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This study aimed to determine shifts in microbial populations regarding richness and diversity from the daily use of a popular over-the-counter nasal spray. In addition, the finding of nasal commensal bacterial species that overlap with the oral microbiome may prove to be potential probiotics for the "gateway microbiomes". Nasal swab samples were obtained before and after using the most popular over-the-counter (OTC) nasal spray in 10 participants aged 18–48. All participants were healthy volunteers with no significant medical histories. The participants were randomly assigned a number by randomizing software and consisted of five men and five women. The sampling consisted of placing a nasal swab atraumatically into the nasal cavity. The samples were preserved and sent to Northwestern University Sequencing Center for whole-genome deep sequencing. After 21 days of OTC nasal spray use twice daily, the participants returned for further nasal microbiome sampling. The microbial analysis included all bacteria, archaea, viruses, molds, and yeasts via deep sequencing for species analysis. The Northwestern University Sequencing Center utilized artificial intelligence analysis to determine shifts in species and strains following nasal spray use that resulted in changes in diversity and richness. [ABSTRACT FROM AUTHOR]

[Display omitted] • Successful and stable high-solid digestion was achieved in both CSTRs and PFRs. • Reduction of volatile solids was 50–54% in both reactor types. • Biogas and methane yields were significantly higher from PFRs than CSTRs. • Bacterial population was dominated by Defluviitoga in PFRs and MBA03 in CSTRs. • Stirring frequency was the likely cause for difference in microbial community. High-solid digestion (HSD) for biogas production is a resource-efficient and sustainable method to treat organic wastes with high total solids content and obtain renewable energy and an organic fertiliser, using a lower dilution rate than in the more common wet digestion process. This study examined the effect of reactor type on the performance of an HSD process, comparing plug-flow (PFR) type reactors developed for continuous HSD processes, and completely stirred-tank reactors (CSTRs) commonly used for wet digestion. The HSD process was operated in thermophilic conditions (52 °C), with a mixture of household waste, garden waste and agricultural residues (total solids content 27–28 %). The PFRs showed slightly better performance, with higher specific methane production and nitrogen mineralisation than the CSTRs, while the reduction of volatile solids was the same in both reactor types. Results from 16S rRNA gene sequencing showed a significant difference in the microbial population, potentially related to large differences in stirring speed between the reactor types (1 rpm in PFRs and 70–150 rpm in CSTRs, respectively). The bacterial community was dominated by the genus Defluviitoga in the PFRs and order MBA03 in the CSTRs. For the archaeal community, there was a predominance of the genus Methanoculleus in the PFRs, and of the genera Methanosarcina and Methanothermobacter in the CSTRs. Despite these shifts in microbiology, the results showed that stable digestion of substrates with high total solids content can be achieved in both reactor types, indicating flexibility in the choice of technique for HSD processes. [ABSTRACT FROM AUTHOR]

Studies have shown that a diverse and metabolically active microbiota exists throughout different stages of coffee processing, from pre- to post-harvest. This microbiota originates from both the cultivation and processing environments. Additionally, microorganisms from the soil can be found on the fruit due to the transfer between them. This study reviews the microbiota present in Arabica coffee fruits and the soils where the plants are grown. It examines how microbial profiles are related to coffee variety, altitude, cultivation region, and processing method, and establishes a connection between the microbiota in soil and fruit. A diverse microbiota was observed in both coffee fruits and soils, with similar microorganisms identified across different growing regions, processing methods, and coffee varieties. However, exclusive detections of some microorganisms were also observed. These differences highlight the influence of terroir on coffee's microbial composition, confirming that environmental conditions, genetic factors, and processing methods shape coffee microbiota. Since microbial development during coffee fermentation can affect the beverage's quality, the data presented in this review offer valuable insights for researchers and producers. Understanding the influence of processing methods, coffee varieties, and cultivation regions on coffee microbiota enables the selection of specific fermentation conditions or starter cultures to enhance terroir characteristics or adjust microbial populations to favor or introduce microorganisms beneficial for coffee quality. [ABSTRACT FROM AUTHOR]

GOOD SOIL can raise the quantity and quality of food. However, the land quality has worsened due to various anthropogenic activities. The present study aimed to assess the effects of land use systems on soil quality over time through specific indicators. A top 30 cm soil sample from six land uses (forest, pasture, orchard, vegetable, maize, and paddy) was analyzed for soil quality index using Principal Component Analysis. The results revealed the highest organic carbon (20.94±1.85 g kg-1), N (537.50±16.7 kg ha-1), and P2O5 (36.51±1.62 kg ha-1) in paddy-based land uses while the minimum OC (8.63±1.23 g kg-1), N (290.30±1.8 kg ha-1) and K2O (201.36±6.2 kg ha-1) respectively with lowest P2O5 (24.22±1.21 kg ha-1) in maize. The forest system showed dense macrofauna (1498 ind. m-2). The microbial population was found in the order of paddy>maize>vegetable>apple>pasture>forest. Particle size distribution of studied land uses varied from silty loam to clay loam. The following order of soil quality: forest>pasture>apple >vegetable>maize>paddy was found after the indexing procedure. It is concluded that further extension and turning of natural forests to agriculture will lead to a more significant loss of stored carbon from soils. [ABSTRACT FROM AUTHOR]

The microbial population in the pig's gastrointestinal tract can be influenced by incorporating fibrous by-products into the diets. This study investigated the impact of including two types of dried olive cake (OC) in pigs' diets on fecal bacterial composition. The correlation between fecal microbiota and growth performance, nutrient digestibility, gut fermentation pattern and slurry gas emissions was also evaluated. Thirty male Pietrain x (Landrace x Large white) pigs (47.9 ± 4.21 kg) were assigned to three groups: a control group (C), a group fed a diet with 20% partially defatted OC (20PDOC), and a group fed a diet with 20% cyclone OC (20COC) for 21 days. Fecal samples collected before and after providing the experimental diets were analyzed for the V3-V4 region of the 16S rRNA gene. Pigs were weighed, and feed intake was recorded throughout the study. Potential ammonia and methane emissions from slurry were measured. No significant differences in alpha diversity indexes were found. The taxonomic analysis revealed that Firmicutes and Bacteroidota phyla were dominant at the phylum level across all groups. Differential abundance analysis using ALDEx showed significant differences among groups for various bacteria at the phylum, genus, and species levels at the end of the experiment. Pigs from 20PDOC and 20COC groups exhibited increased abundances of healthpromoting bacteria, such as Plactomycetota at the phylum level and Allisonella and an unidentified genus from the Eggerthellaceae family at the genus level. These changes influenced short-chain fatty acids' (SCFA) concentration in slurries, leading to greater acetic, butyric, caproic and heptanoic acids in OC-fed groups, especially 20COC pigs. A volatility analysis revealed significant positive correlations (p < 0.05) between Uncultured_Bacteroidales and Unculured_ Selenomonadaceae and energy digestibility. Monoglobus and Desulfovibrio showed a positive significant (p < 0.05) correlation with total SCFA, indicating a high impact on gut fermentation. However, growth performance parameters and potential gas emission displayed no significant correlations with a specific bacterial genus. In conclusion, our results suggest that OC inclusion into pig diets could positively modulate and contribute to the gut microbiota's favorable composition and functionality. Also, nutrient digestibility and gut fermentation patterns can be associated with specific microbial populations. [ABSTRACT FROM AUTHOR]

