Archives of Microbiology

Industrial waste containing hydrophobic pollutants, like oils and hydrocarbons, is toxic and difficult to degrade, posing both ecological and human health risks. Biosurfactants are eco-friendly surface-active compounds produced by microorganisms, known for their ability to lower surface and interfacial tension, enhancing the solubility and bioavailability of hydrophobic compounds, facilitating their breakdown. The current study focuses on isolating biosurfactant-producing bacteria from industrial waste sources near Dhaka, Bangladesh, and characterizing their properties, determining potential usage. Using diesel-enriched nutrient agar, bacterial strains were isolated and screened for biosurfactant production by oil displacement, emulsification index (E24%), and drop collapse assay. The most promising isolates were characterized according to their biochemical activities and 16S rRNA amplicon-based sequencing. Isolation and characterization of the surfactants have been carried out using chromatographic techniques. The identified bacteria passed the drop collapse and oil displacement tests. CTAB agar assay, indicates their anionic nature, showing an emulsification index ranging 10-41%. The potential biosurfactant producers belong to Bacillus, Pseudomonas, Acinetobacter, and Enterobacterium genera. The surfactants showed antibacterial, antifungal, and plant growth promotion activity and have been characterized in terms of pH stability, salinity, adhesion, and temperature tolerance. The study successfully identified and characterized potential biosurfactant-producing bacteria from industrial waste, highlighting their efficiency in breaking down hydrophobic pollutants and hydrocarbons. These microorganisms provide a green and economical substitute for synthetic surfactants due to their biodegradability and lower toxicity. Upon further research and scaling, these bacteria can be a good source of biosurfactants for potential applications in industrial, agricultural, and biomedical fields. IMPORTANCEThe study carries high significance as it creates multi-disciplinary scopes for utilizing these environmentally adapted biosurfactant-producing bacteria in industry, agriculture, and medicine. Since the bacterial isolates have hydrocarbon degradation ability, upon optimization for higher production, industrial usage in oil refinery and other industries can be adopted. Due to their biodegradable nature, usage in wound healing bandages and as antimicrobial agents in medicine will be noteworthy. The isolates have plant growth promotion ability and utilizing them as biofertilizer will reduce the dependency on chemical fertilizers. This is the first detailed report on biosurfactant-producing bacteria from this industrial waste-polluted Turag River of Dhaka City. Moreover, it compiles detailed screening protocols and methods for analyzing such environmentally friendly microbes. Such characterization also opens the scope for optimizing the production of the surfactant compounds on a large scale and utilizing them commercially.

The Bacillus genus comprises physiologically versatile, endospore-forming bacteria widely distributed in natural environments. In this study, we report the isolation and genomic characterization of strain Bva_UNVM-123, recovered from agricultural soil in Pergamino, Argentina. Whole-genome sequencing using Illumina technology yielded a 5.1 Mbp draft genome assembled in 67 contigs with a GC content of 36%. Comparative genomic analyses using the TYGS server and digital DNADNA hybridization (dDDH) values supported its classification as a potentially novel species within the Bacillus sensu lato (s.l.) group. Genome annotation revealed 4,866 protein-coding genes, including multiple determinants conferring resistance to antibiotics (e.g., fosfomycin, tetracycline, beta-lactams) and toxic heavy metals (e.g., arsenic, cadmium, mercury), supporting its potential application in bioremediation. Additionally, PathogenFinder predicted a low probability of human pathogenicity (0.207), reinforcing its safety for environmental use. Functional classification based on Swiss-Prot further supported a metabolically versatile profile and revealed the presence of resistance-related categories associated with environmental adaptation. This study adds to the growing knowledge of environmental Bacillus species and their biotechnological potential

