a lock-and-key manner. This LPS binding defines the range of bacteria that tailocins can kill. Tailocin genomic loci exhibit differential rates of evolution, with conserved genes involved in structural components and variable genes, such as the tail fibers, determining specificity. The maintenance of diverse tailocin variants over time is likely driven by balancing selection, contributing to long-term persistence within bacterial populations. A tradeoff exists between evolving resistance to tailocins and colonizing the host. Tailocin specificity can be easily modified by swapping tail fibers. Phage tail-like bacteriocins (tailocins) are protein complexes produced by bacteria with the potential to kill their neighbors. Widespread throughout Gram-negative bacteria, tailocins exhibit extreme specificity in their targets, largely killing closely related strains. Despite their presence in diverse bacteria, the impact of these competitive weapons on the surrounding microbiota is largely unknown. Recent studies revealed the rapid evolution and genetic diversity of tailocins in microbial communities and suggest that there are constraints on the evolution of specificity and resistance. Given the precision of their targeted killing and the ease of engineering new specificities, understanding the evolution and ecological impact of tailocins may enable the design of promising candidates for novel targeted antibiotics. [ABSTRACT FROM AUTHOR]

Background and methods: The Zéro allergie research clinic (Saguenay, Canada) is a clinical and research initiative in oral immunotherapy (OIT) for managing IgE-mediated food allergy (FA). A total of 183 children with FA and 27 non-allergic siblings were recruited to date in the Zéro allergie cohort (ZAC) to better understand biological mechanisms underlying FA and OIT prognosis. The primary aims are to (a) better understand the genetic, epigenetic, transcriptomic, metabolomic, and microbial diversity associated with FA; (b) establish the multi-omics and microbial diversity profiles of children following OIT to identify predictive prognosis biomarkers, (c) make OIT more accessible to the population of the Saguenay–Lac-Saint-Jean region, and (d) build a biobank of data and biological material. Results: The ZAC constitutes a unique and rich biobank of biological samples (blood, buccal swabs, microbiota samples [intestinal, buccal, nasal, and cutaneous]) combined with clinical data and more than 75 phenotypic characteristics. Conclusions: This represents an innovative interdisciplinary initiative by researchers, allergists, and paediatricians to make FA care accessible to a greater number of children with IgE-mediated FA. Ultimately, it will contribute to provide more accessible treatment options with greater chances of success through a better understanding of the biological nature of FA and OIT. [ABSTRACT FROM AUTHOR]

Carbon sink processes related to the weathering of silicate minerals are often accompanied by physical, chemical, and biological effects. In particular, plant-microbe synergistic effects are important for soil mineral weathering, but relevant correlation analyses and quantitative studies remain sparse. In this research, a standard serpentine test specimens (STSs) with specific specifications were used to study serpentine weathering under different environmental conditions (abiotic or biotic) and correlated it with the microbial community structure under the growth of Setaria viridis. The results showed that the environment with growing S. viridis had the strongest weathering capacity for STSs, which was 35 times higher than that of the abiotic environment group, and a significant increase in soil inorganic and organic carbon contents compared with the abiotic environment and the environment without plant growth. The bacteria with strong weathering ability were enriched in the soil of around STSs, such as Pseudomonas spp. and Sphingomonas spp. In addition, the fungal community of Ascomycetes is also heavily enriched, accelerating STSs weathering. The addition of bacterial agent (Bacillus subtilis) further promoted the STSs weathering under the growth conditions of S. viridis. The soil surrounding the buried STSs was also enriched with heavy metal tolerant Massilia spp. and disease suppressing Lysobacter spp., while the abundance of fungi functionally associated with pathotypes was reduced, thereby benefiting plant growth. This study provides basic information for the serpentine bio-weathering coupled with carbon sequestration by using plant-microbe synergistic effects. [ABSTRACT FROM AUTHOR]