In the dynamic landscape of food technology, where ensuring freshness and extending shelf life are paramount concerns, active packaging stands at the forefront of innovation. This study explores the utilization of natural resources in the development of smart packaging solutions aimed at enhancing the freshness of perishable foods. Specifically, chitosan films incorporating Malva sylvestris mucilage and Rubia tinctorum extract are investigated for their efficacy in preserving the quality of fish products. Through a series of experiments and analyses, this research elucidates the potential of these bio‐based materials to revolutionize packaging practices, offering a sustainable and effective means of prolonging the shelf life of perishable goods while maintaining their quality and safety. Assessment of the antimicrobial properties of Rubia tinctorum hydroethanolic extract revealed that Staphylococcus aureus displayed higher susceptibility to this extract with the lowest MIC value (2.60 ± 0.09 mg/ml) and MBC value (5.20 ± 0.09 mg/ml) as well as the highest inhibition zone (16.33 ± 0.50 mm). For the composites with different concentrations of hydroethanolic Rubia tinctorum extracts, the lightness value significantly (p < 0.05) increased at neutral pH. After days of storage, the pH in the fish sample surpassed the threshold (7), leading to a corresponding change in the indicator film's color. Also, samples coated with higher levels of Rubia tinctorum extract in active/smart chitosan films with Malva sylvestris mucilage had lower pH, thiobarbituric acid, total volatile nitrogen, and microbial population (mesophile, psychrophile, and Enterobacteriaceae). The highest appearance score, surface glaze score, and overall odor acceptance in samples 4 (fish coated with active/smart chitosan with Malva sylvestris containing 0.6% Rubia tinctorum extract) and 5 (fish coated with active/smart chitosan with Malva sylvestris contained 1.2% Rubia tinctorum extract) (p ≤ 0.05) suggest that this application may contribute to the observed perceptual qualities. This novel indicator film has the potential to function as intelligent packaging for monitoring fish freshness. Additional research can delve into the precise mechanisms driving these effects and fine‐tune the formulation for particular applications. [ABSTRACT FROM AUTHOR]

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]

Phage predation is generally assumed to reduce microbial proliferation while not contributing to the spread of antibiotic resistance. However, this assumption does not consider the effect of phage predation on the spatial organization of different microbial populations. Here, we show that phage predation can increase the spread of plasmid-encoded antibiotic resistance during surface-associated microbial growth by reshaping spatial organization. Using two strains of the bacterium Escherichia coli, we demonstrate that phage predation slows the spatial segregation of the strains during growth. This increases the number of cell-cell contacts and the extent of conjugation-mediated plasmid transfer between them. The underlying mechanism is that phage predation shifts the location of fastest growth from the biomass periphery to the interior where cells are densely packed and aligned closer to parallel with each other. This creates straighter interfaces between the strains that are less likely to merge together during growth, consequently slowing the spatial segregation of the strains and enhancing plasmid transfer between them. Our results have implications for the design and application of phage therapy and reveal a mechanism for how microbial functions that are deleterious to human and environmental health can proliferate in the absence of positive selection. The impact of phage predation on spreading antimicrobial resistance is unclear in the context of its effects on microbial community spatial organization. Here, the authors show that phage predation can promote the spread of plasmid-encoded antibiotic resistance by increasing microbial spatial intermixing. [ABSTRACT FROM AUTHOR]

To investigate the effects of kinds of additives on silage quality, the mixture of king grass and rice straw was ensiled with addition of sucrose, citric acid and malic acid at the levels of 0, 1 and 2%, being blank control (CK), citric acid groups (CA1, CA2), malic acid groups (MA1, MA2), citric acid + malic acid groups (CM1, CM2), sucrose groups (SU1, SU2), mainly focusing on fermentation quality, nutrient content, aerobic stability and microbial community of the silages. The results showed that the addition of sucrose decreased (p <  0.05) pH and increased the content of water soluble carbohydrate (p <  0.05). The sucrose groups and mixed acid groups also had a lower (p <  0.01) neutral detergent fiber content. The addition of citric acid and the mixed acid increased (p <  0.01) the aerobic stability of the silage, reduced the abundance of Acinetobacter, and the addition of citric acid also increased the abundance of Lactiplantibacillus. It is inferred that citric acid and malic acid could influence fermentation quality by inhibiting harmful bacteria and improve aerobic stability, while sucrose influenced fermentation quality by by promoting the generation of lactic acid. It is suggested that the application of citric acid, malic acid and sucrose would achieve an improvement effect on fermentation quality of the mixed silage. [ABSTRACT FROM AUTHOR]

This study reports a successful continuous biohydrogen production from rice straw hydrolysate in both 3-L and 20-L dynamic membrane bioreactor (DMBR). In the 3-L DMBR (DMBR I), the maximum average bio-H 2 production performance was 32.13 ± 0.71 L H 2 /L-d, 1.27 ± 0.03 mol H 2 /mol hexose-equiv consumed , and 96.39 ± 2.12 L H 2 /d, respectively. The H 2 production performance of 20-L DMBR (DMBR II) was comparable to DMBR I, which were 33.15 ± 0.42 L H 2 /L-d, 1.46 ± 0.03 mol H 2 /mol hexose-equiv consumed , and 663 ± 8 L H 2 /d, respectively. Rapid decline of hydraulic retention time (HRT) in the early stages of operation led to the metabolic flux of the mixed culture from the lactic acid pathway to the H 2 -producing pathway. Genus Clostridium was the dominant microbial population in DMBR I and DMBR II. This study provides operational criteria and insights in the scale-up design and operation of biohydrogen production from lignocellulosic biomass. • Rice straw was converted to H 2 in 3-L and 20-L dynamic membrane bioreactor. • 663 ± 8 L H 2 /d was recovered continuously from a 20-L bioreactor. • Maximum H 2 production was 33.8 L H 2 /L-d and 1.3 mol H 2 /mol hexose in 20-L bioreactor. • Rapid decrease of HRT in early-stage shifted HLa pathway to H 2 -producing pathway. • Feeding of rice straw hydrolysate shifted H 2 -producing pathway from HBu to HAc. [ABSTRACT FROM AUTHOR]