BackgroundGlobally, seagrass ecosystems are threatened by anthropogenic activities that are leading to increased levels of eutrophication, coastal pollution and thermal conditions. Consequently, there is a growing need to develop new approaches that work to mitigate these stressors and enhance restoration efforts in seagrass meadows. One promising strategy is to identify, isolate and characterize microbial consortia that are likely to support seagrass productivity. However, our current understanding of key microbial functions that support plant growth in marine systems is limited. Based on evidence from terrestrial plant-microbe systems, seagrass-associated bacteria are expected to provide the plant with nitrogen and phosphorus resources while detoxifying sulfur and producing phytohormones. Here, we sequenced 61 bacterial cultures isolated from the rhizosphere, rhizoplane, and endosphere of the seagrass, Zostera marina to identify a consortium of six putative plant growth promoting (PGP) candidates. ResultsOur cultivation approach using plant-based media allowed us to isolate 201 bacteria from Z. marina, which reflected 18% of the total microbial diversity of the starting inoculum. Genomic and phenotypic analyses of the 61-sequenced pure-cultures revealed that most of the sequenced taxa were able to mobilize nitrogen primarily through catabolic pathways, including denitrification (51%), dissimilatory nitrate reduction to ammonia (71%), and C-N bond cleavage (83%). Six of the isolates, which represent new lineages of Agarivorans, coded for the nitrogenase gene cassette. Additionally, 52% of the genomes had genes for sulfur and/or thiosulfate oxidation, 88.5% for phosphorus solubilization, and 60.5% for IAA production. Genomic analysis also revealed that some pathways, including denitrification and dissimilatory nitrite to ammonia DNRA, required cross-species cooperation as no one taxa contained all the genes needed to complete these metabolic pathways. Based on draft genome models and results from phenotypic assays, isolates Streptomyces sp. (Iso23 and Iso384), Mesobacillus sp (Iso127), Roseibuim sp. (Iso195), Peribacillus sp. (Iso49), and Agarivorans sp. (Iso311) represent a minimal microbial community that is likely to promote seagrass growth and enhance restoration efforts. ConclusionOur work provides a detailed genomic and phenotypic analysis of bacteria isolated from Z. marina and identifies a minimal microbial community with complementary PGP traits. Isolating, identifying and characterizing bacteria that promote seagrass growth is critical towards enhancing restoration efforts of seagrass meadows.

Bacteria of the genus Achromatium are known for their large cell sizes and intracellular calcium carbonate deposits. Achromatium inhabit freshwater, brackish, and marine sediments where they accumulate to high abundances at the oxic-anoxic interface. These bacteria alter their vertical position in the sediment along with daily fluctuations in oxygen concentrations. Yet, the mechanism behind their migration in the sediment remains unknown. In this study, we used chemotaxis assays and time-lapse microphotography to analyze the motility and chemotactic behavior of Achromatium oxaliferum. Microscopic observations revealed that rolling and gliding were the main forms of locomotion exhibited by Achromatium. In absence of any stimulant, the movement appeared to be mostly random and changes in direction frequently occurred. Chemotaxis assays showed a negative chemotaxis of Achromatium to oxygen, sulfide, and nitrate, as evidenced by the change from undirected to directed locomotion against the respective chemical gradient. For periods of more than 1 hour, Achromatium cells moved continuously towards regions of low concentration. We further investigated whether the genetic repertoire of Achromatium corresponds to our observations. Based on lab experiments and bioinformatic analyses we conclude that Achomatium motility is propelled by type IV pili guided by a plethora of chemo- and photoreceptors. We conclude that Achromatium uses negative chemo- and phototaxis to confine their distribution in aquatic sediments between opposing oxygen and sulfide gradients. This allows Achromatium to dynamically adjust its position in redox gradients, and thus is likely to have a major contribution to its success in the global colonization of diverse aquatic sediments.

