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To understand insect abundance, distribution and dynamics, we need to understand the relevant drivers of their populations and communities. While microbial symbionts are known to strongly affect many aspects of insect biology, we lack data on their effects on populations or community processes, or on insects' evolutionary responses at different timescales. How these effects change as the anthropogenic effects on ecosystems intensify is an area of intense research. Recent developments in sequencing and bioinformatics permit cost-effective microbial diversity surveys, tracking symbiont transmission, and identification of functions across insect populations and multi-species communities. In this review, we explore how different functional categories of symbionts can influence insect life-history traits, how these effects could affect insect populations and their interactions with other species, and how they may affect processes and patterns at the level of entire communities. We argue that insect-associated microbes should be considered important drivers of insect response and adaptation to environmental challenges and opportunities. We also outline the emerging approaches for surveying and characterizing insect-associated microbiota at population and community scales. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'. [ABSTRACT FROM AUTHOR]

Background: Optimum planting date and appropriate fertilizer module are essential facets of chrysanthemum cultivation, to enhance quality yield, and improve soil health. A field-based study was undertaken over multiple growing seasons in 2022 and 2023, where six different planting dates, viz., P1:June 15, P2:June 30, P3:July 15, P4:July 30, P5:August 15 and P6:August 30 and two fertilizer modules, FM1:Jeevamrit @ 30 ml plant−1 and FM2:NPK @ 30 g m−2 were systematically examined using a Randomized Block Design (factorial), replicated thrice. Results: P6 planting resulted in early bud formation (44.03 days) and harvesting stage (90.78 days). Maximum plant height (79.44 cm), plant spread (34.04 cm), cut stem length (68.40 cm), flower diameter (7.83 cm), stem strength (19.38˚), vase life (14.90 days), flowering duration (24.08 days), available soil N (314 kg ha−1), available P (37 kg ha−1), available K (347 kg ha−1), bacterial count (124.87 × 107 cfu g−1 soil), actinomycetes count (60.72 × 102 cfu g−1 soil), fungal count (30.95 × 102 cfu g−1 soil), microbial biomass (48.79 µg g−1 soil), dehydrogenase enzyme (3.64 mg TPF h−1 g−1 soil) and phosphatase enzyme (23.79 mol PNP h−1 g−1 soil) was recorded in P1 planting. Among the fertilization module, minimum days to bud formation (74.94 days) and days to reach the harvesting stage (120.95 days) were recorded with the application of NPK @30 g m−2. However, maximum plant height (60.62 cm), plant spread (23.10 cm), number of cut stems m−2 (43.88), cut stem length (51.34 cm), flower diameter (6.92 cm), stem strength (21.24˚), flowering duration (21.75 days), available soil N (317 kg ha−1), available P (37 kg ha−1) and available K (349 kg ha−1) were also recorded with the application of NPK @300 kg ha−1. Maximum vase life (13.87 days), OC (1.13%), bacterial count (131.65 × 107 cfu g−1 soil), actinomycetes count (60.89 × 102 cfu g−1 soil), fungal count (31.11 × 102 cfu g−1 soil), microbial biomass (51.27 µg g−1 soil), dehydrogenase enzyme (3.77 mg TPF h−1 g−1 soil) and phosphatase enzyme (21.72 mol PNP h−1 g−1 soil) were observed with the application of Jeevamrit @ 30 ml plant−1. Conclusion: Early planting (P1) and inorganic fertilization (NPK @ 30 g m−2) resulted in improved yield and soil macronutrient content. The soil microbial population and enzymatic activity were improved with the jeevamrit application. This approach highlights the potential for improved yield and soil health in chrysanthemum cultivation, promoting a more eco-friendly and economically viable agricultural model. [ABSTRACT FROM AUTHOR]

The purpose of the current study was to evaluate the impact of various doses of microencapsulated lemongrass and mangosteen peel (MELM) on gas dynamics, rumen fermentation, degradability, methane production, and microbial population in in vitro gas experiments. With five levels of microencapsulated-phytonutrient supplementation at 0, 1, 2, 3, and 4% of substrate, 0.5 g of roughage, and a concentrate ratio of 60:40, the trial was set up as a completely randomized design. Under investigation, the amount of final asymptotic gas volume was corresponding responded to completely digested substrate (b) increased cubically as a result of the addition of MELM (P < 0.01) and a cubic rise in cumulative gas output. The amount of MELM form did not change the pH and NH3-N concentration of the rumen after 12 and 24 h of incubation. However, methane production during 24 h of incubation, the levels were cubically decreased with further doses of MELM (P < 0.01) at 12 h of incubation. Increasing the dosage of MELM supplementation at 2% DM resulted in a significant increase in the digestibility of in vitro neutral detergent fiber (IVNDF) and in vitro true digestibility (IVTD) at various incubation times (P < 0.05), but decreased above 3% DM supplementations. Moreover, the concentration of propionic acid (C3) exhibited the variations across the different levels of MELM (P < 0.05), with the maximum concentration obtained at 2% DM. The populations of Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens, and Megasphaera elsdenii revealed a significant increase (P < 0.05), while the quantity of Methanobacteriales decreased linearly with increasing doses of MELM. In conclusion, the inclusion of MELM at a concentration of 2% DM in the substrate which could enhance cumulative gas production, NDF and true digestibility, C3 production, and microbial population, while reducing methane concentration and Methanobacterial abundance. [ABSTRACT FROM AUTHOR]

We review the process of reconstructing genome-scale metabolic models (GEMs) for single species and microbial communities. We present a detailed compendium of model-building platforms for experts and non-experts. We review and compare the approaches for testing GEMs towards engineering microbial systems. We discuss current challenges and future directions in model development, including the need for standards in microbial community models. Genome-scale metabolic models (GEMs) are consolidating as platforms for studying mixed microbial populations, by combining biological data and knowledge with mathematical rigor. However, deploying these models to answer research questions can be challenging due to the increasing number of available computational tools, the lack of universal standards, and their inherent limitations. Here, we present a comprehensive overview of foundational concepts for building and evaluating genome-scale models of microbial communities. We then compare tools in terms of requirements, capabilities, and applications. Next, we highlight the current pitfalls and open challenges to consider when adopting existing tools and developing new ones. Our compendium can be relevant for the expanding community of modelers, both at the entry and experienced levels. [ABSTRACT FROM AUTHOR]

Multiple diseases can decrease levels and changes in gut microbial populations, while increasing microbiota diversity causes an increase in the immune response. Evidence shows that exercise can affect the gut microbiota and, subsequently, the health of individuals. Also, regular exercise provides many benefits for health, protection against the spread of chronic diseases, and improved quality of life. Exercise can increase the number of helpful microbiota species, enrich microflora diversity, and improve the growth of commensal microbiota. This article reviews recent findings on the interaction of gut microbiota and exercise. Also, another purpose of this research is to suggest different mechanisms that using them can provide the way that the exercise factor can change the gut microbiota. [ABSTRACT FROM AUTHOR]

This review scrutinizes the intricate interplay between the microbiome and the human body, exploring its multifaceted dimensions and far-reaching implications. The human microbiome, comprising diverse microbial communities inhabiting various anatomical niches, is increasingly recognized as a critical determinant of human health and disease. Through an extensive examination of current research, this review elucidates the dynamic interactions between the microbiome and host physiology across multiple organ systems. Key topics include the establishment and maintenance of microbiota diversity, the influence of host factors on microbial composition, and the bidirectional communication pathways between microbiota and host cells. Furthermore, we delve into the functional implications of microbiome dysbiosis in disease states, emphasizing its role in shaping immune responses, metabolic processes, and neurological functions. Additionally, this review discusses emerging therapeutic strategies aimed at modulating the microbiome to restore host–microbe homeostasis and promote health. Microbiota fecal transplantation represents a groundbreaking therapeutic approach in the management of dysbiosis-related diseases, offering a promising avenue for restoring microbial balance within the gut ecosystem. This innovative therapy involves the transfer of fecal microbiota from a healthy donor to an individual suffering from dysbiosis, aiming to replenish beneficial microbial populations and mitigate pathological imbalances. By synthesizing findings from diverse fields, this review offers valuable insights into the complex relationship between the microbiome and the human body, highlighting avenues for future research and clinical interventions. [ABSTRACT FROM AUTHOR]