Objective: The aim of this study was to investigate the effects of Lactiplantibacillus plantarum (L. plantarum) and propionic acid (PA) on fermentation characteristics and microbial community of amaranth (Amaranthus hypochondriaus) silage with different moisture contents. Methods: Amaranth was harvested at maturity stage and prepared for ensiling. There were two moisture content gradients (80%: AhG, 70%: AhS; fresh material: FM) and three treatments (control: CK, L. plantarum: LP, propionic acid: PA) set up, and silages were opened after 60 d of ensiling. Results: The results showed that the addition of L. plantarum and PA increased lactic acid (LA) content and decreased pH of amaranth after fermentation. In particular, the addition of PA significantly increased crude protein content (p < 0.05). LA content was higher in wilted silage than in high-moisture silage, and it was higher with the addition of L. plantarum and PA (p < 0.05). The dominant species of AhGLP, AhSCK, AhSLP and AhSPA were mainly L. plantarum, Lentilactobacillus buchneri and Levilactobacillus brevis. The dominant species in AhGCK include Enterobacter cloacae, and Xanthomonas oryzae was dominated in AhGPA, which affected fermentation quality. L. plantarum and PA acted synergistically after ensiling to accelerate the succession of dominant species from gram-negative to gram-positive bacteria, forming a symbiotic microbial network centred on lactic acid bacteria. Both wilting and additive silage preparation methods increased the degree of dominance of global and overview maps and carbohydrate metabolism, and decreased the degree of dominance of amino acid metabolism categories. Conclusion: In conclusion, the addition of L. plantarum to silage can effectively improve the fermentation characteristics of amaranth, increase the diversity of bacterial communities, and regulate the microbial community and its functional metabolic pathways to achieve the desired fermentation effect. [ABSTRACT FROM AUTHOR]

White cheese is an inseparable part of the Persian breakfast table. However, it has limited shelf life owing to microbial growth and chemical changes. Application of active packaging incorporated with essential oils is an innovative technique to retain quality and extend shelf life of foods. In this study, the effect of chitosan (Ch 1 and 2%) film containing rosemary extract (RE 0.5 and 1%) was studied on the shelf life of white cheese at 4°C for 45 days. The physicochemical evaluation showed that all treated cheeses had higher pH, moisture, and fat content, but acidity and hardness in treated cheeses were lower than the nontreated ones. During storage, pH, moisture, and fat content decreased and acidity and hardness increased. At the end of the storage, the highest acidity (1.79 g lactic acid) and hardness (3.5 N) and the lowest pH (4.1) were observed in the control sample, and the highest moisture (53.92%) and fat (21.84%) content was observed in E2C2 treatment (1% extract + 2% chitosan). The active packaging of cheese caused a significant decrease in the total count of bacteria, coliforms, lactic acid bacteria, mold, and yeast. The population of microorganisms in the control sample increased significantly during storage (p < 0.05). The treated cheeses had acceptable sensory properties. The most effective treatment for maintaining the physicochemical properties and retarding the growth of microorganisms in cheese was the E2C2 sample. Therefore, it can be used in active packaging systems of cheese. [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]

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

The applicability of ionic liquids has grown exponentially over the last few decades. This growth is due to the easy modification of these compounds formed by ions, through the proper choice of both moieties, and the possibility of introducing functional groups into their cations and anions. However, studies of their toxicity and effects on the environment remain scarce. This study analyses firstly the response to adding different concentrations of choline dihydrogen phosphate to the germination of seeds of eight plant species. It also examines the microbial population and the respiration of two soils with contrasting organic matter contents. Seeds were incubated in a Petri dish in a Phytotron with a photoperiod of 16 h under light at 24 °C and 8 h in darkness at 16 °C. The activity of microbial populations of untreated and treated soils was analysed by isothermal microcalorimetry at 25 °C. Basal soil respiration kinetics were measured at optimal moisture (80% of field water retention capacity) and temperature (25 °C) over 10 days. The results indicate that this compound has diverse effects on the different endpoints. Nevertheless, this compound can be classified as non-toxic considering its effects on seeds and on soil, at least in the medium- to long-term. [ABSTRACT FROM AUTHOR]

Agricultural practices profoundly influence soil microbial populations and physicochemical properties, vital for crop growth and quality. This study aims to explore the impact of diverse agrochemical applications on soil microbial dynamics, physicochemical properties, and maize yield and proximate properties. Topsoil samples, collected at depths of 1 to 15 cm, were transported to Jimma University for maize cultivation. Over 120 days, soil and maize samples were collected at specified intervals for analysis, including soil pH, microbial populations, and nutrient content. Statistical analysis using one-way ANOVA (p < 0.05) was conducted. Soil bacterial and fungal populations were measured on days 5, 10, 20, 40, 80, and 120. The highest total mesophilic bacterial count (TMBC) was in compost-treated pots (G) and the lowest in those receiving macronutrient fertilizers and glyphosates (B). The highest total mesophilic fungal count (TMFC) was in pots with glyphosates and compost (F), and the lowest was in pots treated with macronutrient fertilizers and glyphosates (B). Pots treated with macronutrient fertilizers and glyphosates (B), macronutrient fertilizers (A), and micronutrient fertilizers (C) showed the lowest Fe and Zn levels. Maize in pots treated with macronutrient fertilizer combined with glyphosate (B) exhibited the lowest protein, fats, and carbohydrates. Notably, compost-treated soils showed the highest bacterial and fungal counts, Fe, and Zn concentrations, while micro-mineral fertilizer combined with glyphosate (B) depleted the soil. Agrochemical treatments negatively affected maize yield quality, indicating complex treatment-related changes in soil parameters. [ABSTRACT FROM AUTHOR]

Background and Aim: Ruminant enteric methane (CH4) is one of the largest sources of greenhouse gases that contribute to global warming. To minimize environmental harm caused by ruminants' CH4 production, natural substances can be used to suppress it. Chitosan from crustacean sources had been known to obstruct CH4 generation in the rumen. About 18% of silkworm pupae is chitin, but little is known about the impact of silkworm pupae chitosan on rumen methanogenesis. This study investigated the efficacy of the silkworm chitosan extraction method and its impact on rumen fermentation, methanogenesis, and microbial growth in vitro. Materials and Methods: This study employed a randomized complete block design featuring five treatments and four batches for rumen incubation as the blocking factor. In this study, five treatments were implemented: Control (CO) (basal diet with no added chitosan), basal diet with 6% chitosan from the Chinese Silkworm strain 804 (CHI804), basal diet with 6% chitosan from the PS 01 Hybrid Silkworm strain (CHIPS01), basal diet with 6% chitosan from the Hybrid F1 Japanese 102 x Chinese 202 races (CHIJC02), and basal diet with 6% commercial shrimp shell chitosan as the positive control (CHICOMM). The in vitro experiments assessed digestibility, pH, total gas generation, CH4 production, ammonia nitrogen (NH3-N), and short-chain fatty acid levels, along with microbial population. Data were analyzed using a general linear model followed by Duncan's test when applicable. Results: A significant effect on dry matter digestibility (DMD), total gas production, CH4, NH3-N, and rumen microbial populations (Methanogens, Ruminoccocus albus, Ruminoccocus flavefaciens, Selonomonas ruminantium, Butyrivibrio fibrisolvens, Streptoccocus bovis, Prevotella spp., and Bacteroides spp.) was observed (p < 0.05). The extracted chitosan (CHIJC02) used in this study exhibited a similar quality to that of commercial chitosan (CHICOMM). CHI804 treatment could reduce gas production, NH3-N production, and B. fibrisolvens population significantly (p < 0.05), while CHIJC02 could reduce CH4 production, methanogen population, acetate (C2) production, and increase propionate (C3) production significantly (p < 0.05). CHIJC02 and CHICOMM treatments could also increase the population of R. flavefaciens, S. ruminantium, and Bacteroides spp. significantly (p < 0.05). Chitosan addition significantly (p < 0.05) reduced DMD but did not impact organic matter digestibility or pH. Conclusion: The extracted chitosan mimics commercial chitosan in physico-chemical properties. Chitosan derived from Japanese and Chinese F1 hybrid silkworm strains demonstrated superior capacity for inhibiting CH4 generation compared to commercial chitosan. The quality and effects on methanogenesis, rumen fermentation, and rumen microbial populations can differ depending on the origin of chitosan. [ABSTRACT FROM AUTHOR]