The microbiota and microbiome associated with zooplankton remains rather understudied compared to other animal groups and/or taxa. The present study aimed at investigating the whole-body bacterial microbiota of Daphnia spp. in two contrasting Greek lakes, the shallow and hypertrophic Lake Koronia vs. the deep and mesotrophic Lake Vegoritida, including both egg-bearing and non-egg-bearing individuals. In both lakes, 2,060 bacterial operational taxonomic units (OTUs) were found, with 223 of them being conditionally rare (crOTUs) with low contribution even for the dominant phyla, with L. Vegoritida having more crOTUs than L. Koronia. The individuals microbiota had inconsiderable overlap with the surrounding water microbiota in both lakes. The two lakes showed significant differences in their Daphnia -associated microbiota. L. Koronia had richer OTUs and rather homogeneous bacterial communities, with higher occupancy. Overall, no significant differences in between the microbiota of egg-bearing and non-egg-bearing Daphnia individuals in both lakes. However, regarding the most important OTUs (miOTUs), the L. Koronia miOTUs were highly overlapped between the individuals with and without eggs, with only one missing from the individuals without eggs. In L. Vegoritida the individuals without eggs had only six miOTUs and while egg-bearing individuals had nine different ones; the two lakes had no shared miOTUs., considerable differences occurred.. A total of 27 miOTUs, was found and belonged to the Pseudomonadota, unclassified Bacteria, Cyanobacteria, Bacteroidota, Bacillota and Actinomycetota. Those miOTUs, where assignment to the genus level was possible, they were related to Cyanobium, Mucilaginibacter, Flavobacterium and Staphylococcus. This study showed that lake morphotype and ecological status can exert some impact on Daphnia-associated bacterial microbiota, with more pronounced effects on egg-bearing and non-egg-bearing individuals.

Anaerobic methanotrophic (ANME) archaea are important players in the microbial methane cycle, mitigating methane emissions from anoxic environments. ANME are found ubiquitously in methane-rich sediments, where they can couple anaerobic methane oxidation (AOM) to different electron acceptors such as sulfate, metal oxides, and natural organic matter (NOM). However, we still lack understanding of the geochemical niches and preferred metabolic pathways of most ANME subclades. Here, we investigated the genomic potential and ecophysiology of ANME-2a with respect to metal-dependent AOM in brackish metal-rich coastal sediments. We assembled several high-quality ANME MAGs from subclades with high strain heterogeneity and analyzed the genomic potential for metal-AOM. Additionally, we monitored long-term enrichments with various electron acceptors from the same sediments. Ultimately, we recovered 8 novel genomes of ANME-2a that clustered with an uncharacterized genus with only 2 representatives in public databases for which we propose the name Candidatus Methanoborealis. The analysis of the MAGs showed two different clusters within this genus; one comprising of MAGs from the Baltic Sea that showed high potential for extracellular electron transfer (EET) required for metal-AOM, and another cluster form more diverse environments with less EET potential. The Baltic Sea Ca. Methanoborealis were the only canonical methanotrophs in the incubations during active methane oxidation and metal reduction. Our results contribute to the understanding of the phylogenomic and metabolic diversity in ANME subclades, which will help to further characterize novel ANME lineages from complex sediment samples.

Phosphorus is a vital nutrient required for the functioning of living organisms. In aquatic environments, dissolved inorganic phosphate is considered its most bioavailable form. However, phosphate can be scarce, which has the potential to limit microbial metabolism and ecosystem functioning. To overcome phosphate scarcity, microbes produce alkaline phosphatase (AP) to access dissolved organic phosphorus (DOP). Here, we conducted a year-long study of alkaline phosphatase activity (APA) at the Ellen Browning Scripps Memorial Pier, a nutrient-rich coastal site. APA was observed throughout the year despite phosphate-replete conditions, suggesting that the role of APs in microbial nutrition is not completely understood. We tested the hypothesis that APA may promote acquisition of organic carbon liberated from DOP hydrolysis by growing the heterotrophic marine bacterium Ruegeria pomeroyi on three DOP compounds as sole carbon sources and assessing APA. Controlling for carbon concentration, all DOP sources supported growth, but at lower levels than glucose, with the highest growth observed on glucose-6-phosphate (G6P), followed by adenosine monophosphate (AMP) and adenosine triphosphate (ATP). Moreover, cell-specific APA was significantly enhanced in carbon-deplete conditions and during growth on G6P, relative to cultures grown on replete glucose or nucleotides. These findings suggest alkaline phosphatases (APs) are part of a generic carbon stress response and likely play a role in acquiring certain forms of organic carbon by R. pomeroyi, with implications for other taxa. Overall, this study helps advance the current state of knowledge regarding microbial phosphorus cycling and carbon utilization in aquatic environments.