Phleum pratense is an allergenic grass that pollinates in spring in Pakistan. Databases Allergenonline.org and Allergen.org record ten P. pratense allergens and their isoforms. Phl P 1, Phlp 5, and Phl p 11 are major P. pratense-pollen allergens with demonstrated basophil activity and skin test reactivity. Little is known about P. pratense pollen adaptive variations in different climatic regions and pollen-associated microbial diversity. In this study, we collected P. pratense-pollen and soils in the spring season 2022. Samples were collected from three climatic regions in Pakistan (R1, R2 and R3) with differences in mean monthly air temperature, mean monthly precipitation and elevation. The morphology of pollen was observed by light microscopy, scanning electron microscopy (SEM), biochemical fingerprint analysis, and composition of pollen were investigated by fourier-transform infrared spectroscopy (FTIR). The pollen-associated bacterial populations were identified through a Biolog GEN III microplate system. The pollen water-soluble proteins were isolated and stabilized in phosphate buffer saline (PBS) and tested for allergenicity responses through dot blots and western blots analysis. The morphology study found difference in pollen biochemical composition. Biolog identified Brevibacterium epidermidis and Pantoea agglomerans from P. pratense pollen. Protein extract quantification and sodium dodecyl sulfate-poly acrylamide gel electrophoresis (SDS-PAGE) gel found decreased protein expression in R1 region pollen compared to R2 and R3 region pollen. Allergenicity studies found differential expression of beta-expansin and profilin allergens in pollen obtained from the three regions. Beta-expansin and profilin were suppressed in R1 pollen and expressed in compared to R2 and R3 pollen. This is the first study to identify B. epidermidis and P. agglomerans growth on P. pratense pollen. Variable allergen expression in P. pratense pollen has also been observed in different regions. Soil pH, an increase in mean monthly temperature and a decrease in mean monthly precipitation correlated with pollen biochemical composition, and reduced beta-expansin and profilin expression involved in pollen growth and development. The findings of this research are unique, which enhances basic knowledge and understanding of P. pratense-pollen associated microbiota and climate change impacts on the pollen allergen expression. [ABSTRACT FROM AUTHOR]

[Display omitted] • Natural material manufactured using soil and plant has the potential to mimic exposure to diverse environmental microbiota. • The natural material retains a high diversity of microbiota found in the natural environment. • Sterilized natural material is safe for use in immune-mediated disease-prone mice. It has been suggested that reduced contact with microbiota from the natural environment contributes to the rising incidence of immune-mediated inflammatory disorders (IMIDs) in western, highly urbanized societies. In line with this, we have previously shown that exposure to environmental microbiota in the form of a blend comprising of soil and plant-based material (biodiversity blend; BDB) enhances the diversity of human commensal microbiota and promotes immunoregulation that may be associated with a reduced risk for IMIDs. To provide a framework for future preclinical studies and clinical trials, this study describes how the preparation of BDB was standardized, its microbial content analysed and safety assessments performed. Multiple batches of BDB were manufactured and microbial composition analysed using 16S rRNA gene sequencing. We observed a consistently high alpha diversity and relative abundance of bacteria normally found in soil and vegetation. We also found that inactivation of BDB by autoclaving effectively inactivates human and murine bacteria, viruses and parasites. Finally, we demonstrate that experimental mice prone to develop IMIDs (non-obese diabetic, NOD, mouse model) can be exposed to BDB without causing adverse effects on animal health and welfare. Our study provides insights into a potentially safe, sustainable, and cost-effective approach for simulating exposure to natural microbiota, which could have substantial impacts on health and socio-economic factors. [ABSTRACT FROM AUTHOR]

Background: The skin microbiota maintains a physical and immunological barrier to the environment. Little is known about how the microbiome changes over time or the effect of hand hygiene practices and moisturizer use. Objectives: To assess sex‐specific changes in skin bacteria over time, and how the microbiome is related to self‐reported hand eczema, hand hygiene practices and use of moisturizers. Methods: Swab samples from the dorsal hand were collected at baseline and 6.5 years later during the COVID‐19 pandemic, in 168 participants from the RHINESSA study in Bergen, Norway. The skin samples were analysed by 16S rRNA amplicon sequencing. Results: The alpha diversity of the hand microbiome increased from baseline to follow‐up, and beta diversity differed by sex at both time points. The relative abundance increased for several bacteria from baseline to follow‐up, with sex‐specific differences. Current hand eczema and aggravating hand eczema during the COVID‐19 pandemic were associated with an increase in Staphylococcus. High hand washing frequency at home was associated with lower alpha diversity and with higher abundance of Staphylococcus, Corynebacterium, Finegoldia, and Pseudomonas and lower abundance of Propionibacterium and Pelomonas. The alpha diversity increased with increasing time passing between hand washing and sampling, whereas more frequent moisturizer use was associated with significantly lower alpha diversity, and a change in abundance for some bacteria, such as more Pseudomonas. Conclusions: This longitudinal study revealed an overall increase in skin microbial diversity over a 6‐year period, which was unexpected since follow‐up was performed during the COVID‐19 pandemic when vigorous hand hygienic practices were introduced. Sex‐specific differences were identified at both time points. Individuals with hand eczema seem to develop a more dysbiotic skin bacterial community over time. Hand washing and use of moisturizers, with typically gender‐specific habitual patterns, may lead to change in bacterial composition. [ABSTRACT FROM AUTHOR]