In the ongoing battle against antimicrobial resistance, phenotypic drug tolerance poses a formidable challenge. This adaptive ability of microorganisms to withstand drug pressure without genetic alterations further complicating global healthcare challenges. Microbial populations employ an array of persistence mechanisms, including dormancy, biofilm formation, adaptation to intracellular environments, and the adoption of L-forms, to develop drug tolerance. Moreover, molecular mechanisms like toxin-antitoxin modules, oxidative stress responses, energy metabolism, and (p)ppGpp signaling contribute to this phenomenon. Understanding these persistence mechanisms is crucial for predicting drug efficacy, developing strategies for chronic bacterial infections, and exploring innovative therapies for refractory infections. In this comprehensive review, we dissect the intricacies of drug tolerance and persister formation, explore their role in acquired drug resistance, and highlight emerging therapeutic approaches to combat phenotypic drug tolerance. Furthermore, we outline the future landscape of interventions for persistent bacterial infections. • Phenotypic drug tolerance and its significance for healthcare challenges. • Diverse active molecular mechanisms involved in drug tolerance. • Extending concept of persistence beyond bacteria to fungi, parasites, and cancer. • Evolutionary significance of phenotypic drug tolerance in acquired drug resistance. • Evolving therapies for persistent infections and future landscape of interventions. [ABSTRACT FROM AUTHOR]

Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome-assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750-m deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon-fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin–Benson–Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1–10 mM. However, out of all the active carbon-fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon. [ABSTRACT FROM AUTHOR]

Simple Summary: The development of the sheep industry plays an important role in increasing the income of farmers and herdsmen and promoting rural revitalization. Genetic improvement is the key to improving the competitiveness of the sheep industry. Tianhua mutton sheep, as China's first mutton fine wool sheep adapted to alpine pastures, have a key advantage over Gansu alpine fine wool sheep in terms of adaptive ability. In order to show the differences in rumen development and microbial structure between Tianhua mutton sheep and Gansu alpine fine wool sheep, the present study was conducted to comprehensively investigate the rumen of the two types of fine wool sheep by Hematoxylin Eosin (H&E) staining, volatile fatty acids (VFAs) assay, and full-length sequencing of 16S rRNA. The results showed that Tianhua mutton sheep had a better performance in the rumen volatile fatty acid content, rumen tissue development, and rumen microorganisms compared with Gansu alpine fine wool sheep, and this study provided a good theoretical explanation for the better adaptation of Tianhua mutton sheep to alpine pastures compared with Gansu alpine fine wool sheep. The purpose of this experiment was to investigate the differences in rumen tissue morphology, volatile fatty acid content, and rumen microflora between Tianhua mutton sheep and Gansu alpine fine wool sheep under the same grazing conditions. Twelve 30-day-old lambs were randomly selected from two different flocks in Duolong Village and grazed together for a period of 150 days. The rumen tissue was fixed with 4% paraformaldehyde and brought back to the laboratory for H&E staining, the volatile fatty acid content of the rumen contents was detected by gas chromatography, and the rumen flora structure was sequenced by full-length sequencing of the bacterial 16S rRNA gene using the PacBio sequencing platform. The acetic acid and total acid contents of the rumen contents of Tianhua mutton sheep were significantly higher than those of Gansu alpine fine wool sheep (p < 0.05). The rumen papillae height of Tianhua mutton sheep was significantly higher than that of Gansu alpine fine wool sheep (p < 0.05). The diversity and richness of the rumen flora of Tianhua mutton sheep were higher than those of Gansu alpine fine wool sheep, and Beta analysis showed that the microflora structure of the two fine wool sheep was significantly different. At the phylum level, Firmicutes and Bacteroidetes dominated the rumen flora of Tianhua mutton sheep and Gansu alpine fine wool sheep. At the genus level, the dominant strains were Christensenellaceae_R_7_group and Rikenellaceae_RC9_gut_group. LEfSe analysis showed that Prevotella was a highly abundant differential species in Tianhua mutton sheep and lachnospiraccac was a highly abundant differential species in Gansu alpine fine wool sheep. Finally, both the KEGG and COG databases showed that the enrichment of biometabolic pathways, such as replication and repair and translation, were significantly higher in Tianhua mutton sheep than in Gansu alpine fine wool sheep (p < 0.05). In general, there were some similarities between Tianhua mutton sheep and Gansu alpine fine wool sheep in the rumen tissue morphology, rumen fermentation ability, and rumen flora structure. However, Tianhua mutton sheep had a better performance in the rumen acetic acid content, rumen papillae height, and beneficial bacteria content. These differences may be one of the reasons why Tianhua mutton sheep are more suitable for growing in alpine pastoral areas than Gansu alpine fine wool sheep. [ABSTRACT FROM AUTHOR]

Simple Summary: Dragon fruit peel polyphenolic extract is a potential ruminal modulator endorsed by consumers for its inherent safety and acceptability. This in vitro study demonstrated that dragon fruit peel polyphenolic extract increased the concentration of volatile fatty acids in the rumen, reduced gas production, and enhanced the rumen bacterial abundances. These findings suggest that dragon fruit peel polyphenol extract has the potential to improve ruminal fermentation of sika deer and provides a theoretical basis for dragon fruit peel polyphenol extract to be used as a functional feed additive for Sika deer. The aim of this study is to investigate the effect of dragon fruit peel polyphenolic extract (DFPE) on gas production, rumen fermentation, and bacterial communities in sika deer using an in vitro technique. Three treatments with different DFPE levels (DFPE0, base diet; DFPE5, base diet + 5 mg/g DFPE; DFPE10, base diet + 10 mg/g DFPE, respectively; n = 6) were implemented. The phenolic composition of DFPE, gas production (GP), ammonia nitrogen (NH3-N), volatile fatty acid (VFA), and bacteria communities was evaluated after 24 h of incubation. The results showed that GP and NH3-N were reduced by DFPE supplementation. Total VFA, isovaleric acid, and valeric acid were increased (p < 0.05) by the addition of DFPE. No changes (p > 0.05) were observed in pH, acetic acid, propionic acid, isobutyric acid, butyric acid, and the ratio of acetic acid to propionic acid. Additionally, the alpha indexes, including Sobs, Shannon, and Ace, were increased by DFPE supplementation. Moreover, at the phylum level, DFPE supplementation increased (p = 0.01) Bacteroidota but reduced (p < 0.01) Firmicutes. At the genus level, compared to DFPE0, the DFPE10 had increased relative abundances of Rikenellaceae_RC9_gut_group (p < 0.01), norank_f_Muribaculaceae (p = 0.01), Lachnospiraceae_NK3A20_group (p < 0.01), Christensenellaceae_R-7_group (p < 0.01), and NK4A214_group (p < 0.01), decreased relative abundances of Streptococcus (p < 0.01), Oribacterium (p = 0.01), and Enterococcus (p < 0.01). Compared to DFPE0, DFPE5 had no change (p > 0.05) in all bacteria at the genus level except for decreased relative abundance of Enterococcus (p < 0.01). These results indicated that DFPE may be able to be used as a feed additive to enhance fermentation parameters and improve ruminal bacteria communities in Sika deer. [ABSTRACT FROM AUTHOR]

In order to maintain a healthy soil, organic farming (OF) and natural farming (NF) should be practiced in addition to conventional farming. In order to evaluate soil fertility and productivity, a field experiment was conducted to study the microbial populations, dehydrogenase activities and biomass carbon in rhizosphere soils of cabbage under different farming systems over two years. Generally, microbial populations are expressed as colony forming units (CFU). Significantly higher microbial populations such as bacteria (34.15 × 106 CFU g−1of soil), fungi (19.08 × 103 CFU g−1of soil), actinomycetes (20.18 × 104 CFU g−1of soil), phosphate solubilizing microorganisms (11.45 × 104 CFU g−1of soil) and nitrogen fixers (14.78 × 104 CFU g−1of soil) were observed in rhizosphere soils after harvest of cabbage in organic farming followed by natural farming treatment. Dehydrogenase activity and microbial biomass carbon were significantly higher under organic farming. Lower microbial populations, dehydrogenase activity and microbial biomass carbon were found in conventional farming practices. It is concluded that application of organic farming inputs farm yard manure (FYM) and natural farming inputs, i.e. liquid organic manure (jeevamrutha), solid organic manure (ghanajeevamrutha) enhanced the soil microflora, dehydrogenase activity and microbial biomass carbon activities when compared to the conventional farming system. [ABSTRACT FROM AUTHOR]