Simple Summary: This study investigated whether COS in the diet can improve the digestion and rumen health of beef cattle under in vitro fermentation conditions. A total of 24 fermentation tanks were randomly allocated into four groups. Each treatment had six replicates, with one tank per replicate. Each group received a different concentration of 0.02% COS, 0.04% COS, 0.08% COS, and a control group (CON). The results demonstrated that the addition of COS facilitates a shift in rumen fermentation from the acetate model to the propionate model. This is achieved by influencing the microbial population, resulting in alterations to the fermentation level, nutrient disappearance rate, and gas production. These changes have the potential to enhance rumen health. The study aimed to investigate the effect of dietary chitosan oligosaccharides (COS) meal levels on the nutrient disappearance rate, rumen fermentation, and microflora of beef cattle in vitro. A total of 24 fermentation tanks were randomly divided into four treatments containing 0% COS (CON), 0.02% COS, 0.04% COS, and 0.08% COS for an 8-day experiment period, with each treatment comprising six replicates. The disappear rates of DM, CP, EE, and total gas production were quadratically increased with increasing COS levels. The disappear rates of DM, CP, EE, and ADF were greatest, whereas the total gas production was lowest in the 0.08% COS group. The pH, NH3-N, MCP, the content of propionate, isobutyrate, butyrate, valerate, and the A/P were quadratically increased with increasing COS levels, while the A/P were linearly decreased. The pH, MCP, and the content of propionate, and butyrate were highest, whereas the NH3-N and the content of acetate, isobutyrate, valerate, and the A/P were lowest in the 0.08% COS group. Microbiomics analysis showed that the rumen microbial diversity was not altered between the CON and the 0.08% COS group. However, the relative abundance of Methanosphaera, Ruminococcus, Endomicrobium, and Eubacterium groups was increased, and the relative abundance of pathogenic bacteria Dorea and Escherichia-Shigella showed a decrease in the 0.08% COS group. Overall, the 0.08% COS was the most effective among the three addition levels, resulting in an increase in the disappearance rate of in vitro fermented nutrients and improvements in rumen fermentation indexes and microbial communities. This, in turn, led to the maintenance of rumen health. [ABSTRACT FROM AUTHOR]

This study aimed to evaluate the effects of essential oils (EOs) extracted from Cannabis sativa L. and Cannabis indica Lam. on in vitro ruminal fermentation characteristics, selected rumen microbial populations, and methane production. GC-MS analyses allowed us to identify 89 compounds in both EOs. It was found that E-β-caryophyllene predominated in C. sativa (18.4%) and C. indica (24.1%). An in vitro (Ankom) test was performed to analyse the control and monensin groups, as well as the 50 µL or 100 µL EOs. The samples for volatile fatty acids (VFAs), lactate, and microbiological analysis were taken before incubation and after 6 and 24 h. The application of EOs of C. indica resulted in an increase in the total VFAs of acetate and propionate after 6 h of incubation. The applied EOs had a greater impact on the reduction in methane production after 6 h, but no apparent effect was noted after 24 h. Lower concentrations of C. sativa and C. indica had a more pronounced effect on Lactobacillus spp. and Buryrivibrio spp. than monensin. The presented findings suggest that C. sativa and C. indica supplementation can modify ruminal fermentation, the concentrations of specific volatile fatty acids, and methane production. [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]

[Objective] The study was conducted to clarify the microbial community structure in soil with continuous cropping of Curcuma wenyujin and fumigation treatment, aiming to lay a foundation for alleviating continuous cropping obstacles in C. wenyujin cultivation. [Method] The soil under a continuous cropping of C. wenyujin for 3 years was selected and fumigated with dazomet one month before planting C. wenyujin. After 7-month cultivation of C. wenyujin, we collected soil samples from three types of plots: continuous cropping, fumigated and uncultivated. Total soil DNA was extracted, and the population and diversity of microbial communities (fungi and bacteria) were analyzed by using PacBio Sequel third-generation sequencing. [Result] The results showed that C. wenyujin plants in the fumigated soil exhibited good growth and minimal disease incidence, while those in the continuous cropping soil had poor growth and severe seedling death. Analysis of bacterial communities at the phylum level revealed that the abundance of AD3, TK10 and WPS-2 decreased in rhizosphere soil after continuous cropping compared with those in uncultivated soil. Fumigation of continuous cropping soil increased the abundance of beneficial bacteria with biocontrol functions such as Bacillus and Sphingomonas. Among the three soil types, 5 fungal phyla were abundant, including Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, and unclassified_k_ Fungi. Ascomycota had the lowest abundance in uncultivated C. wenyujin soil, but continuous cropping significantly increased its abundance, while Basidiomycota showed a significant decrease. Several beneficial fungal genera, including Chaetomium, Penicillium, Aspergillus, Myrothecium, Thielavia, Humicola, Rhizophlyctis, Microdochium, Ramicandelaber, Albifi mbria, Curvularia, Gigaspora, Nigrospora, Neocosmospora, Talaromyces, Roussoella, Rhytidhysteron, Boothiomyces, Apiotrichum, Ochroconis, Saitozyma, Trichosporon and Phoma, had higher abundance in fumigated soil than that in continuous cropping soil. In contrast, continuous cropping soil had a higher accumulation of pathogenic microorganisms. [Conclusion] Continuous cropping of C. wenyujin leads to the accumulation of harmful soil microorganism, resulting in continuous cropping obstacles. Fumigation with dazomet can reduce the number of soil-borne pathogens and increase the abundance of beneficial microbial populations, thereby mitigating continuous cropping obstacles in C. wenyujin cultivation. [ABSTRACT FROM AUTHOR]