This study investigated the ideal performance of non-recirculating Anaerobic Fluidized Bed Reactors (AnFBRs) for treating organic wastewater of varying strengths under low Hydraulic Retention Time (HRT). Four 4.58 L AnFBRs were used to treat synthetic wastewater with an Organic Loading Rate (OLR) ranging from 4.50 to 40.11 gCOD/L-d, and HRT between 1.1 and 4.4 hours. The AnFBRs achieved high removal efficiencies ranging from 83 % to 96 % at steady state, except during the organic shock load, which reduced removal performance to 12 %. Shortened HRT conditions led to a decreasing trend in reactor pH due to an incomplete anaerobic cycle. The modified Stover-Kincannon model estimated the maximum substrate utilization rate of AnFBR's to be 196.08 gCOD/L-d, with a correlation coefficient of 0.98. Under shortended HRT, microbial diversity analysis identified predominant non-filamentous bacterial families, such as Streptococcaceae and Veillonellaceae, which collaborate during biofilm development in anaerobic environments. It was suggested that the porous media provided secure attachment sites for the biomass growth and biofilm formation under shock load and high shear force conditions. While these results offer valuable insights, further studies are needed to confirm these findings and enhance the understanding of the use porous media in non-recirculating AnFBRs. [Display omitted] • Low-density media allow fluidization in a non-recirculating configuration. • The reactor contributes to good performance under severe conditions. • The downward trend in environmental parameters stands for practical limitation. • Microbial diversity result signifies a new assumption in use of porous media. • Maximum utilization rate 196.08 in unit of organic load present ideal conditions [ABSTRACT FROM AUTHOR]

As two kinds of increasingly popular pets, the saliva of cat or canine is most likely to be left at the crime scene compared with the common types of body fluids in forensics. Accurately identifying the species of saliva samples found at the crime scene involving pets will help the investigators find available testing materials, reduce the consumption of reagents and save the investigative time of the case. Therefore, it is necessary to explore the characteristics and differences of saliva microbiomes of cat, canine and human. In this study, 16S rRNA gene amplicon sequencing technology was used to reveal microbial communities of saliva samples of healthy human, cat, and canine. Alpha diversity analyses indicated that canine saliva demonstrated the highest microbial diversity, followed by cat saliva, whereas human saliva microbial diversity was the lowest. The saliva samples of the three species all had their own unique microbial community compositions, and the dominant phyla of canine and cat salivas were Proteobacteria and Bacteroidete, while the dominant phyla of human saliva were Firmicutes and Proteobacteria. There was no significant statistical difference in the salivary microbiota obtained by the two collection methods (cotton swab and liquid saliva). The gender of cats and canines might have no effect on the salivary microbiota, but the different breeds had an impact on their saliva microbiomes. Principal coordinates analysis, non-metric multidimensional scaling analysis and random forest analysis all indicated significant differences in microbial community structures among the three species, allowing inference on the species sources of saliva samples by microbiome method. Differential microbial biomarkers for the salivas of three species were screened out using a variety of bioinformatics analyses, and the results demonstrated that Prevotella melaninogenica, Veillonella parvula, and Haemophilus parainfluenzae could be used as species-specific microbial biomarkers of human saliva. The detections of human species-specific microbes provide a potential method for determining human saliva. [ABSTRACT FROM AUTHOR]