Cooperation via shared public goods is ubiquitous in nature, however, noncontributing social cheaters can exploit the public goods provided by cooperating individuals to gain a fitness advantage. Theory predicts that this dynamic can cause a Tragedy of the Commons, and in particular, a 'Collapsing' Tragedy defined as the extinction of the entire population if the public good is essential. However, there is little empirical evidence of the Collapsing Tragedy in evolutionary biology. Here, we experimentally demonstrate this outcome in a microbial model system, the public good-producing bacterium Pseudomonas aeruginosa grown in a continuous-culture chemostat. In a growth medium that requires extracellular protein digestion, we find that P. aeruginosa populations maintain a high density when entirely composed of cooperating, protease-producing cells but completely collapse when non-producing cheater cells are introduced. We formulate a mechanistic mathematical model that recapitulates experimental observations and suggests key parameters, such as the dilution rate and the cost of public good production, that define the stability of cooperative behavior. We combine model prediction with experimental validation to explain striking differences in the long-term cheater trajectories of replicate cocultures through mutational events that increase cheater fitness. Taken together, our integrated empirical and theoretical approach validates and parametrizes the Collapsing Tragedy in a microbial population, and provides a quantitative, mechanistic framework for generating testable predictions of social behavior. [ABSTRACT FROM AUTHOR]

The objective of present research is to evaluate the changes in the chemical, microbial, and biogenic amines in Persian fish sauce (Mahyaveh) during 40 days of fermentation. In the current survey, the parameters of salt percentage, pH, total nitrogen concentration, amino nitrogen concentration, Brix, color features, cadaverine, and histamine concentration were measured in the fish sauce. The amino nitrogen content, total protein, Brix, and salt were increased along with the progression of fermentation process. The microbial population of Mahyaveh sauce demonstrated that lactic acid bacteria (LAB), total bacterial count, and Enterobacteriaceae decreased during fermentation. The population of lactic acid bacteria and the total count of bacteria were around one logarithmic cycle lower in the presence of 10% salt than under low salt conditions. Histamine and cadaverine concentrations increased to 43.49 and 42.76 mg/kg during the fermentation period, respectively. As a result, the population density of histamine‐producing bacteria rose from 3.00 log CFU/mL at the beginning to 4.58 log CFU/mL at the end of process. The population density of cadaverine‐producing bacteria was 3.43 and 5.24 log CFU/mL on the 20th and 40th days of fermentation, respectively. Sensory evaluation results indicated that our sample of fish sauce had an overall acceptability score of 5.1 (good). On the other hand, Principal Component Analysis (PCA) demonstrated a positive correlation between the most of chemical parameters and the fermentation period. The concentration of cadaverine and histamine has a positive association with the pH and type of bacteria producing the biogenic amines. [ABSTRACT FROM AUTHOR]

In order to evaluate the effect of Artemisia sieberi extract from different habitats on the shelf life of Iranian white cheese, this research was conducted in 2022 in the research laboratory of Qom University, Iran. A factorial experiment was conducted based the completely randomized design, and cheese in terms of chemical and microbial characteristics in the conditions of no extract (control) and the use of extract containing 1% of the weight of the fresh material of A. sieberi from three habitats of Venan, Tajkhatun and Abbas Abad was checked on the 1st, 1 5 th and 30th. The results showed that the population of cheese microorganisms increased with the increase of the storage period, and the extract of Venan better controlled the population of microorganisms than other extracts. The amount of pH and protein in the dry matter decreased with the increase of the storage period, and the amount of moisture, salt, fat, dry matter, phenol and antioxidant activity increased. Venan extract increased the quality and shelf life of cheese more than other extracts, which may be due to the higher amount of total phenol in Venan extract compared to other extracts. In general, the extract of Artemisia sieberi significantly increased the shelf life and quality of cheese, and with further studies, the extract of this valuable plant can be used to increase the shelf life and quality of food products, especially dairy products. [ABSTRACT FROM AUTHOR]

Metagenomics has now evolved as a promising technology for understanding the microbial population in the environment. By metagenomics, a number of extreme and complex environment has been explored for their microbial population. Using this technology, researchers have brought out novel genes and their potential characteristics, which have robust applications in food, pharmaceutical, scientific research, and other biotechnological fields. A sequencing platform can provide a sequence of microbial populations in any given environment. The sequence needs to be analysed computationally to derive meaningful information. It is presumed that only bioinformaticians with extensive computational skills can process the sequencing data till the downstream end. However, numerous open-source software and online servers are available to analyse the metagenomic data developed for a biologist with less computational skills. This review is focused on bioinformatics tools such as Galaxy, CSI-NGS portal, ANASTASIA and SHAMAN, EBI- metagenomics, IDseq, and MG-RAST for analysing metagenomic data. [ABSTRACT FROM AUTHOR]

Insects harbor a remarkable diversity of gut microbiomes critical for host survival, health, and fitness, but the mechanism of this structured symbiotic community remains poorly known, especially for the insect group consisting of many closely related species that inhabit the Qinghai‐Tibet Plateau. Here, we firstly analyzed population‐level 16S rRNA microbial dataset, comprising 11 Parnassius species covering 5 subgenera, from 14 populations mostly sampled in mountainous regions across northwestern‐to‐southeastern China, and meanwhile clarified the relative importance of multiple factors on gut microbial community structure and evolution. Our findings indicated that both host genetics and larval host plant modulated gut microbial diversity and community structure. Moreover, the effect analysis of host genetics and larval diet on gut microbiomes showed that host genetics played a critical role in governing the gut microbial beta diversity and the symbiotic community structure, while larval host plant remarkably influenced the functional evolution of gut microbiomes. These findings of the intimate insect–microbe–plant interactions jointly provide some new insights into the correlation among the host genetic background, larval host plant, the structure and evolution of gut microbiome, as well as the mechanisms of high‐altitude adaptation in closely related species of this alpine butterfly group. [ABSTRACT FROM AUTHOR]

Soil amendment with biochar from oil palm biomass has been found to improve the quality of the infertile weathered soils and enhance crop productivity in the humid tropics. Meanwhile, the field information on microbial responses to oil palm-derived biochar application and its residual effect in acidic tropical soils is still limited. A field study was carried out over three cropping cycles of sweet corn on a Haplic Acrisol of Peninsular Malaysia. The soil was amended once with oil palm kernel shell (OPKS) biochar before the first cropping cycle, with or without inorganic fertiliser. Soil samples were taken at each harvesting stage and analysed for soil pH, cation exchange capacity (CEC), organic C, total N, available P, microbial biomass (C (MBC), N (MBN), and P (MBP)). Microbial biomass ratios (MBC : MBN, MBC : MBP) were calculated. The total bacterial and fungal populations were quantified from soil genomic DNA, employing qPCR amplification of the 16S rDNA and ITS gene. The sole application of biochar and its combined application with fertiliser, increased soil pH, CEC, organic C and N. Coapplication of OPKS biochar and NPK fertiliser hindered N loss in the second cycle. The bacterial and fungal abundance was stimulated following biochar treatment majorly due to the elevation of soil pH and CEC. The ratio of MBC : MBN had a significant negative correlation with N, signifying that this ratio could reflect soil N content and be used as a soil fertility indicator. [ABSTRACT FROM AUTHOR]

Lactic acid bacteria (LAB) are probiotic bacteria that have many health benefits. The aim of study was to determinate LAB from traditional cheeses (Gedebey, Ivanovka, Karabakh) consumed in Azerbaijan. The microbial content and loading of three traditional samples were explored using counting methods and a culture-independent approach. The average count of total bacteria in both of samples ranged between 105 and 107 cfu/g. In all samples, aerobic bacteria and lactic acid bacteria were more >4.9 × 105 cfu/g. The V3-V4 region of 16S rDNA was amplified from total DNA extracted from traditional cheese samples and microbial communities and lactic acid bacteria were determined. In general, the diversity of microbial populations in cheese samples were Lactobacillus, Lactococcus, Streptococcus. Among the three samples, Gedebey sample showed the highest richness. Obtained data can be use in the food industry. In addition, lactic acid bacteria analysis could help the determination of potential strains for traditional cheese production. In conclusion, determination and identification of LAB strains in traditional cheeses will reveal the traditional food microbiota and will help to find potential probiotic bacteria for health and industry. [ABSTRACT FROM AUTHOR]