Nitrate poses a potential threat to aquatic ecosystems. This study focuses on the sulfur autotrophic denitrification mechanism in the process of water culture wastewater treatment, which has been successfully applied to the degradation of nitrogen in water culture farm effluents. However, the coexistence of organic acids in the treatment process is a common environmental challenge, significantly affecting the activity of denitrifying bacteria. This paper aims to explore the effects of adding benzoic acid and lactic acid on denitrification performance, organic acid removal rate, and microbial population abundance in sulfur autotrophic denitrification systems under optimal operating conditions, sulfur deficiency, and high hydraulic load. In experiments with 50 mg·L−1 of benzoic acid or lactic acid alone, the results show that benzoic acid and lactic acid have a stimulating effect on denitrification activity, with the stimulating effect significantly greater than the inhibitory effect. Under optimal operating conditions, the average denitrification rate of the system remained above 99%; under S/N = 1.5 conditions, the average denitrification rate increased from 88.34% to 91.93% and 85.91%; under HRT = 6 h conditions, the average denitrification rate increased from 75.25% to 97.79% and 96.58%. In addition, the addition of organic acids led to a decrease in microbial population abundance. At the phylum level, Proteobacteria has always been the dominant bacterial genus, and its relative abundance significantly increased after the addition of benzoic acid, from 40.2% to 61.5% and 62.4%. At the genus level, Thiobacillus, Sulfurimonas, Chryseobacterium, and Thermomonas maintained high population abundances under different conditions. Practitioner Points: Employing autotrophic denitrification process for treating high‐nitrate wastewater.Utilizing organic acids as external carbon sources.Denitrifying bacteria demonstrate high utilization efficiency towards organic acids.Organic acids promote denitrification more than they inhibit it.The promotion is manifested in the enhancement of activity and microbial abundance. [ABSTRACT FROM AUTHOR]

1. Effects of cereal type and conditioning temperature (CT) on protein and carbohydrate (CHO) molecular structures, nutrient retention, carcass and blood characteristics, caecal microbial population and growth criteria of broilers fed pellet diet were evaluated for a total period of 35 d. 2. In total, 336-day-old Cobb 500 broiler chicks were randomly allotted into a 2 × 2 factorial arrangement with two different cereal types (maize or wheat) processed in two different temperatures (CT; 68°C or 90°C) with seven pen replicates containing 12 birds each. 3. Chicks fed the maize-based diets significantly gained higher body weight (BW) and lower feed conversion ratio (FCR) in comparison to the chicks fed wheat-based diets during the whole grow-out period (p < 0.01). Overall, the highest BW and feed intake (FI) were seen in birds fed wheat-based diets conditioned at 68°C, but the lowest FCR was observed in maize-based diet conditioned at 90°C at 7, 14 and 21 d of age (p < 0.01). However, BW was higher and FCR lower in chicks fed maize-based diets conditioned at 90°C in the grower period (28 and 35 d; p < 0.01). 4. The α-helix height was higher in wheat-based starter diets in comparison to the maize-based diet (p < 0.01). Ratio of amide I to II area and total CHO peak height were increased when diets were processed at 90°C in both maize and wheat-based starter diet (p < 0.05). Increasing the CT from 68°C to 90°C reduced CHO peak 1 and 2 height by 11.6% and 3.95%, respectively, in maize-based starter diets, while increasing the CT from 68°C to 90°C reduced CHO peak 1 and 2 height by 54.3% and 57.2%, respectively, in wheat-based starter diets. In the grower diets, increasing the CT from 68°C to 90°C increased CHO peak 1 by 23% in maize-based diets, but reduced CHO peak 1 by 24.5% in wheat-based diets. 5. Calcium and phosphorous retention were highest in chicks fed wheat-based diets conditioned at 90°C and lowest in chicks fed maize-based diets conditioned at 90°C (p < 0.01). Salmonella, E. coli and coliforms in the caeca reduced significantly (p < 0.05) in chicks fed wheat-based diets conditioned at 90°C on d 11 and increased with the same diet at 35 d of age compared to the chicks fed maize-based diets conditioned at both 68°C and 90°C or wheat-based diets conditioned at 68°C. 6. Conditioning the wheat-based diets at 68°C improved production responses without causing any adverse effects on protein and CHO molecular structures, however increasing the conditioning temperature to 90°C impaired performance due to alteration of protein and CHO molecular structures. In contrast, conditioning of the maize-based diets at 90°C had the opposite effect, and improved production performance compared to diets conditioned at 68°C. [ABSTRACT FROM AUTHOR]

Background: Maize popularly known as "Queen of cereals". Weeds resulted in the highest crop loss (33%), followed by pathogens (26%), insects (20%), storage pests (7%), rodents (6%) and others (8%) in India. Application of herbicides will affect various soil microbial processes and enzymatic activities in the soil, whose activity is very important for maintaining the soil fertility. Methods: The present field experiment was conducted during Rabi, 2017-18 and 2018-19 under irrigated conditions at wetland farm of S.V. Agricultural College, Tirupati Andhra Pradesh, with ten treatments and three replications in a randomized block design. Result: Higher kernel and stover yield of maize was recorded with hand weeding twice at 15 and 30 DAS and the yield loss was comparatively lower with atrazine 1.0 kg ha-1as PE fb topramezone 30 g ha-1or tembotrione 120 g ha-1 as PoE or atrazine 1.0 kg ha-1 as PE fb HW at 30 DAS, while these were lowest with weedy check. Soil microbial count and enzyme activity was statistically comparable in all the pre followed by post emergence herbicide treatments. [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]

Introduction: Intratumoral microbes play an important role in the development of colorectal cancer (CRC). However, studying intratumoral microbes in CRC faces technical challenges, as tumor microbe communities are often contaminated by fecal microbes due to the structure of the gut folds and villi. The present study aimed to develop a new method for isolating tumor cellassociated microbiota and comparing microbial populations from different compartments. Materials and methods: The distribution of intestinal bacteria was detected using immunohistochemistry combined with 5R-16s rRNA gene sequencing to explore the effects of the sampling site and number of washes on the detection of microbiota. The 5R-16s rRNA gene sequencing was performed using 44 samples from 11 patients with CRC, including CRC tumor tissues (TT), normal tissues adjacent to CRC (NT), tumor cells (TC), and normal cells (NC). TC and NC were obtained from the TT and NT using an enzymatic digestion method. The microbiota and their potential functions in the four groups were analyzed and compared to determine the differential microbiota related to CRC. Results: Bacteria were mainly distributed in the feces covering intestinal tissues and in the epithelial cells and macrophages within the tissues. Different sampling sites and number of washes led to detection of different microbiota distributions. Although the cleaningmethod could be controlled, sampling sites varied and led to different microbiota distributions. The phyla of Firmicutes and Bacteroidetes were highly abundant in the conventionally used tissue samples, whereas Proteobacteria was the most abundant phyla in the cell samples isolatedwith the newmethod (i.e., after cell enzymatic hydrolysis). Detection of CRC cell-associated microbiota using a cell enzymatic digestion method showed that some bacteria, such as Fusobacterium, Eikenella, Shewanella, and Listeria, were more abundant in TT than NT, whereas the abundance of Akkermansia was lower in TT than NT. The tumor/normal ratios of some bacteria, such as Gemella, Escherichia, Shigella, and Blautia, were different between the cell and tissue samples. Conclusion: The cell enzymatic digestion method reduced fecal bacterial contamination, enabling low biomass intratumoral microbiota to be detected and allowing prediction of bacterial distributions. [ABSTRACT FROM AUTHOR]