Microbial communities play a central role in compost-bedded pack (CBP) systems by driving organic matter decomposition and nutrient cycling. The objective of this study was to characterize and compare the bacterial community structure of CBP from two dairy farms in Cordoba, Argentina, using 16S rRNA gene sequencing. Two CBP systems were evaluated: Martin Bono (MB; 30 months in operation) and Angela Teresa (AT; 20 months). The MB system was established on natural soil without bedding addition and included concrete feed alleys, whereas AT was initiated with peanut shell bedding and lacked concrete alleys. In both systems, compost was tilled twice daily. Two samples per farm were collected at a depth of 30 cm during winter 2019. Raw Illumina reads were processed using the DADA2 pipeline, including quality filtering, error modeling, denoising, and chimera removal. A total of four samples yielded 2,503 amplicon sequence variants (ASVs), with approximately 76% of reads retained after filtering and chimera removal, indicating high-quality sequencing data. Taxonomic analysis revealed that bacterial communities in both systems were dominated by phyla typically associated with compost environments, including Actinobacteriota, Proteobacteria, and Firmicutes. Differences in relative abundance between systems suggested shifts in community composition associated with management conditions.

Yarrowia lipolytica is a yeast of industrial interest exhibiting remarkable lipolytic and proteolytic capacities, with a high potential for white biotechnology applications. This yeast can be isolated from a wide range of natural, polluted or anthropogenic environments, including various food products. The present study aims to increase the data on Y. lipolytica phenotypic diversity by evaluating the growth parameters and secreted enzymatic activities of 28 wild-type Y lipolytica (and Yarrowia sp.) strains isolated from various environments across 10 countries. These data could facilitate the selection of appropriate strains for specific research purposes, particularly when wild-type strains are prioritized over genetically engineered ones, like for food-related applications. Notably, strain SWJ-1b exhibited an outstanding combination of favourable characteristics, with optimum (or near) performances for both growth and enzymatic parameters.

Hydrogenotrophic methanogens are of high environmental and biotechnological importance, converting CO2 with H2 into CH4. Despite their common metabolism, variations in the energy metabolism among these methanogens exist, likely affecting their H2 thresholds and growth yields. However, a systematic comparison of these traits for a wide range of hydrogenotrophic methanogens has been lacking. Here, we measured the H2 thresholds and growth yields of nine different hydrogenotrophic methanogens. The H2 threshold, i.e. the H2 partial pressure at which H2 consumption halts, ranged over two orders of magnitude from 1.0 {+/-} 0.5 Pa for Methanobrevibacter arboriphilus to 120 {+/-} 10 Pa for Methanosarcina mazei. Growth yields in our experimental conditions ranged from 0.51 {+/-} 0.28 gDCWx(mol CH4)-1 for Methanococcus maripaludis to 5.28 {+/-} 1.25 gDCWx(mol CH4)-1 for Methanosarcina mazei. The ATP gains, estimated from both H2 thresholds and growth yields, correlated reasonably well, confirming that these variations are due to differences in energy conservation strategies. Our results strongly differentiated the two previously proposed groups of hydrogenotrophic methanogens: methanogens with cytochromes had a high H2 threshold ([&ge;] 21 Pa) and high growth yield (> 4.0 gDCWx(mol CH4)-1), whereas methanogens without cytochromes had lower H2 threshold ([&le;] 7 Pa) and low growth yield (< 1.7 gDCWx(mol CH4)-1). Moreover, our H2 thresholds indicated that additional variations in energy metabolism exist within both groups. Overall, this study found strong variations between hydrogenotrophic methanogens, which are important to understand their environmental prevalence and biotechnological applicability.