• Fe 2 O 3 and TiO 2 NPs restrained As(V) release, and stimulated As(III) release. • The released As co-precipitated with Fe after Fe 2 O 3 NPs addition. • The released As adsorbed on TiO 2 NPs after TiO 2 NPs addition. • NPs additions changed the relative abundance of soil bacterial community. • NPs additions had a negative impact on soil microbial population in a long term. Environmental effects of nano remediation engineering of arsenic (As) pollution need to be considered. In this study, the roles of Fe 2 O 3 and TiO 2 nanoparticles (NPs) on the microbial mediated As mobilization from As contaminated soil were investigated. The addition of Fe 2 O 3 and TiO 2 NPs restrained As(V) release, and stimulated As(III) release. As(V) concentration decreased by 94% and 93% after Fe 2 O 3 addition, and decreased by 89% and 45% after TiO 2 addition compared to the Biotic and Biotic+Acetate (amended with sodium acetate) controls, respectively. The maximum values of As(III) were 20.5 and 27.1 µg/L at 48 d after Fe 2 O 3 and TiO 2 NPs addition, respectively, and were higher than that in Biotic+Acetate control (12.9 µg/L). The released As co-precipitated with Fe in soils in the presence of Fe 2 O 3 NPs, but adsorbed on TiO 2 NPs in the presence of TiO 2 NPs. Moreover, the addition of NPs amended with sodium acetate as the electron donor clearly promoted As(V) reduction induced by microbes. The NPs addition changed the relative abundance of soil bacterial community, while Proteobacteria (42.8%-70.4%), Planctomycetes (2.6%-14.3%), and Firmicutes (3.5%-25.4%) were the dominant microorganisms in soils. Several potential As/Fe reducing bacteria were related to Pseudomonas, Geobacter, Desulfuromonas , and Thiobacillus. The addition of Fe 2 O 3 and TiO 2 NPs induced to the decrease of arrA gene. The results indicated that the addition of NPs had a negative impact on soil microbial population in a long term. The findings offer a relatively comprehensive assessment of Fe 2 O 3 and TiO 2 NPs effects on As mobilization and soil bacterial communities. [Display omitted] [ABSTRACT FROM AUTHOR]

Romaine lettuce outer leaves, as opposed to the more commonly marketed heart, are typically discarded and present an opportunity for upcycling as dried powders. Duquesne Romaine lettuce was evaluated to quantify and compare quality attributes of fresh outer and heart leaves, dried powders following hot air drying, and dried powders following an infrared (IR) blanching pretreatment before drying. Attributes measured for fresh leaves included moisture, water activity (Aw), color, total soluble phenolics (TSP), and antioxidant capacity (AC). Drying kinetics and time/energy saving through IR blanching were evaluated. Attributes measured for dried powders included moisture, Aw, color, true density, water vapor isotherms, TSP, AC, cadmium (Cd) content, and pesticide residues. TSP, AC, Cd, and pesticide residues were higher, whereas moisture content and Aw were lower in fresh outer versus heart leaves. Hot air drying reduced TSP and AC to 63.6% and 35.2% of fresh values, respectively, whereas IR blanching further reduced TSP and AC to 37.3% and 25.4% in outer leave powders. On the other hand, TSP and AC increased 237% and 151%, respectively, for unblanched heart powders. Higher increase of TSP than AC in heart leaf powder may indicate synthesis of phenolic compounds activated by abiotic stresses such as cutting and high temperatures at the initial drying stage. IR blanching resulted in significant time/energy savings for drying of outer leaves. Microbial loads were substantially reduced during drying, although microbial population on outer leaves were more resistant. Safe to eat outer leaf Romaine lettuce powders can be produced, assuming appropriate agricultural practices. [ABSTRACT FROM AUTHOR]

Renal cell carcinoma (RCC) accounts for about 2% of cancer diagnoses and deaths worldwide. Recent studies emphasized the critical involvement of microbial populations in RCC from oncogenesis, tumor growth, and response to anticancer therapy. Microorganisms have been shown to be involved in various renal physiological and pathological processes by influencing the immune system function, metabolism of the host and pharmaceutical reactions. These findings have extended our understanding and provided more possibilities for the diagnostic or therapeutic development of microbiota, which could function as screening, prognostic, and predictive biomarkers, or be manipulated to prevent RCC progression, boost anticancer drug efficacy and lessen the side effects of therapy. This review aims to present an overview of the roles of microbiota in RCC, including pertinent mechanisms in microbiota-related carcinogenesis, the potential use of the microbiota as RCC biomarkers, and the possibility of modifying the microbiota for RCC prevention or treatment. According to these scientific findings, the clinical translation of microbiota is expected to improve the diagnosis and treatment of RCC. [ABSTRACT FROM AUTHOR]

Anaerobic ammonium oxidation (anammox) is a promising and efficient biological nitrogen removal process, which can economically treat wastewater without organic supplement and aeration. However, to date, the insufficient nitrite in wastewater is the foremost problem encountered in anammox process. This restriction hinders full-scale application of anammox worldwide. Nitrite can be provided by innovative processes such as autotrophic denitrification and denitrifying anaerobic methane oxidation (DAMO). Therefore, the synergy between them and anammox is feasible means to solve the bottleneck. This review unravels the advantages and operating strategies of autotrophic denitrification, DAMO and their coupled processes with anammox. Besides, different electron donors such as reductive sulfur, iron, hydrogen, manganese and methane are analyzed in the two processes. The characteristics of microbial populations and their synergies in microbial communities are deciphered, and nitrogen removal contributions through different microbes are also highlighted. Still, nitrogen conversion pathways are clarified in the processes with different electron donors, and metabolic mechanisms of both autotrophic denitrifiers and DAMO microbes are revealed. Finally, the challenges to be focused in autotrophic denitrification and DAMO processes are proposed, and future perspectives on their coupled process with anammox are also put forward. [ABSTRACT FROM AUTHOR]

The present study assessed the influence of the preceding crop (crotalaria or corn) on the bromatological, digestibility and microbiological aspects of the EMBRAPA 139 black oat hay (Avena strigosa) cultivar. A randomized block design was used, with subplots divided according to time, whereby the preceding crop (crotalaria or corn) was allocated to the main plot and hay storage times (baling, 30, 60 and 90 days of storage) to the subplots, with five repetitions. Crotalaria as predecessor resulted in lower indigestible fiber and higher protein contents in black oat hay, both in acid detergent, as well as higher pH. Corn as the preceding crop provided better hay digestibility due to lower neutral detergent insoluble protein content and higher in vitro neutral detergent fiber digestibility. The preceding crop did not significantly affect the drying time of forage and the microorganism population. [ABSTRACT FROM AUTHOR]

Physiological and metabolic behavior of photoheterotrophic mixed cultures (PHMCs), monocultures of Rhodopseudomonas palustris , Clostridium pasteurianum and Syntrophomonas wolfei and a designed microbial consortium (DMC), consisting of these microorganisms that emulates natural consortia were studied. Growing and photoheterotrophic nongrowing conditions to simulate the use of dark fermentative effluents were used. Under growing conditions, C. pasteurianum showed higher bioH 2 production (8.5 mmol) and molar bioH 2 yield (21 mmoLH 2 /gCOD), while R. palustris did not produce this gas. Under nongrowing conditions, DMC reached the highest bioH 2 production (10 mmol) and bioH 2 yield (78.6 mmoLH 2 /gCOD) together with Poly-hydroxy-alkanoates (PHA), followed for PHMC-C2 (7.5; 59.6) and the monocultures. Higher bioH 2 and PHA production of the PHMC and the DMC suggest that these conditions promote the use of nonconventional energy pathways, and interactions among microbial populations that allow for the survival and sustain bioH 2 production. This study forms the basis for more in-depth studies of the metabolic behavior of photosynthetic natural and designed cultures. [Display omitted] • Metabolic behavior of natural and designed photoheterotrophic cultures was evaluated. • Nongrowing conditions promote the highest bioH 2 production in microbial consortia. • Microbial interactions allow for the survival and sustain bioH 2 production. • BioH 2 and PHA production are involved in the metabolic energy conservation. • Feasibility of design a microbial community for high bioH 2 production was demonstrated. [ABSTRACT FROM AUTHOR]

Inflammatory bowel disease (IBD) is one of the most prevalent chronic inflammations of the gastrointestinal tract (GIT). The gut microbial population, the cytokine milieu, the aryl hydrocarbon receptor (AHR) expressed by immune and nonimmune cells and the intrinsic pathway of Th-cell differentiation are implicated in the immunopathology of IBD. AHR activation requires a delicate balance between regulatory and effector T-cells; loss of this balance can cause local gut microbial dysbiosis and intestinal inflammation. Thus, the study of the gut microbiome in association with AHR provides critical insights into IBD pathogenesis and interventions. This review will focus on the recent advancements to form conceptional frameworks on the benefits of AHR activation by commensal gut bacteria in IBD. [ABSTRACT FROM AUTHOR]