This study aimed to investigate the effect of prickly ash seeds (PAS) on the microbial community found in rumen microbes of Hu sheep by adding different percentages of prickly ash seeds and to carry out research on the relation between rumen flora and production performance. Twenty-seven male lambs of Hu sheep were classified into three groups based on the content of prickly ash seeds (PAS) fed for 90 days, i.e., 0%, 3%, and 6%. At the end of the feeding trial, rumen fluid samples were collected from six sheep in each group for 16S amplicon sequencing. The results showed that the addition of prickly ash seeds significantly increased both Chao1 and ACE indices (P < 0.05), and the differences between groups were greater than those within groups. The relative content of Bacteriodota decreased, and the relative content of Fusobacteriota, Proteobacteria, Acidobacteriota, and Euryarchaeota increased. The relative content of Papillibacter and Saccharofermentans was increased at the genus level, and the relative content of Bacteroides and Ruminococcus was decreased. The test group given 3% of prickly ash seeds was superior to the test group given 6% of prickly ash seeds. In addition, the addition of 3% of prickly ash seeds improved the metabolism or immunity of sheep. Fusobacteriota and Acidobacteriota were positively correlated with total weight, dressing percentage, and average daily gain (ADG) and negatively correlated with average daily feed intake (ADFI), feed-to-gain ratio (F/G), and lightness (L*). Methanobrevibacter and Saccharofermentans were positively correlated with ADG and negatively correlated with ADFI and L*. In conclusion, under the present experimental conditions, the addition of prickly ash seeds increased the abundance and diversity of rumen microorganisms in Hu sheep and changed the relative abundance of some genera. However, the addition of 6% prickly ash seedsmay negatively affect the digestive and immune functions in sheep rumen. [ABSTRACT FROM AUTHOR]

This study investigated the effect of molasses addition on the fermentation quality, chemical composition, and bacterial community of seed pumpkin peel residue (SPPR) mixed with sunflower straw (SS) in microstorage feed. Molasses additions on a dry matter basis (DM) were divided into three groups: 0% control (CON), 1% (MA), and 2% (MB), and the raw materials underwent mixed microstorage for a period of 60 days. MA exhibited the highest content of dry matter (DM), the lowest content of neutral detergent fiber (NDF), acid detergent fiber (ADF), and ammoniacal nitrogen (NH3-N), as well as the lowest microbial diversity abundance and the highest relative abundance of lactobacilli (p < 0.05). MB demonstrated the highest crude protein (CP) content and acetic acid (AA) and propionic acid (PA) concentrations, with the lowest pH. In conclusion, the addition of molasses could enhance the quality of mixed microsilage feeds composed of seeded pumpkin peel pomace (SPPR) and sunflower straw (SS), with the optimal addition of molasses being 1% on a DM basis. [ABSTRACT FROM AUTHOR]

Despite the high abundance and potential toxicity of ferrocyanide in the environment, data on the bioremediation of these complexes in contaminated soils are missing. In this study we isolated forty bacterial species presented in soil highly contaminated with ferrocyanide complexes, originating from a Manufactured Gas Plant (MGP). All bacterial strains were resistant to ferrocyanide (500 mg L−1). Six isolates showed better growth in the presence of ferrocyanide and were able to use it as a sole nitrogen source. One of them was able to assimilate ferrocyanide‐derived nitrogen and carbon. The strains varied in their tolerance to the ferrocyanide. The Minimum Inhibitory Concentration (MIC) values determined in the rich medium ranged from 1400 mg L−1 to 2000 mg L−1 and in all cases were greater than those set on the minimal medium. Molecular analysis revealed that the investigated isolates had the highest similarity to the Bacillus and Rummeliibacillus lineages. Rummeliibacillus was recognized for the first time for its ferrocyanide-degrading potential. Soil samples collected from MGP sites indicated that the overall indigenous population of microorganisms was low. Total cyanide content ranged from 220 mg kg−1 to 346 mg kg−1. Additionally, elevated Pb concentrations and an imbalanced C:N:P ratio were observed. Our study provides new information about the presence of a well-acclimated bacterial community associated with long-term ferrocyanide-contaminated soil. This bacterial community could play an important role in MGP site bioremediation processes and has the potential for application for other bioremediation purposes; however, it is likely limited due to unfavorable environmental conditions. [ABSTRACT FROM AUTHOR]

Although Astragalus membranaceus root (AMR) has been noted as an ingredient in ruminant feed, the impacts of AMR feeding on rumen fermentation and the microbial community structure within the rumen are yet to be evaluated. This study investigated the effects of AMR supplementation on rumen fermentation characteristics and microbial community structures in goats. In two sets of feeding experiments, four Japanese native goats were fed AMR (10 g/kg DM/day/head) for three weeks per experiment. The rumen fluid samples were analyzed using high-performance liquid chromatography for fermentation products and next-generation sequencing for microbial analysis. The rumen fluid samples in the second experiment were also subject to an in vitro anaerobic fermentation test. The results indicated a significant modification, with a higher volatile fatty acid (VFA) content in the rumen fluid of goats in the feeding period than before feeding (p < 0.01). The microbial analysis revealed a significant increase in community diversity (p < 0.05) following AMR feeding, and the rumen bacterial community increased in two families belonging to the order Oscillospirales in Firmicutes (p < 0.05). The phylum Verrucomicrobiota was observed to be significantly less abundant after AMR feeding than during the control period (p < 0.05). Notably, the linear discriminant analysis revealed that the families with largely unknown functions in the rumen (Oscillospiraceae, Rikenellaceae, Muribaculaceae, and vadinBB97) were the determinants of the community split between control and AMR feeding. Increased fermentation rate by AMR feeding was also supported by an in vitro culture experiment, which resulted in faster VFA production without affecting methane production in total gas production. The study demonstrated that AMR can significantly facilitate change in the bacterial community structure in the goat rumen involving a shift of the favoring fibrolytic bacteria towards VFA production. The long-term effects of AMR supplementation and its applicability across different ruminant species, with potential benefits for animal health and productivity, should be addressed. [ABSTRACT FROM AUTHOR]