Leaf diseases pose a serious threat to faba bean production. Leaf blotch of faba bean, caused by Alternaria spp., has become increasingly widespread and destructive in several countries. Leaf diseases pose a serious threat to faba bean production. The infection of plant by pathogens can be influenced by various factors associated with the host plant, environmental conditions and presence of other microorganisms. The phyllosphere and endosphere play a critical role in plant health and disease development. This study aimed to evaluate the factors shaping the structure and diversity of fungal communities associated with faba beans. Plant samples were collected in 2004 from two intensively managed faba bean production fields in the central region of Latvia. Fungal assemblages were characterized using an ITS region metabarcoding approach based on Illumina MiSeq sequencing. Among the assigned amplicon sequence variant (AVS), 65% belonged to the phylum Ascomycota, while approximately 4% were classified as Basidiomycota. Alternaria and Cladosporium were the dominant genera across samples. The alfa and beta diversities of fungal communities was higher during flowering of faba beans to compare with ripening. The higher abundance of Basidiomycota yeasts were observed during flowering, in contrast, Cladosporium genus was significantly more abundant during ripening. Alternaria DNA was found on leaves that showed no symptoms of the disease. The diversity and composition of fungal communities were significantly influenced by sampling time and presence of leaf blotch, caused by Alternaria spp.

Formate is emerging as an important molecule in carbon capture and utilization technologies. However, its low electron density makes formate less attractive for energy storage. Some hydrogenotrophic methanogens can reduce formate to methane, thereby upgrading it into an established energy carrier. The bottleneck in this process is that 75% of the carbon is lost as carbon dioxide, and achieving a complete formate-to-methane conversion requires co-feeding hydrogen. However, hydrogen-dependent genetic regulation of formate metabolism inhibits simultaneous formate and hydrogen utilization in hydrogenotrophic methanogens. Here, we compared the catalytic performance of the genetically modified strain Methanothermobacter thermautotrophicus {Delta}H (pFdh) with M. thermautotrophicus Z-245 by conducting continuous cultivation at different hydrogen concentrations. While M. thermautotrophicus Z-245 is a natural formatotroph, M. thermautotrophicus {Delta}H (pFdh) was engineered to enable formate utilization via episomal expression of a formate dehydrogenase-gene cassette. We found that M. thermautotrophicus {Delta}H (pFdh) can simultaneously utilize formate and hydrogen. It continuously consumed formate at {approx} 0.1 mM dissolved hydrogen, enabling a 75.6% formate-to-methane conversion efficiency. M. thermautotrophicus Z-245 showed a declining formate consumption at {approx} 0.016 mM and only reached a maximum stable efficiency of 36.3%. These results suggest that M. thermautotrophicus {Delta}H (pFdh) is largely insensitive to hydrogen-induced genetic regulation; however, it still faces redox-related metabolic limitations at dissolved hydrogen concentrations above 0.4 mM. Overall, the findings reveal a potential strategy to circumvent hydrogen-induced regulation of formate metabolism and identify M. thermautotrophicus {Delta}H (pFdh) as a promising biocatalyst for formate-to-methane conversion.

O_LIPhyllosphere microbiomes are subject to microbial import from various sources and undergo substantial changes during phenological changes of plants. However, these processes are still poorly understood for forest canopies. We propose that phenology-driven changes in host properties, and rainwater-mediated, within-canopy transport shape the phyllosphere microbiome in temperate forests. Leaves and throughfall samples were collected from oak, ash and linden trees at top, mid, and bottom canopy positions at the Leipzig canopy crane facility (Germany) at time points representing early, mid and late phenological stages. Bacterial community composition was assessed by 16S rRNA gene amplicon sequencing. C_LIO_LIPhenological stages explained 19% of phyllosphere bacterial community variation, followed by tree species identity (12%) and canopy position (2%). Later phenological stages exhibited more homogeneous and functionally redundant phyllosphere communities along with a strong decline of plant pathogens and increasing potential for microbially mediated biocontrol mechanisms. Throughfall transported up to 1011 bacterial cells per litre with maximum bacterial fluxes at the canopy top. C_LIO_LIOur findings demonstrate that in temperate forests, phenology-driven effects on the phyllosphere microbiome are far more important than tree species specific effects. Extent and selectivity of throughfall-mediated mobilization may play a crucial role for the spatial heterogeneity of microbial communities in tree crowns. C_LI