Litter decomposition has historically been attributed to soil microbial community at local scale, but which fundamental process directly contributes to carbon release from decomposing litter remains not fully understood. Here we used in situ microcosms to assess the temporal changes in soil microbial biomass, taxonomic composition, alpha and beta diversity, network complexity and carbon-degrading functional genes during litter decomposition of a subtropical dominant species (Castanopsis carlesii) in an older (45-years) and a younger (9-years) evergreen broadleaved forests. The soil phospholipid fatty acids, bacterial and fungal community composition, α-diversity indexes and network topological properties were not changed significantly after short-term litter input when litter was decomposed by approximately 70%. However, the absolute abundance of functional genes involved in the decomposition of starch, pectin, hemicellulose, cellulose, chitin and lignin were up-regulated, and these variations were associated with soil α-1.4-glucosidase, β-glucosidase and cellobiohydrolase activities in contributing to litter carbon release during decomposition. These results suggest that the upregulation of functional genes rather than microbial community composition and diversity controls local-scale litter decomposition by encoding and secreting enzymes in these subtropical forests. [ABSTRACT FROM AUTHOR]

Silkworm excrement (SE) and silkworm excrement-derived biochar (BC) were applied to atrazine-contaminated soil at the rates of 0% and 0.5% (w/w), respectively. The effect of organic amendments on sorption capacity, microbial biomass carbon, enzyme activity (dehydrogenase, urease and catalase) and bacterial composition in soil were evaluated. Atrazine significantly decreased the microbial activity and diversity in soil. Both SE and BC treatments increased the sorption of atrazine in soil. SE treatment significantly increased the microbial biomass carbon and enzyme activity in contaminated soil. Unlike the addition of silkworm excrement, BC treatment had no significant effect on dehydrogenase activity. Additionally, Illumina-MiSeq sequencing analyses showed that the two organic amendments increased the Shannon index of bacteria. SE treatment improved the relative abundance of Bacteroidetes. BC treatment improved the Proteobacteria in atrazine contaminated soil. [ABSTRACT FROM AUTHOR]

Ceftriaxone is an antibiotic that increases central nervous system (CNS) protein expression of the glutamate transporters GLT-1 and xCT and ameliorates pathological behaviors in rodent models of neurological disease and substance use disorder. However, little ceftriaxone passes through the blood–brain barrier, the CNS binding partner of ceftriaxone is unknown, and ceftriaxone does not consistently upregulate GLT-1 and xCT in cell culture. Ceftriaxone alters the gut microbiome composition in rodents and humans, and the microbiome–gut–brain axis regulates drug-seeking. Thus, here we test the hypothesis that ceftriaxone reduces alcohol intake while ameliorating alcohol-induced disruption of the gut microbiome composition. Male and female Sprague–Dawley rats received intermittent access to alcohol (IAA) while controls received access to only water. Following 17 IAA sessions, ceftriaxone/vehicle treatment was given for 5 days. Analysis of the gut microbiome composition was assessed by 16S rRNA gene amplicon sequencing conducted on fecal pellets collected prior to and after alcohol consumption and following ceftriaxone treatment. Male rats displayed escalated alcohol intake and preference over the course of the 17 sessions; however, total alcohol intake did not differ between the sexes. Ceftriaxone reduced alcohol intake and preference in male and female rats. While alcohol affected a diverse set of amplicon sequencing variants (ASV), ceftriaxone markedly reduced the diversity of microbial communities reflected by a blooming of the Enterococcaceae family. The remaining effects of ceftriaxone, however, encompassed families both affected and unaffected by prior alcohol drinking and highlight the Ruminococcaceae and Muribaculaceae families as bidirectionally modulated by alcohol and ceftriaxone. Altogether, our study confirms that ceftriaxone reduces alcohol intake in rats and partially reverses alcohol-induced dysbiosis. • Total amount of alcohol intake did not differ by sex. • Ceftriaxone reduced alcohol intake and preference in male and female rats. • Ceftriaxone markedly reduced the diversity of microbial communities. • Ceftriaxone partially reverses alcohol-induced dysbiosis. [ABSTRACT FROM AUTHOR]