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Introduction: Cardiovascular diseases, including myocardial infarction, remain a leading cause of death globally. Emerging evidence suggests the gut microbiota plays a crucial role in cardiovascular health. This study aims to explore the impact of gut microbiota on myocardial infarction using a mouse model. Methods: The research utilizes a multi-omics approach, including 16S rDNA sequencing and LC-MS-based metabolomics to analyze fecal and serum samples from mice modeled to mimic myocardial infarction. This methodology allows for a comprehensive analysis of microbial populations and their metabolic output. Results: The findings reveal a significant reduction in gut microbiota a-diversity in mice with induced myocardial infarction compared to healthy controls. Notably, there is an increase in populations of Fusobacteria and Clostridia. Metabolomic analysis indicates disruptions in amino acid and energy metabolism, suggesting a metabolic dysregulation linked to myocardial health. Discussion: The study proposes a novel microbiota-metabolite-myocardium axis, where specific microbial metabolites may directly affect heart health. This connection points to the gut microbiota as a potential player in the pathogenesis of myocardial infarction and may open new therapeutic avenues targeting the gut microbiome to combat cardiovascular diseases. [ABSTRACT FROM AUTHOR]

Introduction: Intensive beef cattle production systems are frequently implicated as a source of bacteria that can be transferred to nearby humans and animals via effluent water, manure used as fertilizer, or airborne particulate matter. It is crucial to understand microbial population dynamics due to manure pack desiccation, antibiotic usage, and antibiotic alternatives within beef cattle and their associated feedyard environment. Understanding how bacterial communities change in the presence of antibiotics can also improve management practices for reducing the spread of foodborne bacteria. Methods: In this study, we aimed to compare the microbiomes within cattle feces, the feedyard environment and artificially produced airborne particulate matter as a function of pen change and treatment with tylosin or probiotics. We utilized 16S rRNA sequencing to compare bacterial communities among sample types, study days, and treatment groups. Results: Bacterial community diversity varied as a function of sampling day and pen change (old or new) within fecal and manure pack samples. Manure pack samples from old pens and new pens contained diverse communities of bacteria on days 0 and 84; however, by day 119 of the study these taxonomic differences were less evident. Particulate matter samples exhibited significant differences in community diversity and predominant bacterial taxa compared to the manure pack they originated from. Treatment with tylosin did not meaningfully impact bacterial communities among fecal, environmental, or particulate matter samples; however, minor differences in bacterial community structure were observed in feces from cattle treated with probiotics. Discussion: This study was the first to characterize and compare microbial communities within feces, manure pack, and airborne particulate matter from the same location and as a function of tylosin and probiotic treatment, and pen change. Although fecal and environmental samples are commonly used in research studies and other monitoring programs to infer public health risk of bacteria and antimicrobial resistance determinants from feedyard environments, our study suggests that these samples may not be appropriate to infer public health risk associated with airborne particulate matter. [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]

Phytoplankton blooms provoke bacterioplankton blooms, from which bacterial biomass (necromass) is released via increased zooplankton grazing and viral lysis. While bacterial consumption of algal biomass during blooms is well-studied, little is known about the concurrent recycling of these substantial amounts of bacterial necromass. We demonstrate that bacterial biomass, such as bacterial alpha-glucan storage polysaccharides, generated from the consumption of algal organic matter, is reused and thus itself a major bacterial carbon source in vitro and during a diatom-dominated bloom. We highlight conserved enzymes and binding proteins of dominant bloom-responder clades that are presumably involved in the recycling of bacterial alpha-glucan by members of the bacterial community. We furthermore demonstrate that the corresponding protein machineries can be specifically induced by extracted alpha-glucan-rich bacterial polysaccharide extracts. This recycling of bacterial necromass likely constitutes a large-scale intra-population energy conservation mechanism that keeps substantial amounts of carbon in a dedicated part of the microbial loop. Phytoplankton blooms provoke bacterioplankton blooms, from which bacterial biomass (necromass) is released via zooplankton grazing and viral lysis. Here, Beidler et al. show that the bacterial biomass, including alpha-glucan polysaccharides generated from the consumption of algal organic matter, is reused by microbes in vitro and during a diatom-dominated bloom. [ABSTRACT FROM AUTHOR]

Background: The rumen microbiome enables ruminants to digest otherwise indigestible feedstuffs, thereby facilitating the production of high-quality protein, albeit with suboptimal efficiency and producing methane. Despite extensive research delineating associations between the rumen microbiome and ruminant production traits, the functional roles of the pervasive and diverse rumen virome remain to be determined. Results: Leveraging a recent comprehensive rumen virome database, this study analyzes virus-microbe linkages, at both species and strain levels, across 551 rumen metagenomes, elucidating patterns of microbial and viral diversity, co-occurrence, and virus-microbe interactions. Additionally, this study assesses the potential role of rumen viruses in microbial diversification by analyzing prophages found in rumen metagenome-assembled genomes. Employing CRISPR–Cas spacer-based matching and virus-microbe co-occurrence network analysis, this study suggests that the viruses in the rumen may regulate microbes at strain and community levels through both antagonistic and mutualistic interactions. Moreover, this study establishes that the rumen virome demonstrates responsiveness to dietary shifts and associations with key animal production traits, including feed efficiency, lactation performance, weight gain, and methane emissions. Conclusions: These findings provide a substantive framework for further investigations to unravel the functional roles of the virome in the rumen in shaping the microbiome and influencing overall animal production performance. 3QAbSJqYZPn2njEBJ23VpA Video Abstract [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]

Objective. To characterize by microbiology the native strains associated to the intestinal tract of the species Panaque cochliodon. Materials and methods. Three adult specimens captured in the Magdalena River that were transported and sacrificed under animal welfare regulations were used. Dissection of the intestinal tract was performed, obtaining samples for microbiological isolation, using culture media, purifying the microorganisms, performing metabolic biochemical tests and API 20E (Biomeriux) tests for their identification. Results. Information on the microbial population structure was obtained, reporting the phylum Proteobacteria with the species: Pantoea sp, Erwinia sp, Providencia stuarti, Providencia alcalifaciens, Serratia ficaria, Citrobacter koseri and the phylum Firmicutes with the species: Bacillus sphaericus, Bacillus subtilis, Bacillus thurigiensis, Bacillus mycoides, Bacillus coagulans and Bacillus circulans. Conclusion. The predominant culturable microorganisms in P. cohliodon belong to the phylum Proteobacteria and the phylum Firmicutes. [ABSTRACT FROM AUTHOR]

Fire blight, a disease of pome fruits caused by the bacterium Erwinia amylovora, has become increasingly difficult to manage after the emergence of streptomycin-resistant strains. Alternative antibiotics and copper are available; however, these chemicals have use restrictions in some countries and also can carry risks of phytotoxicity. Therefore, there is growing interest in biological-based management options, with bacteriophage (phages) showing promise, as these naturally occurring pathogens of bacteria are easy to isolate and grow. However, there are several technical challenges regarding the implementation of phage biocontrol in the field, as the viral molecules suffer from ultraviolet radiation (UVR) degradation and can die off rapidly in the absence of the host bacterium. In this work, we assessed the efficacy of Erwinia phages and a commercial phage product for blossom blight control in the field across multiple locations in the eastern United States. In these tests, disease control ranged from 0.0 to 82.7%, and addition of a UVR protectant only resulted in significantly increased disease control in 2 of 12 tests. We also analyzed microbial community population changes in response to phage application. Changes in bacterial community diversity metrics over time were not detected; however, relative abundances of target taxa were temporarily reduced after phage applications, indicating that these phage applications did not have deleterious effects on the flower microbiome. We have demonstrated that biological control of fire blight with phages is achievable, but a better understanding of phage-pathogen dynamics is required to optimize disease control efficacy. [ABSTRACT FROM AUTHOR]