The study of microbial volatile organic compounds (mVOCs) is a growing area of research, with applications ranging from agriculture to human health. The majority of the mVOC data are from in vitro liquid cultures, while few analyses of bacterial and fungal volatilomes on solid media cultures exist. Studies comparing liquid versus solid cultures of bacteria and fungi show significant changes to the soluble metabolites that are produced, suggesting that large differences would be observed for mVOCs based on the culture conditions. To test this idea, we characterized the volatilomes of Chromobacterium violaceum (strain ATCC(R) 12472) and C. vaccinii (strain MWU328), and those of their isogenic cviR- quorum sensing mutants cultured on solid versus liquid Kings Medium B media. VOCs were sampled using thin-film solid-phase microextraction (TF-SPME) and analyzed by two-dimensional gas chromatography-time-of-flight mass spectrometry (GCxGC-TOFMS). Of the three variables examined - Chromobacterium species, media type, and quorum sensing ability - growth on liquid versus solid media caused the most significant differences in the volatilomes. Bacterial species and quorum sensing ability were also influential, but to a lesser degree. Our findings indicate the importance of growth conditions in microbial volatilomics, and therefore, more consideration should be given to how microorganisms are cultured for volatilome analyses. ImportanceThe purpose of this work is to elucidate the differences in the volatile metabolic profiles of Chromobacterium spp. by exploring them through the lens of three variables: growth conditions, species, and the ability to quorum sense. Work on organismal metabolic differences stemming from factors such as liquid versus solid media types remains broadly overlooked. Understanding these effects will allow future researchers to design more robust experiments that better translate to native microbial ecosystems such as rhizosphere and phyllosphere, where volatile compounds may influence plant-pathogen or plant-saprobe interactions.

BackgroundPelagic Sargassum has undergone significant range expansion and dramatic blooms in the Atlantic over the past 15 years. This algaes microbiome provides symbiotic functions that are believed to contribute to its ecological success. Recent research shows that Sargassum-associated bacteria are enriched in integrated prophages compared to the surrounding seawater and that these prophages are inducible by chemical and ultraviolet treatment. ResultsHere, we investigated a Sargassum-derived in vitro multispecies biofilm encompassing the dominant heterotrophic microbial members associated with Sargassum to probe the impacts of prophage induction on the composition of Sargassum microbiomes. Induction was quantified by coverage-based virus-to-host ratios in chemically induced treatments with Mitomycin C and non-induced controls, and the community composition and metabolic profiles were analyzed after a period of recovery post-induction. Chemical induction led to a significant increase in abundance and virus-to-host ratio of viral genomes linked to Vibrio metagenome-assembled genomes. This was accompanied by altered biofilm community composition, with a reduction in Vibrio bacterial abundance that opened niche space for other biofilm members in the genera Pseudoalteromonas, Alteromonas, and Cobetia. The induced Vibrio-associated phages encoded genes involved in quorum sensing, biofilm formation, virulence, and host metabolism. Induction led to a relative loss of 17 metabolic modules, including functions related to energy metabolism and nitrogen utilization. ConclusionDue to the high frequency of lysogeny in the Sargassum microbiome and the susceptibility of prophages to chemical and ultraviolet light induction, these results suggest that prophage integration and induction are mechanisms that significantly contribute to structuring the Sargassum microbiome and its functional profiles, potentially aiding in microbiome flexibility in changing environmental contexts.

Bacterial interactions-whether positive or negative - are crucial for the functioning of microbial communities. Though bacterial interactions are mainly expected to be negative, the sign and strength of interactions are predicted to be context dependent, with interactions typically being more positive in more stressful and nutrient-poor conditions. However, systematic studies investigating how the environment affects interactions between multiple taxa are lacking. Here, we determine if interactions between a panel of natural soil isolates change in response to the environment in which they are grown, with two different artificial media used (one simple and one complex) and a more ecologically relevant soil wash. To maximise natural variation in interactions, we collected multiple isolates from multiple sites: co-occurring (sympatric) isolates were predicted to show more negative interactions than allopatric isolates because of greater overlap in resource use. Pairwise interactions were in general negative, but more negative when grown in a complex lab-derived medium (Tryptic Soy Broth). Mutually beneficial interactions were most common in a simple resource medium (M9 minimal media) and exploitative interactions were most frequent in a soil broth. These patterns were independent of whether species originated from the same or a different site. The study supports the prediction that nutrient rich environments promote more negative interactions, and that measuring interactions of soil isolates in standard lab media is likely to misrepresent interactions occurring in natural environments.