In Japan, Japanese Black cattle, known for their exceptional meat quality owing to their abundant intramuscular fat, undergo a unique three-stage feeding system with varying concentrate ratios. There is limited research on physiological and rumen microbial changes in Japanese Black cattle during these stages. Therefore, this study aimed to examine Japanese Black steers in these three stages: early (T1, 12–14 months), middle (T2, 15–22 months), and late (T3, 23–30 months). The rumen bacteria of 21 cattle per phase was analyzed using 16S rRNA gene sequencing. Rumen bacterial diversity was significantly higher in T1, with a distinct distribution, than in T2 and T3. Specific phyla and genera were exclusive to each stage, reflecting the shifts in feed composition. Certain genera dominated each stage: T1 had Flexilinea, Streptococcus, Butyrivibrio, Selenomonas, and Kandleria; T2 had Bifidobacterium, Shuttleworthia, and Sharpea; and T3 had Acetitomaculum, Mycoplasma, Atopobium, and Howardella. Correlation analysis revealed significant associations between certain microbial populations and physiological parameters. These findings indicate that changes in energy content and feed composition are associated with physiological and ruminal alterations. This study may guide strategies to improve rumen health and productivity in Japanese Black cattle by modifying diets to specific fattening stages. [ABSTRACT FROM AUTHOR]

This study investigated the effects of additives on fermentation quality, in vitro digestibility and microbial communities of Korshinsk peashrub (Caragana korshinskii Kom.) silages at different maturity stages. Korshinsk peashrub was harvested at budding (S1) and blooming (S2) stages, and ensiled without additives (CON), or with 5% molasses (M0), or a combination of 5% molasses and either L. plantarum CLP (M1) or L. plantarum L694 (M2). Each treatment was triplicated and ensiled for 60 days. Delayed harvest increased water soluble carbohydrates (WSC), neutral detergent fibre (aNDF) and acid detergent fibre (ADF) in silages at S2 stage, whereas crude protein (CP) was lower in silages at S1 stage. Compared with the CON group, the additives treated silages had lower pH, greater lactic acid (LA), acetic acid (AA), and WSC concentrations (p <.05). Application of molasses alone or in combination with CLP had a noticeable effect on bacterial communities, with an increase in Lactobacillus in silages at both stages, whereas M2 silages presented more unfavourable microorganisms. Spearman's rank correlation analysis showed that LA concentration in silage was positively correlated with Lactobacillus relative abundance at both stages, while ammonia nitrogen (NH3‐N) concentration was positively correlated with the relative abundances of unclassified‐f‐Enterobacteriaceae and Enterobacter. In conclusion, delayed harvest could result in greater WSC and aNDF but lower CP in Korshinsk peashrub silage. Low WSC is the primary limiting factor affecting silage quality, and ensiling with molasses accelerated lactic acid fermentation in Korshinsk peashrub silage, providing a high‐quality forage resource for livestock production. [ABSTRACT FROM AUTHOR]

Definition: The rumen is the largest of the four chambers of the "stomach" in ruminant animals, which harbors an incredibly dense, diverse, and dynamic microbial community crucial for feedstuff degradation, animal health, and production. The primary objective of this article is to enhance knowledge and comprehension of rumen microbiology by providing an introductory-level overview of the field of rumen microbiology. Ruminants possess a distinctive digestive system optimized for the microbial breakdown of complex plant materials. The ruminant "stomach" consists of four chambers (e.g., reticulum, rumen, omasum, and abomasum), which is home to a microbial population that degrades feedstuffs consumed by ruminant animals. Dr. Robert Hungate and Dr. Marvin Bryant's groundbreaking research in the 1960s laid the foundation for understanding the function of the ruminal microbial ecosystem. Recent advancements (e.g., next-generation sequencing) have provided the field with deeper insight into populations, boosting our understanding of how the microbial population of the rumen functions in a variety of conditions. The ruminal microbial ecosystem is comprised of bacteria, along with archaea, protozoa, bacteriophage, and fungi, each contributing to the symbiotic relationship between the microbial ecosystem and the host animal that is essential for optimal animal health and efficient animal production. Traditional anaerobic growth techniques have facilitated the study of individual anaerobic bacteria but have been limited by dependence on growth in laboratory conditions. The development of 16S rRNA sequencing allows the identification of microbial populations that cannot be grown and allows an unbiased view of microbial diversity. Diet shapes the rumen microbial population composition, influencing animal production metrics such as feed efficiency, methane emissions, and immunological functions. Feed additives (e.g., essential oils, eubiotics) hold promise by manipulating and unraveling the microbial biochemical potential for improving animal health, feed efficiency, environmental impacts, and overall production sustainability. Future research impacts include the development of probiotics, prebiotics, and genetic strategies for optimizing the rumen microbiome's multifaceted impacts. [ABSTRACT FROM AUTHOR]

The Type VI Secretion System (T6SS) is a widespread and highly effective mechanism of microbial warfare; it confers the ability to efficiently kill susceptible cells within close proximity. Due to its large physical size, complexity, and ballistic basis for intoxication, it has widely been assumed to incur significant growth costs in the absence of improved competitive outcomes. In this study, we precisely examine the fitness costs of constitutive T6SS firing in the bacterium Vibrio cholerae. We find that, contrary to expectations, constitutive expression of the T6SS has a negligible impact on growth, reducing growth fitness by 0.025 ± 0.5% (95% CI) relative to a T6SS− control. Mathematical modeling of microbial populations demonstrates that, due to clonal interference, constitutive expression of the T6SS will often be neutral, with little impact on evolutionary outcomes. Our findings underscore the importance of precisely measuring the fitness costs of microbial social behaviors and help explain the prevalence of the T6SS across Gram‐negative bacteria. [ABSTRACT FROM AUTHOR]

The objective of this study was to evaluate various wheat supplementation levels on rumen microbiota and fermentation parameter in Tibetan sheep. A total of ninety ram with an average 12.37 ± 0.92 kg at the age of 2 months were randomly allocated to three treatments: 0% wheat diet (CW, N = 30), 10% wheat diet (LW, N = 30), and 15% wheat diet (HW, N = 30) on a dry matter basis. The experiment was conducted over a period of 127 days, including 7 days of adaption to the diets. Our results showed that sheep fed 10% wheat exhibited optimal average daily gain and feed gain ratio compared with HW group (p < 0.05). The serum alkaline phosphatase concentration was the lowest when fed the 10% wheat diet (p < 0.05), whereas serum aspartate aminotransferase concentration was the highest (p < 0.05). Both acetate and propionate increased with increase in dietary wheat ratio (p < 0.05), while a greater decrease in concentrations of NH3‐N was observed (p < 0.05). In rumen fluid, 3413 OTUs were obtained with 97% consistency. Phylum Firmicutes was the predominant bacteria and accounted for 49.04%. The CW groups supported significantly increased the abundance of Bacteroidetes (p < 0.05), as compared with the HW group. The abundance of Bacteroidales_UCG‐001, Ruminococcus, and Mitsuokella possessed a higher relative abundance in HW group (p < 0.05). No differences in the bacterial community and fermentation parameters were observed between the sheep fed 0% and 10% wheat (p > 0.05). Ruminal bacterial community structure was significantly correlated with isobutyrite (r2 = 0.4878, p = 0.035) and valerate (r2 = 0.4878, p = 0.013). In conclusion, supplementation of 10% wheat in diet promoted the average daily gain and never altered microbial community structure and fermentation pattern, which can be effectively replace partial corn in Chinese Tibetan Sheep. [ABSTRACT FROM AUTHOR]

The effects of the addition of molasses (5 and 10% of dry matter: DM basis; M5 and M10 respectively) with or without urea (2%; U2, U2 + M5 and U2 + M10) on chemical and mineral composition, silage quality, microbial populations, buffering capacity and fermentation/digestion characteristics of common reed (Phragmites australis) ensiled under anaerobic conditions were investigated. The additives changed the silage quality of common reed compared with the control. Crude protein content was significantly (p < 0.0001) increased in urea‐containing silages, whereas ash‐free neutral detergent fibre concentration decreased in M10 compared with the control (p = 0.05). Treatment with 2% urea (U2) resulted in the reduction of most measured minerals with a severe decrease in iron concentration. The amount of gas produced after 96 h of incubation was, respectively, higher for U2, M10, U2M10, U2M5 and M5 compared with the control (p < 0.0001). Although the greatest in vitro dry matter digestibility and in vitro organic matter digestibility (96 h) were observed in U2 (p < 0.0001), no significant differences were found between U2 and M10. Supplementation with 10% molasses (M10) significantly increased lactic acid concentration, aerobic stability and total bacteria compared with other treatments (p < 0.0001). Moreover, DM loss (p = 0.0004), total yeast and mould (p < 0.0001) were significantly decreased as a result of 10% molasses treatment. Overall, it can be suggested that treating silage with 10% molasses (M10) has the potential to efficiently improve the nutritive value of common reed. [ABSTRACT FROM AUTHOR]