This study examined the risk of intrauterine infection associated with radical trachelectomy (RT) in early‐stage cervical cancer patients. This procedure preserves fertility but is linked to increased risk of intrauterine infection due to cervical defects during pregnancy. DNA was extracted from the formalin‐fixed paraffin‐embedded (FFPE) placental specimens of 23 pregnant post‐RT patients and 16S rRNA gene sequencing was used for bacterial identification. The prevalence of Lactobacillus crispatus and Burkholderia stabilis was significantly higher in the non‐chorioamnionitis group. In contrast, alpha diversity analysis using the PD index showed significantly higher diversity in the chorioamnionitis group (P = 0.04). The demonstrated relationship between chorioamnionitis and microbial diversity affirms the importance of controlling the genital bacterial flora in pregnancies following RT. [ABSTRACT FROM AUTHOR]

The low-salt fermented shrimp pastes with 10% (w/w) salt addition were made using acetes chinensis as the substrates and Bacillus amyloliquefaciens Y11 and Bacillus velezensis Y12 as fermentation starter cultures to investigate the impact of Bacillus amyloliquefaciens Y11 and Bacillus velezensis Y12 on the quality and bacterial community diversity. Sensory evaluation, flavor analysis, MDA content, TVB-N value, and bacterial community were examined to compare the quality and microbial diversity changes of shrimp paste fermented using single-strain and mixed-strain fermentation methods. The results revealed that shrimp paste subjected to mixed-strain fermentation using two Bacillus strains exhibited higher sensory evaluation scores, color, and flavor assessment than the single-strain and natural fermentation shrimp paste. For the shrimp paste fermented with mixed Bacillus strains, the pH was between 7.5 and 8.0, and remained relatively stable throughout the fermentation process. The MDA content decreased from 0.98 mg/kg to 0.33 mg/kg with an increased fermentation time, and the lowest TVB-N value (33.32 mg/100 g) was observed after 10 days of fermentation. Amplicon sequencing of the fermented shrimp paste indicated the addition of starter cultures had a significant impact on the relative abundance of bacterial communities in the early stage of fermentation. At the end of fermentation, the relative abundance of Alkalibacterium, Atopistipes, Staphylococcus, and Tetragonococcus was relatively high in different groups. These findings provide a theoretical foundation for utilizing Bacillus strains as fermentation agents in producing shrimp paste and other related seafood products. [ABSTRACT FROM AUTHOR]

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Copyright of China Condiment is the property of China Condiment and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Obstacles related to the continuous cropping of sweet potatoes (Ipomoea batatas (L.) Lam.) restrict its intensive production. However, the effects of continuous cropping on soil properties and/or the rhizosphere microbial community are largely unclear. In this study, we analyzed changes in rhizosphere soil chemical properties and microbial communities of sweet potatoes across different cultivation years. We observed that the microbial diversity and complexity of the fungal ecological network in rhizosphere soils of sweet potatoes were decreased after 5 years of continuous cropping, with significant enrichment in Sphingobium, Gemmatimonas, Volutella, and Neoidriella. Tuber yield, soil pH, and available potassium (AK) content were significantly reduced after continuous cropping, with the soil microbial community having the highest correlation with pH, AK, and ammonium nitrogen (NH4+‐N). Specifically, soil pH and AK were positively correlated with Bacillus and Gaiella, and negatively correlated with some plant‐pathogenic fungi (Volutella and Neoidriella), while NH4+‐N showed the opposite trend. In addition, soil pH, AK, and the relative abundance of Bacillus were positively correlated with tuber yield, while Volutella showed the opposite trend. In summary, the continuous cropping of sweet potatoes negatively affects rhizosphere soil health, resulting in imbalanced soil fertility and an increased abundance of pathogens. These results improve our understanding of factors driving obstacles faced with the continuous cropping of sweet potatoes, enabling future studies and the development of technologies to overcome these obstacles. [ABSTRACT FROM AUTHOR]