Functional dairy products are increasingly recognized for their ability to provide both essential nutrition and additional health benefits. This study aimed to develop and evaluate a synbiotic yogurt enriched with Lactobacillus plantarum as a probiotic and Stevia rebaudiana extract (1% w/v) as a prebiotic source. Thirteen lactic acid bacteria (LAB) strains were isolated from fermented dairy and vegetable samples and evaluated for probiotic potential through tests for acid and bile tolerance, hydrophobicity, aggregation abilities, and pathogen co-aggregation. Isolate PG1 (Lactobacillus plantarum) demonstrated the highest prebiotic growth stimulation index (49%) in the presence of stevia extract and was selected for yogurt formulation. Yogurt samples were prepared and stored at 4{degrees}C for 10 days. Physicochemical properties (pH, titratable acidity, and protein content), microbiological viability, total phenolic and flavonoid content, antioxidant activity (DPPH assay), and sensory attributes were monitored. The synbiotic yogurt (St-Y) showed enhanced functional properties, with a total phenolic content of 16.67 {micro}g GAE/g, a flavonoid content of 6.28 {micro}g QE/g, and 57.84% antioxidant activity. Additionally, it showed improved protein content and superior sensory scores compared to control samples. These findings suggest that S. rebaudiana fortified probiotic yogurt can serve as a nutritious, antioxidant-rich, and sensory-acceptable functional dairy product.

Enteric methane emissions from ruminant livestock contribute to global warming, creating an urgent need for effective mitigation strategies that do not compromise animal productivity and welfare. Methanogenic archaea within the rumen microbiome drive enteric methane emissions. However, large-scale rumen-fluid sampling in commercial production systems is impractical, due to its invasive nature and the associated logistical challenges. This study hypothesised that rumination enables the capture of rumen microbial signals within the oral cavity and using oral microbiome profiles to provide a practical, non-invasive alternative method for proxy methane phenotyping in commercial production systems. To test the hypothesis, we estimated the oral microbiability, defined as the proportion of phenotypic variance in methane emissions explained by oral microbiome variation. Samples were collected from 209 animals across two trials in Queensland, Australia. Oral microbiome samples were obtained from all animals, with paired rumen samples in one trial, and methane emissions were measured using either the sulphur hexafluoride (SF6) tracer technique or the GreenFeed system. Microbial features were characterised using taxonomic and functional annotations, and microbiability was estimated using mixed linear models incorporating microbiome-based relationship matrices. Although the small sample size limited strong conclusions, the oral microbiability estimates reported in this study were comparable to those derived from rumen samples. Functional microbial profiles generally explained a greater proportion of methane variation than taxonomic profiles, suggesting that microbial function is more closely linked to methane production than community composition alone. However, these differences were not statistically significant due to large standard errors. These findings suggest that oral microbiome sampling potentially provides a practical, minimally invasive, scalable proxy method for methane emissions of individual cattle in grazing systems, where direct methane gas measurements are labour-intensive and difficult to implement. Integrating oral microbiome profiles in the existing breeding model with the host genetics, weight and environmental factors could provide a promising pathway for enabling selection for low emissions and advancing reduced emissions livestock farming under real-world production conditions. Lay summaryCattle produce methane as part of their normal digestion and this contributes to climate change. Reducing methane emission in grazing livestock systems is therefore important. However, measuring methane from individual grazing animals is difficult, costly, and often impractical under commercial conditions. The rumen microbiome has been used as a proxy for estimating methane emissions, but collecting rumen samples is invasive and impractical for large-scale use. Because rumination transfers material from the rumen to the mouth, we investigated whether microbes found in cattle mouths could also be used to estimate how much methane an individual animal produced. We suggest that mouth-swab sampling method can be an alternative to rumen fluid sampling because it was less invasive, relatively quick and practically applicable in commercial conditions. Importantly, the microbiome explained a meaningful proportion of the between-animal variation for methane emission. This suggests that collection of mouth swabs is a potentially scalable alternative proxy method to identify cattle that naturally produce less methane. Overall, our findings support the potential use of oral ruminant microbial information to improve breeding and management strategies aimed at reducing methane emissions while maintaining productive livestock systems. Teaser TextThis study demonstrates that collecting oral swabs from the mouths of grazing beef cattle could provide a scalable method to estimate individual methane emissions in commercial production systems, offering a practical alternative to invasive rumen sampling and complex gas measurement systems. These findings support the development of scalable breeding and management strategies for methane mitigation in large-scale livestock production systems.