Hydrogen creates water during combustion. Therefore, it is expected to be the most promising environmentally friendly energy alternative in the coming years. This study used extract liquid obtained from the waste nigella sativa generated by the black cumin oil industry. The performance of biological hydrogen manufacturing via dark fermentation was investigated in the fluidized bed reactor (FBR) and completely stirred tank reactor (CSTR) under the operation conditions of pH 5.0, 4.0, and 6.0 and a hydraulic retention time (HRT) of 36 and 24 h. The performance of hydrogen manufacturing was determined to be good under an organic loading ratio (OLR) of 6.66 g.nigella sativa extract/L and pH 4.0. According to these conditions, the maximum amount of hydrogen in CSTR and FBR was found to be 20.8 and 7.6 mL H2/day, respectively. The operating process of the reactors displayed that a reduction in HRT augmented biohydrogen manufacturing. The work that used mixed culture found that the dominant microbial population at pH 4.0 involved Hydrogenimonas thermophila, Sulfurospirillum carboxydovorans, Sulfurospirillum cavolei, Sulfurospirillum alkalitolerans, and Thiofractor thiocaminus. No research on waste black cumin extract was found in biohydrogen studies, and it was determined that this substrate source is applicable for biological hydrogen manufacturing. [ABSTRACT FROM AUTHOR]

Simple Summary: This review summarizes the main findings about the human seminal microbiome regarding its biological origins, microbial populations, and relationship with fertility and health, as well as the factors that may affect its composition and the potential sources of data variability. Although the microbial communities from seminal fluid were an unexplored field some decades ago, their characteristics and potential roles are gradually coming to light. Therefore, a complex and specific microbiome population with commensal niches and fluctuating species has started to be revealed. In fact, certain clusters of bacteria have been associated with fertility and health, while the outgrowth of several species is potentially correlated with infertility indicators. This constitutes a compelling reason for outlining the external elements that may induce changes in the seminal microbiome composition, like lifestyle factors, gut microbiota, pathologies, prebiotics, and probiotics. In this review, we summarize the main findings about seminal microbiome, its origins and composition, its relationship with fertility, health, and influence factors, while reminding readers of the limitations and advantages introduced from technical variabilities during the experimental procedures. [ABSTRACT FROM AUTHOR]

Aims This study investigated the antimicrobial efficacy of ultrasound technology (US) in combination with two different disinfectants (Disinfectant A and Disinfectant B), containing peracetic acid (PAA) and quaternary ammonium compounds (QACs), respectively, against two sporigenic pathogens, Aspergillus brasiliensis and Bacillus subtilis. Methods and results The microbicidal activity of the coupled treatment was compared with the use of the disinfectants alone, and the efficacy of the disinfection strategies was evaluated by the log reduction of the population of the microorganism inoculated onto stainless-steel surface. The combination treatment resulted in a log reduction of 5.40 and 3.88 (Disinfectant A + US) against A. brasiliensis and B. subtilis , at 850 and 500 ppm PAA, compared to 265 and 122 (Disinfectant A only). For Disinfectant B, in combination with US, showed a logarithmic reduction of 5.04 and 4.79 against A. brasiliensis and B. subtilis at 078% v v−1 and 392% v v−1 QACs, respectively, vs. 1.58 and 1.64 (Disinfectant B only). Moreover, no colonies or not statistically significant growth was observed within the US bath containing the disinfectant. Conclusions The antimicrobial efficacy of the two disinfectants was greatly enhanced when used in combination with US, and this also makes it possible to avoid the overuse of chemicals for disinfection. [ABSTRACT FROM AUTHOR]

There is scanty information about the microbial composition of poultry manure processed through several bioprocessing interventions such as anaerobic digestion (AD) and vermicomposting. Here, we investigated the changes in microbial population and parasitic load of poultry manure (both litter and excreta separately) undergoing AD and vermicomposting . The study was conducted for a period of three months. Six biogas digesters and seven vermicompost units were used comprising of different treatments. Broiler litter was pretreated with 0.1 and 0.2 mol/L NaOH prior to AD while the layer excreta was subjected to different dilutions in water (1:6, 1:8, 1:10) for the production of biogas. Further, the substrates were also used for vermicompost production wherein similar treatment was given to the broiler litter while different carbonaceous materials (16-20 kg of leaves, rice husk, saw dust and wheat straw per 100 kg of poultry waste) were incorporated to the layer excreta. The microbiota changes were studied which comprised of changes in total bacterial count (TBC), coliform count and Salmonella spp. count in all the treatments at regular intervals. The parasitic load was also measured by counting eggs per gram (EPG) in all the treatments at regular interval. The results of the study showed a significant (P <0.01) reduction in the microbial populations of pathogens (upto 44-54%) as well as parasitic load (92-100%) with the advancement in time and proved AD and vermicomposting of broiler litter and layer excreta at the defined pretreatment conditions as an effective technique to treat poultry waste prior to safe disposal and utilization. [ABSTRACT FROM AUTHOR]

Triclosan (TCS), a broad-spectrum antibacterial chemical, is detected in human urine, breast milk, amniotic fluid, and feces; however, little is known about its impact on the intestinal microbiome and host mucosal immunity during pregnancy and early development. Pregnant female rats were orally gavaged with TCS from gestation day (GD) 6 to postpartum (PP) day 28. Offspring were administered TCS from postnatal day (PND) 12 to 28. Studies were conducted to assess changes in the intestinal microbial population (16S-rRNA sequencing) and functional analysis of microbial genes in animals exposed to TCS during pregnancy (GD18), and at PP7, PP28 and PND28. Microbial abundance was compared with the amounts of TCS excreted in feces and IgA levels in feces. The results reveal that TCS decreases the abundance of Bacteroidetes and Firmicutes with a significant increase in Proteobacteria. At PND28, total Operational Taxonomic Units (OTUs) were higher in females and showed correlation with the levels of TCS and unbound IgA in feces. The significant increase in Proteobacteria in all TCS-treated rats along with the increased abundance in OTUs that belong to pathogenic bacterial communities could serve as a signature of TCS-induced dysbiosis. In conclusion, TCS can perturb the microbiome, the functional activities of the microbiome, and activate mucosal immunity during pregnancy and early development. [ABSTRACT FROM AUTHOR]

In Japan, Japanese Black cattle, known for their exceptional meat quality owing to their abundant intramuscular fat, undergo a unique three-stage feeding system with varying concentrate ratios. There is limited research on physiological and rumen microbial changes in Japanese Black cattle during these stages. Therefore, this study aimed to examine Japanese Black steers in these three stages: early (T1, 12–14 months), middle (T2, 15–22 months), and late (T3, 23–30 months). The rumen bacteria of 21 cattle per phase was analyzed using 16S rRNA gene sequencing. Rumen bacterial diversity was significantly higher in T1, with a distinct distribution, than in T2 and T3. Specific phyla and genera were exclusive to each stage, reflecting the shifts in feed composition. Certain genera dominated each stage: T1 had Flexilinea, Streptococcus, Butyrivibrio, Selenomonas, and Kandleria; T2 had Bifidobacterium, Shuttleworthia, and Sharpea; and T3 had Acetitomaculum, Mycoplasma, Atopobium, and Howardella. Correlation analysis revealed significant associations between certain microbial populations and physiological parameters. These findings indicate that changes in energy content and feed composition are associated with physiological and ruminal alterations. This study may guide strategies to improve rumen health and productivity in Japanese Black cattle by modifying diets to specific fattening stages. [ABSTRACT FROM AUTHOR]