In this study, fresh-cut cucumbers were subjected to near-freezing temperature storage at -2 °C (NF) for 12 d, and microbial population (aerobic bacteria and coliforms), physicochemical properties (weight loss, color, firmness, and pH), and O2 consumption were compared with samples stored at 5 °C (C). Observation indicated that no sample showed any critical freezing phenomena during near-freezing temperature storage. Results showed that the microbial population (aerobic bacteria and coliforms) was suppressed in NF samples but increased significantly in C samples compared with the stored samples on day 0. Results of physicochemical properties showed that weight loss and total color difference of NF samples were less than those of C samples. Moreover, near-freezing temperature storage at -2 °C inhibited O2 consumption compared with storage at 5 °C. These results provide new insights into the application of near-freezing temperature storage for fruits and vegetables in the food cold chain. [ABSTRACT FROM AUTHOR]

The vast array of interconnected microorganisms across Earth's ecosystems and within holobionts has been called the "Internet of Microbes." Bacteria and archaea are masters of energy and information collection, storage, transformation, and dissemination using both "wired" and wireless (at a distance) functions. Specific tools affecting microbial energy and information functions offer effective strategies for managing microbial populations within, between, and beyond holobionts. This narrative review focuses on microbial management using a subset of physical modifiers of microbes: sound and light (as well as related vibrations). These are examined as follows: (1) as tools for managing microbial populations, (2) as tools to support new technologies, (3) as tools for healing humans and other holobionts, and (4) as potential safety dangers for microbial populations and their holobionts. Given microbial sensitivity to sound, light, and vibrations, it is critical that we assign a higher priority to the effects of these physical factors on microbial populations and microbe-laden holobionts. We conclude that specific sound, light, and/or vibrational conditions are significant therapeutic tools that can help support useful microbial populations and help to address the ongoing challenges of holobiont disease. We also caution that inappropriate sound, light, and/or vibration exposure can represent significant hazards that require greater recognition. [ABSTRACT FROM AUTHOR]

This experiment aimed to examine the impact of Salicornia europaea L. extract on sheep growth performance, rumen fermentation variables, nutrient apparent digestibility, and gastrointestinal microbial diversity. Forty-eight male Altay sheep, weighing 32.5±2.8kg and approximately 3.5months old, were chosen. Four dietary treatments, each consisting of four replicates and three sheep per replicate, were distributed randomly to the sheep. The pelleted total mixed ration containing Salicornia europaea L. extract at 0.0, 0.2, 0.4, and 0.6% DM was freely available to the sheep in the four treatment groups. The 56-day experiment consisted of 45days of measurements followed by 11days of adaptation. The growth performance was not affected by nutrition Salicornia europaea L. extract (p ≤ 0.05), but the feed-togain ratio was reduced when the extract was given at 0.4% DM (p ≤ 0.05). Compared to the 0 and 0.2% treatments, the apparent digestibility of DM, OM, NDF, and ADF was substantially greater in the 0.4, and 0.6% treatments. Furthermore, compared to sheep in the 0 and 0.2% groups, sheep in the 0.6% group had a noticeably higher apparent digestibility of CP. As the amount of Salicornia europaea L. extract added to the rumen fluid rose, the molar ratio of acetic acid increased. In contrast, the molar ratio of propionic acid gradually decreased, and the total volatile fatty acid content gradually reduced. Thus, adding a suitable quantity of Salicornia europaea L. extract to the sheep ration is natural and secure, which may improve the environmental sustainability of small ruminant production systems. [ABSTRACT FROM AUTHOR]

We used microbiology and molecular biology techniques to screen out high-temperature and low-temperature-resistant saprobiotics for compost and prepared a compound fermentation bacteria agent to rapidly ferment cattle manure into high-quality organic fertilizer in low-temperature season. Conventional composting and high-throughput techniques were used to analyze the changes of physical and chemical indexes and biodiversity in the process of composting, from which high and low-temperature-resistant strains were obtained, and high-temperature and low-temperature-resistant solid composite bactericides were prepared and added to composting to verify the effects of composite bactericides on composting. The conventional composting cycle took 22 days, and the diversity of microflora increased first and then decreased. Composting temperature and microbial population were the key factors for the success or failure of composting. Two strains of high-temperature-resistant bacteria and six strains of low-temperature-resistant bacteria were screened out, and they were efficient in degrading starch, cellulose, and protein. The high-temperature and low-temperature-resistant solid bacterial agent was successfully prepared with adjuvant. The preparation could make the compost temperature rise quickly at low temperature, the high temperature lasted for a long time, the water content, C/N, and organic matter fell quickly, the contents of total phosphorus and total potassium were increased, and the seed germination index was significantly improved. Improve the composting effect. The solid composite bacterial agent can shorten the composting time at low temperature and improve the composting efficiency and quality. [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]

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]

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]

This study investigated the effects of defective pear fermentation (DPF) diets on growth performance and gastrointestinal microbial communities in 60 healthy male small-tailed Han sheep, aged 90 days. The sheep were randomly divided into four groups, each consisting of three replicates with five sheep per replicate. Initially, all groups received a basal diet for seven days during the adaptation stage. Subsequently, for 60 days, group C (control) was fed a basal diet, group X received a basal diet with 2% DPF, group Y had a basal diet with 4% DPF, and group Z was fed a basal diet with 6% DPF. The results indicated that group Y experienced a significant increase in average daily gain (ADG) and average daily feed intake (ADFI). The addition of DPF significantly elevated the levels of GSH-Px and notably reduced MDA content compared to group C. Analysis of gastrointestinal microbiota showed that groups receiving DPF had increased relative abundances of Lachnospiraceae_NK3A20_group, norank_f p-2534-18B5_gut_group, Acetitomaculum, Actinobacteriota, Bacteroidota and Ruminococcus_gauvreauii_group, and decreased abundances of Proteobacteria, Prevotella, Staphylococcus, and Psychrobacter compared to group C. Group X exhibited the highest relative abundance of Olsenella, while group Y showed a significant increase in unclassified_f Lachnospiraceae compared to the other groups. Bacterial function prediction indicated that pathways related to energy metabolism were more prevalent in group X and Y. This study preliminarily confirms the feasibility of using DPF as feed additives, providing a foundation for further research and evaluation of DPF's application in animal production. [ABSTRACT FROM AUTHOR]