Objective. To evaluate the diagnostic and prognostic significance of C reactive protein (CRP) level dynamics within the first five days after surgery for the early detection of surgical site infections (SSI) and to identify independent risk factors, taking into account regional specifics of surgical management (types of surgeries, duration of procedures), as well as the local hospital microbial landscape. Materials and Methods. A single-center retrospective cohort analysis of data from 127 patients who underwent surgical procedures between 2022 and 2024 was conducted. CRP levels on postoperative days 1, 3, and 5 were assessed, and delta values were calculated. Descriptive statistics, ROC analysis, and multivariate logistic regression were used to identify predictors of SSI. Results. Patients with SSI lacked the physiological decrease in CRP levels by day 5. The most informative indicator was the CRP level on day 3: a threshold of >106 mg/L was associated with a high risk of SSI (AUC=0.76; sensitivity 85%, specificity 63%). Independent predictors of SSI included surgery duration (OR=1.015 per 1 min; p<0.001) and the increase in CRP between days 3 and 5 (delta CRP3-5: OR=1.027; p=0.023). A combined model (clinical parameters + CRP) demonstrated the highest predictive ability (AUC=0.79). Conclusion. Monitoring CRP dynamics, particularly on days 3 and 5, is a highly informative and accessible method for the early diagnosis of SSI. A CRP threshold of >100 mg/L on day 3 and its subsequent increase should serve as a trigger for in-depth diagnostic investigation and rationalization of antimicrobial therapy. Keywords: C reactive protein, postoperative complications, surgical site infection, antibiotic therapy, predictive factors, diagnosis

AimsSponge microbiomes have been extensively studied, in part due to their potential as sources of novel antimicrobials and other biologics, with most research focusing on Demosponges. Here, we investigate the Hexactinellid sponge Pheronema carpenteri, previously identified as a promising source of antibiotic-producing bacteria. MethodsUsing next-generation sequencing of bacterial 16S rRNA genes and a single sponge metagenome, we examined the composition of bacterial communities of P. carpenteri sponges recovered from the Porcupine Seabight, along with local water and sediment samples. ResultsOur results show that P. carpenteri harbours a microbiome abundant in Proteobacteria (47.1-59.4%) and Actinobacteria (11.5-27.5%), with consistent intra-aggregation similarities and structured intra-sponge communities. A metagenomic analysis revealed the presence of several nitrogen cycling genes (nirK, nosZ, nirS homologues of proteobacterial origin), supporting a suggestion that these sponges may play a role in nitrogen cycling, while biosynthetic gene clusters (BGCs) were limited (4 complete clusters). Notably, bacterial community structures within P. carpenteri aggregations resemble those observed in both low and high microbial abundance (LMA/HMA) sponges. ConclusionsHexactinellids are traditionally considered LMA sponges, so identifying species that deviate from this dichotomy provides new insights into sponge microbiome ecology. Integrating Hexactinellids into both culture-dependent and culture-independent studies will advance our broader understanding of sponge-associated microbial diversity and could inform biodiscovery programmes in marine environments. Impact StatementOur findings support the suggestion that a combination of culture-based and molecular analyses is required to generate a comprehensive picture of the biosynthetic potential of P. carpenteri sponges. We also reveal insights into the ecosystem services that sponge microbiomes may contribute towards. These observations could facilitate a deeper understanding of the biotechnological and environmental value of key marine resources.