To assess the possible impact of climatic variation on microbial community composition in organic winemaking, we employed a metabarcoding approach to scrutinize the microbiome in a commercial, organic, Pinot noir wine production system that utilizes autochthonous fermentation. We assessed microbial composition across two vintages (2018 and 2021) using biological replicates co-located at the same winery. Microbial dynamics were monitored over four important fermentation time points and correlated with contemporaneous climate data. Bacterial (RANOSIM = 0.4743, p = 0.0001) and fungal (RANOSIM = 0.4738, p = 0.0001) compositions were different in both vintages. For bacteria, Lactococcus dominated the diversity associated with the 2018 vintage, while Tatumella dominated the 2021 vintage. For fungal populations, while Saccharomyces were abundant in both vintages, key differences included Starmerella, copious in the 2018 vintage; and Metschnikowia, substantive in the 2021 vintage. Ordination plots correlated the climatic variables with microbial population differences, indicating temperature as a particularly important influence; humidity values also differed significantly between these vintages. Our data illustrates how climatic conditions may influence microbial diversity during winemaking, and further highlights the effect climate change could have on wine production. [ABSTRACT FROM AUTHOR]

Although the pesticide hexachlorocyclohexane (HCH) and its isomers have long been banned, their presence in the environment is still reported worldwide. In this study, we investigated the bioaccumulation potential of α, β, and δ hexachlorocyclohexane (HCH) isomers in black alder saplings (Alnus glutinosa) to assess their environmental impact. Each isomer, at a concentration of 50 mg/kg, was individually mixed with soil, and triplicate setups, including a control without HCH, were monitored for three months with access to water. Gas chromatography–mass spectrometry revealed the highest concentrations of HCH isomers in roots, decreasing towards branches and leaves, with δ-HCH exhibiting the highest uptake (roots—14.7 µg/g, trunk—7.2 µg/g, branches—1.53 µg/g, leaves—1.88 µg/g). Interestingly, α-HCH was detected in high concentrations in β-HCH polluted soil. Phytohormone analysis indicated altered cytokinin, jasmonate, abscisate, and gibberellin levels in A. glutinosa in response to HCH contamination. In addition, amplicon 16S rRNA sequencing was used to study the rhizosphere and soil microbial community. While rhizosphere microbial populations were generally similar in all HCH isomer samples, Pseudomonas spp. decreased across all HCH-amended samples, and Tomentella dominated in β-HCH and control rhizosphere samples but was lowest in δ-HCH samples. [ABSTRACT FROM AUTHOR]

The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population's mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of a simulated evolving population subject to a standard serial dilution protocol. Through extensive numerical experimentation, we find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that increasing the level of clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but leaves the rate of growth invariant when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape. The simulation package for this work may be found at https://github.com/nmboffi/spin_glass_evodyn. [ABSTRACT FROM AUTHOR]

The discharge of hydrothermal vents on the seafloor provides energy sources for dynamic and productive ecosystems, which are supported by chemosynthetic microbial populations. These populations use the energy gained by oxidizing the reduced chemicals contained within the vent fluids to fix carbon and support multiple trophic levels. Hydrothermal discharge is ephemeral and chemical composition of such fluids varies over space and time, which can result in geographically distinct microbial communities. To investigate the foundational members of the community, microbial growth chambers were placed within the hydrothermal discharge at Axial Seamount (Juan de Fuca Ridge), Magic Mountain Seamount (Explorer Ridge), and Kamaʻehuakanaloa Seamount (Hawai'i hotspot). Campylobacteria were identified within the nascent communities, but different amplicon sequence variants were present at Axial and Kamaʻehuakanaloa Seamounts, indicating that geography in addition to the composition of the vent effluent influences microbial community development. Across these vent locations, dissolved iron concentration was the strongest driver of community structure. These results provide insights into nascent microbial community structure and shed light on the development of diverse lithotrophic communities at hydrothermal vents. [ABSTRACT FROM AUTHOR]

An exposure to diverse microbial population early in life is important for the development of immunity against various non‐communicable diseases including asthma, childhood leukaemia and other cancers. Social mixing in daycare settings helps with exposure to a variety of microbes. However, social isolation and a high emphasis on workplace hygiene during the COVID pandemic may have affected children's exposure to diverse microbiota. The structure of microbial communities and their role in developing immunity to various diseases are not well understood. In this study, we investigated the structure of microbial communities in daycare and home settings during the pandemic. Interestingly, microbial diversity was relatively higher in dust samples collected from homes, with human‐associated taxa being more prevalent compared to those from daycare settings. Environmental microbes were more abundant in dust samples from daycare providers. These results potentially suggest that cleaning practices during the pandemic may have influenced the diversity and microbial abundance of the daycare samples. Several bacterial taxa detected in both the environments are known to induce anti‐inflammatory and immunomodulatory responses, conferring protection from various diseases. Therefore, exposure to diverse microbial population in early childhood may play an important role in developing immunity against various non‐communicable and infectious diseases. [ABSTRACT FROM AUTHOR]

Bacterial transcription is not monolithic. Microbes exist in a wide variety of cell states that help them adapt to their environment, acquire and produce essential nutrients, and engage in both competition and cooperation with their neighbors. While we typically think of bacterial adaptation as a group behavior, where all cells respond in unison, there is often a mixture of phenotypic responses within a bacterial population, where distinct cell types arise. A primary phenomenon driving these distinct cell states is transcriptional heterogeneity. Given that bacterial mRNA transcripts are extremely short-lived compared to eukaryotes, their transcriptional state is closely associated with their physiology, and thus the transcriptome of a bacterial cell acts as a snapshot of the behavior of that bacterium. Therefore, the application of single-cell transcriptomics to microbial populations will provide novel insight into cellular differentiation and bacterial ecology. In this review, we provide an overview of transcriptional heterogeneity in microbial systems, discuss the findings already provided by single-cell approaches, and plot new avenues of inquiry in transcriptional regulation, cellular biology, and mechanisms of heterogeneity that are made possible when microbial communities are analyzed at single-cell resolution. [ABSTRACT FROM AUTHOR]

The objective of this study was to evaluate the effects of cashew nut shell extract (CNSE) and monensin on ruminal in vitro fermentation, CH 4 production, and ruminal bacterial community structure. Treatments were as follows: control (CON, basal diet without additives); 2.5 μ M monensin (MON); 0.1 mg CNSE granule/g DM (CNSE100); and 0.2 mg CNSE granule/g DM (CNSE200). Each treatment was incubated with 52 mL of buffered ruminal content and 500 mg of total mixed ration for 24 h using serum vials. The experiment was performed as a complete randomized block design with 3 runs. Run was used as a blocking factor. Each treatment had 5 replicates, in which 2 were used to determine nutrient degradability, and 3 were used to determine pH, NH 3 -N, volatile fatty acids, lactate, total gas, CH 4 production, and bacterial community composition. Treatment responses for all data, excluding bacterial abundance, were analyzed with the GLIMMIX procedure of SAS v9.4. Treatment responses for bacterial community structure were analyzed with a PERMANOVA test run with the R package vegan. Orthogonal contrasts were used to test the effects of (1) additive inclusion (ADD: CON vs. MON, CNSE100, and CNSE200); (2) additive type (MCN: MON vs. CNSE100 and CNSE200); and (3) CNSE dose (DOS: CNSE100 vs. CNSE200). We observed that pH, acetate, and acetate:propionate ratio in the CNSE100 treatment were lower compared with CNSE200, and propionate in the CNSE100 treatment was greater compared with CNSE200. Compared with MON, CNSE treatments tended to decrease total lactate concentration. Total gas production of CON was greater by 2.63% compared with all treatments, and total CH 4 production was reduced by 10.64% in both CNSE treatments compared with MON. Also, compared with MON, in vitro dry matter degradabilities in CNSE treatments were lower. No effects were observed for NH 3 -N or in vitro neutral detergent fiber degradability. Finally, the relative abundances of Prevotella , Treponema , and Schwartzia were lower, whereas the relative abundances of Butyrivibrio and Succinivibrio were greater in all treatments compared with CON. Overall, the inclusion of CNSE decreased CH 4 production compared with MON, making CNSE a possible CH 4 mitigation additive in dairy cattle diets. [ABSTRACT FROM AUTHOR]