The diversity of the microbial community structure plays a crucial role in the flavor and nutritional value of Shanxi aged vinegar in fermentation. Illumina Miseq high-throughput sequencing identified thirteen bacterial genera, with Lactobacillales (44.89%) and Acetobacter (21.04%) being the predominant species. Meanwhile, the fermentation characteristics of selected lactic acid bacteria strains isolated from Shanxi aged vinegar were studied in different media. The results showed that the biomass, and physical and chemical indices, as well as flavor compounds of the four strains of lactic acid bacteria in the simulated vinegar fermented grains medium were superior to those in barley and pea medium and sorghum juice medium. The bacterial interaction was conducted to investigate the effects on growth, the physicochemical indices, and flavor substances in order to determine the optimal combination. Furthermore, the interaction between pure cultures and co-cultures of lactic acid bacteria in a simulated vinegar culture medium was investigated, with a focus on the impact of this interaction on strain growth, fermentation characteristics, and flavor compound production. Compared with the pure culture, when strains L7 and L729 were co-inoculated, the reducing sugar content was 0.31 ± 0.01 g/100 g, total acid content was 3.02 ± 0.06 g/100 g, acetoin content was 2.41 ± 0.07 g/100 g, and total organic acid content was 3.77 ± 0.17 g/100 g. In terms of flavor compounds, the combined culture system exhibited higher levels of esters, aldehydes, and acids compared to pure cultures or other co-culture systems. This study revealed the fermentation characteristics of selected lactic acid strains in Shanxi aged vinegar under different conditions and their interaction in simulated vinegar fermentation media, which could provide theoretical support for the safety and health evaluation of aged vinegar. [ABSTRACT FROM AUTHOR]

Introduction: The Asian elephant (Elephas maximus) is a giant herbivore classified as an endangered wildlife species by the International Union for Conservation of Threatened Species. This study aims to investigate and compare the core gut microbiota of captive Asian elephants from three different locations in Yunnan Province, China, to explore the impact of environmental and husbandry factors on microbial diversity. Methods: We collected fecal samples from 29 captive Asian elephants from three locations and performed full-length 16S rRNA gene sequencing. Microbial diversity was assessed using alpha diversity (Chao1 and Shannon indexes) and beta diversity (Bray-Curtis and Euclidean distance metrics). Principal coordinate analysis (PCoA) was used to visualize microbial variation among groups. Results: Alpha diversity analysis showed that the microbial diversity in the Yexianggu group was higher than that in the other groups. Bray-Curtis and Euclidean metrics revealed significant differences among the microbial communities. Bacteroidetes and Firmicutes, which are key cellulose-degrading bacteria, were the dominant phyla in all groups. Synergistaceae was the most abundant family in the Menghai group, while Lachnospiraceae and Pirellulaceae were more abundant in the Yexianggu and Yuantongshan groups, respectively. Genus p-1008-a5-gut-group was more abundant in Yexianggu, and Prevotella was predominant in Menghai. Discussion: These results indicate that habitat and husbandry practices significantly influence the gut microbiota of captive Asian elephants. The identification of bacterial species such as Lactobacillus fermentum, Clostridium neonatale, Enterococcus mundtii, Klebsiella huaxiensis, Corynebacterium nasicanis, and Streptococcus equinus highlights the potential role of specific microbes in maintaining host-microbial interactions. Promoting microbial diversity through improved captive conditions could enhance the health of these endangered animals. [ABSTRACT FROM AUTHOR]

The present study investigated the effects of water extracts of Artemisia annua L. (WEAA) on rumen immune and antioxidative indexes, fermentation parameters and microbial diversity in lambs. A total of 32 3-month-old Dorper × Han female lambs having comparable body weights (24±0.09 kg) were selected and were randomly assigned to four treatments, with eight repetitions for each treatment. The basal diet, consisting of 45% concentrate and 55% forage, was solely provided to the control group. For the other treatment groups, the basal diet was supplemented with WEAA at dosages of 500, 1000, and 1500 mg/kg diet, respectively. Rumen tissue samples were collected for the analysis of immune and antioxidative parameters, as well as related gene expression. Rumen fluid samples were collected to assess rumen fermentation parameters on days 30 and 60 and to evaluate the microbiota on day 60. Results showed that WEAA supplementation linearly or quadratically increased the content of sIgA, IL-4, IL-2 and the gene expression level of MyD88, IκB-α, IL-4, COX-2, iNOS in rumen tissue (p < 0.05), as well as the bacteria negatively associated with IL-6 (g_ [Eubacterium] _cellulosolvens_group). Furthermore, the addition of WEAA linearly or quadratically increased rumen T-SOD, GSH-Px (p < 0.05) and the gene expression level of Nrf2, SOD2, GSH-Px, HO-1 (p < 0.05), and decreased the rumen concentration of malondialdehyde (MDA) and gene expression level of Keap1 (p < 0.05), as well as the bacteria positively associated with T-AOC, T-SOD and GSH-Px (g_Lachnospiraceae_NK3A20_group, g_Saccharofermentans, g__Marvinbryantia, g_unclassified_f_Eggerthellaceae). The supplementation of WEAA caused the concentration of microprotein (MCP), total volatile fatty acids (TVFA), propionate to increase either linearly or quadratically, while reducing the concentration of NH3-N and the acetate/propionate ratio (A:P) in rumen fluid (p < 0.05). The addition of WEAA linearly or quadratically increased the abundance of Actinobacteriota, Cyanobacteria and Lachnospiraceae_NK3A20_group (p < 0.10), and g__Lachnospiraceae_NK3A20_group, g_Saccharofermentans, g_Marvinbryantia, g_Bifidobacterium were significantly abundant as specific microflora in the 1000 mg/kg WEAA supplementation group. In conclusion, dietary inclusion of 1000 mg/kg WEAA improved the rumen immune function, antioxidant status, rumen fermentation, and composition of rumen microbes in lambs. [ABSTRACT FROM AUTHOR]

Introduction: The phenomenon in which the damage of plant diseases is suppressed by continuous cropping is defined as "suppressiveness" and the development of suppressive soils and key beneficial microorganisms have been identified through various previous studies. However, no studies have been conducted on microbial communities related to disease occurrence before the initial occurrence of diseases in crop monoculture. Methods: We aimed to investigate the ecological modifications of pathogen population density in soil, disease occurrence rate, and microbiota community shifting during ginseng monoculture to better understand the tripartite social relationships in the monoculture system. To achieve the study's objectives, a long-term monoculture of ginseng was established. The microbial diversity and community structure were analyzed using high-throughput sequencing, and the pathogen population density and disease occurrence rate were determined using qPCR and observation. Results and discussion: The results showed that the initial rhizosphere bacterial community of ginseng had already collapsed before the development of the root rot disease. The study also identified the crucial role of soil-borne pathogens in causing disease and the loss of initial keystone taxa populations in the early stages of monoculture. Our study revealed a novel aspect of soil microbiota dynamics during ginseng monoculture, with seven distinct microbes (Beijerinckiaceae, Comamonadaceae, Devosiaceae, Rhizobiaceae, Sphingobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae) participating in soil nitrogen metabolism as an 'initial community' that regulates root rot disease through nutritional competition. The findings contribute to ecological research on disease-suppressiveness soil, disease management, and sustainable agriculture. [ABSTRACT FROM AUTHOR]

Prokaryotes play a crucial role in marine ecosystem health and drive biogeochemical processes. The northern Ninety East Ridge (NER) of the Indian Ocean, a pivotal yet understudied area for these cycles, has been the focus of our study. We employed high-throughput 16S rRNA gene sequencing to analyze 35 water samples from five stations along the ridge, categorized into three depth- and dissolved oxygen-level-based groups. Our approach uncovered a clear stratification of microbial communities, with key bioindicators such as Prochlorococcus MIT9313, Sva0996 marine group, and Candidatus Actinomarina in the upper layer; Ketobacter, Pseudophaeobacter, Nitrospina, and SAR324 clade in the middle layer; and Methylobacterium-Methylorubrum, Sphingomonas, Sphingobium, and Erythrobacter in the deep layer. Methylobacterium-Methylorubrum emerged as the most abundant bacterial genus, while Nitrosopumilaceae predominated among archaeal communities. The spatial and depth-wise distribution patterns revealed that Ketobacter was unique to the northern NER, whereas Methylobacterium-Methylorubrum, UBA10353, SAR324 clade, SAR406, Sva0996_marine_group, Candidatus Actinomarina were ubiquitous across various marine regions, exhibiting niche differentiation at the OTU level. Environmental factors, especially dissolved oxygen (DO), silicate, nitrate, and salinity, significantly influence community structure. These findings not only reveal the novelty and adaptability of the microbial ecosystem in the northern NER but also contribute to the broader understanding of marine microbial diversity and its response to environmental heterogeneity. [ABSTRACT FROM AUTHOR]

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Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems. [ABSTRACT FROM AUTHOR]