Ruminal ciliates are a fundamental constituent within the rumen microbiome of ruminant animals. The complex interactions between ruminal ciliates and other microbial guilds within the rumen ecosystems are of paramount importance for facilitating the digestion and fermentation processes of ingested feed components. This review underscores the significance of ruminal ciliates by exploring their impact on key factors, such as methane production, nitrogen utilization efficiency, feed efficiency, and other animal performance measurements. Various methods are employed in the study of ruminal ciliates including culture techniques and molecular approaches. This review highlights the pressing need for further investigations to discern the distinct roles of various ciliate species, particularly relating to methane mitigation and the enhancement of nitrogen utilization efficiency. The promotion of establishing robust reference databases tailored specifically to ruminal ciliates is encouraged, alongside the utilization of genomics and transcriptomics that can highlight their functional contributions to the rumen microbiome. Collectively, the progressive advancement in knowledge concerning ruminal ciliates and their inherent biological significance will be helpful in the pursuit of optimizing rumen functionality and refining animal production outcomes. [ABSTRACT FROM AUTHOR]

Objective: The objective of this study was to evaluate the growth performance, rumen fermentation parameters and bacterial community of post-weaning dairy calves in response to five diets varying in corn silage (CS) inclusion. Methods: A total of forty Holstein weaned bull calves (80±3 days of age;128.2±5.03 kg at study initiation) were randomized into five groups (8 calves/group) with each receiving one of five dietary treatments offered as total mixed ration in a 123-d feeding study. Dietary treatments were control diet (CON; 0% CS dry matter [DM]); Treatment 1 (T1; 27.2% CS DM); Treatment 2 (T2; 46.5% CS DM); Treatment 3 (T3; 54.8% CS DM); and Treatment 4 (T4; 67.2% CS DM) with all diets balanced for similar protein and energy concentration. Results: Results showed that calves offered CS had greater average daily gain, body length and chest depth growth, meanwhile altered rumen fermentation indicated by decreased rumen acetate concentrations. Principal coordinate analysis showed the rumen bacterial community structure was affected by varying CS inclusion diets. Bacteroidetes and Firmicutes were the predominant bacterial phyla in the calf rumens across all treatments. At the genus level, the abundance of Bacteroidales_RF16_group was increased, whereas Unclassified_ Lachnospiraceae was decreased for calves fed CS. Furthermore, Spearman's correlation test between the rumen bacteria and rumen fermentation parameters indicated that Bacteroidales_ RF16_group and Unclassified Lachnospiraceae were positively correlated with propionate and acetate, respectively. Conclusion: The results of the current study suggested that diet CS inclusion was beneficial for post-weaning dairy calf growth, with 27.2% to 46.5% CS of diet DM recommended to achieve improved growth performance. Bacteroidales_RF16_group and Unclassified Lachnospiraceae play an important role in the rumen fermentation pattern for post-weaning calves fed CS. [ABSTRACT FROM AUTHOR]

Carbon near the Earth's surface cycles between the production and consumption of organic carbon; the former sequesters carbon dioxide while the latter releases it. Microbes attempt to close the loop, but the longer organic matter survives, the slower microbial degradation becomes. This aging effect leaves observable quantitative signatures: Organic matter decays at rates that are inversely proportional to its age, while microbial populations and concentrations of organic carbon in ocean sediments decrease at distinct powers of age. Yet mechanisms that predict this collective organization remain unknown. Here, I show that these and other observations follow from the assumption that the decay of organic matter is limited by progressively rare extreme fluctuations in the energy available to microbes for decomposition. The theory successfully predicts not only observed scaling exponents but also a previously unobserved scaling regime that emerges when microbes subsist on the minimum energy flux required for survival. The resulting picture suggests that the carbon cycle's age-dependent dynamics are analogous to the slow approach to equilibrium in disordered systems. The impact of these slow dynamics is profound: They preclude complete oxidation of organic carbon in sediments, thereby freeing molecular oxygen to accumulate in the atmosphere. [ABSTRACT FROM AUTHOR]

Background: The mare-foal relationship is essential for the well-being and growth of a foal. Mare's milk provides a foal with nutrients, protective immunity, and microbes. Within the first two weeks of life, there is a risk for a foal to suffer from diarrhea, particularly "foal heat diarrhea" which happens at about the time of a mare's estrus cycle but is more likely due to transitions in the microbiota in the foal's gastrointestinal (GI) tract. We hypothesized that this GI microbiota transition could be caused by changes in lysozyme and microbial populations in the mare's milk. To test this hypothesis, fifteen mare-foal pairs were followed in the first 15 days post-foaling. Every other day milk was collected from mares and rectal swabs were collected from foals. Lysozyme activity in the mare's milk was measured using a fluorescence assay. Microbial DNA was isolated from the milk and swabs and the V4 domain of 16 S rRNA genes were PCR amplified and sequenced using Illumina MiSeq technology. Microbial populations were analyzed using DADA2 and phyloseq within R. Results: Mare's milk lysozyme activity peaked for samples at Day 1 and levels dropped to 72.5% of Day 1 activity by Day 15; however, microbial populations in the mare's milk did not vary significantly over the two weeks. Furthermore, levels of microbial diversity found in foal rectal swabs were initially similar to microbial diversity seen in mare's milk; however, over the first fifteen days, diversity increased for the foal rectal swab microbiota and swab microbial populations differed from milk microbes. A transition occurred shifting from microbes from the phylum Proteobacteria early in rectal swabs to those primarily from the phyla Firmicutes and Bacteroidota after the first few days post-foaling. These phyla contained several families and genera of microbes that promote utilization of milk components in healthy gut transition. Microbial abundance levels correlated more with days post-parturition than with lysozyme activity and mare's milk microbial populations. Conclusions: The findings suggest that much of the microbial populations responsible for the transition of the foal's gut comes from sources outside of mare's milk species and levels of lysozyme activity. [ABSTRACT FROM AUTHOR]

Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relationships with their microbiome based on the reciprocal exchange of chemical currencies. Among these, the dicarboxylate metabolite azelaic acid (Aze) appears to play an important, but heterogeneous, role in modulating these microbiomes, as it is used as a carbon source for some heterotrophs but is toxic to others. However, the ability of Aze to promote or inhibit growth, as well as its uptake and assimilation mechanisms into bacterial cells are mostly unknown. Here, we use transcriptomics, transcriptional factor coexpression networks, uptake experiments, and metabolomics to unravel the uptake, catabolism, and toxicity of Aze on two microalgal-associated bacteria, Phycobacter and Alteromonas, whose growth is promoted or inhibited by Aze, respectively. We identify the first putative Aze transporter in bacteria, a 'C4-TRAP transporter', and show that Aze is assimilated through fatty acid degradation, with further catabolism occurring through the glyoxylate and butanoate metabolism pathways when used as a carbon source. Phycobacter took up Aze at an initial uptake rate of 3.8×10-9 nmol/cell/hr and utilized it as a carbon source in concentrations ranging from 10 µM to 1 mM, suggesting a broad range of acclimation to Aze availability. For growth-impeded bacteria, we infer that Aze inhibits the ribosome and/or protein synthesis and that a suite of efflux pumps is utilized to shuttle Aze outside the cytoplasm. We demonstrate that seawater amended with Aze becomes enriched in bacterial families that can catabolize Aze, which appears to be a different mechanism from that in soil, where modulation by the host plant is required. This study enhances our understanding of carbon cycling in the oceans and how microscale chemical interactions can structure marine microbial populations. In addition, our findings unravel the role of a key chemical currency in the modulation of eukaryote-microbiome interactions across diverse ecosystems. [ABSTRACT FROM AUTHOR]

Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and genome stability. In a growing cell culture, genomic regions that are replicated early should be more abundant than regions that are replicated late. This abundance pattern can be experimentally measured using deep sequencing. However, a general quantitative theory linking this pattern to the replication program is still lacking. In this paper, we predict the abundance of DNA fragments in asynchronously growing cultures from any given stochastic model of the DNA replication program. As key examples, we present stochastic models of the DNA replication programs in budding yeast and Escherichia coli. In both cases, our model results are in excellent agreement with experimental data and permit to infer key information about the replication program. In particular, our method is able to infer the locations of known replication origins in budding yeast with high accuracy. These examples demonstrate that our method can provide insight into a broad range of organisms, from bacteria to eukaryotes. Author summary: Biological cells replicate their genome in a planned manner. One way of obtaining experimental information about this plan is by deep sequencing a growing culture of cells. The idea underlying these experiments is that genomic regions that are replicated earlier would be present in higher abundances than regions replicated at a later stage. In this paper, we make use of this idea to obtain precise quantitative information on replication programs from sequencing. As a main application, we infer the locations of origins of replication in budding yeast from sequencing data. Our inference is consistent with direct experimental evidences on the locations of these origins. Our method can be in principle be applied to any organism that can be cultured and sequenced, and has therefore the potential to shed light on the replication program of a broad class of organisms. [ABSTRACT FROM AUTHOR]