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BACKGROUND: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens. RESULTS: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments. CONCLUSIONS: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.

The oxygenation of Earths atmosphere represents the quintessential transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution; molecular clock models indicate the diversification and ecological expansion of respiratory metabolisms in the several hundred million years following atmospheric oxygenation. Across this same interval, the geological record preserves 13C enrichment in some carbonate rocks, called the Lomagundi-Jatuli excursion (LJE). By combining data from geologic and genomic records, a self-consistent metabolic evolution model emerges for the LJE. First, fermentation and methanogenesis were major processes remineralizing organic carbon before atmospheric oxygenation. Once an ozone layer formed, shallow water and exposed environments were shielded from UVB/C radiation, allowing the expansion of cyanobacterial primary productivity. High primary productivity and methanogenesis led to preferential removal of 12C into organic carbon and CH4. Extreme and variable 13C enrichments in carbonates were caused by 13C-depleted CH4 loss to the atmosphere. Through time, aerobic respiration diversified and became ecologically widespread, as did other new metabolisms. Respiration displaced fermentation and methanogenesis as the dominant organic matter remineralization processes. As CH4 loss slowed, dissolved inorganic carbon in shallow environments was no longer highly 13C enriched. Thus, the loss of extreme 13C enrichments in carbonates marks the establishment of a new microbial mat ecosystem structure, one dominated by respiratory processes distributed along steep redox gradients. These gradients allowed the exchange of metabolic by-products among metabolically diverse organisms, providing novel metabolic opportunities. Thus, the microbially induced oxygenation of Earths atmosphere led to the transformation of microbial ecosystems, an archetypal example of planetary microbiology.IMPORTANCEThe oxygenation of Earths atmosphere represents the most extensive known chemical transformation of a planetary surface by microbial processes. In turn, atmospheric oxygenation transformed metabolic evolution by providing oxidants independent of the sites of photosynthesis. Thus, the evolutionary changes during this interval and their effects on planetary-scale biogeochemical cycles are fundamental to our understanding of the interdependencies among genomes, organisms, ecosystems, elemental cycles, and Earths surface chemistry through time.

Methane (CH4) is a potent greenhouse gas emitted by archaea in anaerobic environments such as wetland soils. Tidal freshwater wetlands are predicted to become increasingly saline as sea levels rise due to climate change. Previous work has shown that increases in salinity generally decrease CH4 emissions, but with considerable variation, including instances where salinization increased CH4 flux. We measured microbial community composition, biogeochemistry, and CH4 flux from field samples and lab experiments from four different sites across a wide geographic range. We sought to assess how site differences and microbial ecology affect how CH4 emissions are influenced by salinization. CH4 flux was generally, but not always, positively correlated with CO2 flux, soil carbon, ammonium, phosphate, and pH. Methanogen guilds were positively correlated with CH4 flux across all sites, while methanotroph guilds were both positively and negatively correlated with CH4 depending on site. There was mixed support for negative relationships between CH4 fluxes and concentrations of alternative electron acceptors and abundances of taxa that reduce them. CH4/salinity relationships ranged from negative, to neutral, to positive and appeared to be influenced by site characteristics such as pH and plant composition, which also likely contributed to site differences in microbial communities. The activity of site-specific microbes that may respond differently to low-level salinity increases is likely an important driver of CH4/salinity relationships. Our results suggest several factors that make it difficult to generalize CH4/salinity relationships and highlight the need for paired microbial and flux measurements across a broader range of sites.

Subtropical oceans contribute significantly to global primary production, but the fate of the picophytoplankton that dominate in these low-nutrient regions is poorly understood. Working in the subtropical Mediterranean, we demonstrate that subduction of water at ocean fronts generates 3D intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic zone into the dark ocean. These contain fresh picophytoplankton assemblages that resemble the photic-zone regions where the water originated. Intrusions propagate depth-dependent seasonal variations in microbial assemblages into the ocean interior. Strikingly, the intrusions included dominant biomass contributions from nonphotosynthetic bacteria and enrichment of enigmatic heterotrophic bacterial lineages. Thus, the intrusions not only deliver material that differs in composition and nutritional character from sinking detrital particles, but also drive shifts in bacterial community composition, organic matter processing, and interactions between surface and deep communities. Modeling efforts paired with global observations demonstrate that subduction can flux similar magnitudes of particulate organic carbon as sinking export, but is not accounted for in current export estimates and carbon cycle models. Intrusions formed by subduction are a particularly important mechanism for enhancing connectivity between surface and upper mesopelagic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.

Diversity-generating retroelements (DGRs) are used by bacteria, archaea, and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these targeted genes. However, the function and benefits of DGR-diversified proteins in cellular hosts remain elusive. We find that 82% of DGRs from one of the major monophyletic lineages of DGR reverse transcriptases are encoded by multicellular bacteria, which often have two or more DGR loci in their genomes. Using the multicellular purple sulfur bacterium Thiohalocapsa sp. PB-PSB1 as an example, we characterized nine distinct DGR loci capable of generating 10282 different combinations of target proteins. With environmental metagenomes from individual Thiohalocapsa aggregates, we show that most of PB-PSB1s DGR target genes are diversified across its biogeographic range, with spatial heterogeneity in the diversity of each locus. In Thiohalocapsa PB-PSB1 and other bacteria hosting this lineage of cellular DGRs, the diversified target genes are associated with NACHT-domain anti-phage defenses and putative ternary conflict systems previously shown to be enriched in multicellular bacteria. We propose that these DGR-diversified targets act as antigen sensors that confer a form of adaptive immunity to their multicellular consortia, though this remains to be experimentally tested. These findings could have implications for understanding the evolution of multicellularity, as the NACHT-domain anti-phage systems and ternary systems share both domain homology and conceptual similarities with the innate immune and programmed cell death pathways of plants and metazoans.

Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

Discovering new deep hydrothermal vent systems is one of the biggest challenges in ocean exploration. They are a unique window to elucidate the physical, geochemical, and biological processes that occur on the seafloor and are involved in the evolution of life on Earth. In this study, we present a molecular analysis of the microbial composition within the newly discovered hydrothermal vent field, JaichMaa ja ag, situated in the Southern Pescadero Basin within the Gulf of California. During the cruise expedition FK181031 in 2018, 33 sediment cores were collected from various sites within the Pescadero vent fields and processed for 16S rRNA amplicon sequence variants (ASVs) and geochemical analysis. Correlative analysis of the chemical composition of hydrothermal pore fluids and microbial abundances identified several sediment-associated phyla, including Thermotogota, that appear to be enriched in sediment horizons impacted by hydrothermal fluid flow. Comparative analysis of Thermotogota with the previously explored Auka hydrothermal vent field situated 2 km away displayed broad similarity between the two locations, although at finer scales (e.g., ASV level), there were notable differences that point to core-to-core and site-level factors revealing distinct patterns of distribution and abundance within these two sediment-hosted hydrothermal vent fields. These patterns are intricately linked to the specific physical and geochemical conditions defining each vent, illuminating the complexity of this unique deep ocean chemosynthetic ecosystem.

Ocean spring phytoplankton blooms are dynamic periods important to global primary production. We document vertical patterns of a diverse suite of eukaryotic algae, the prasinophytes, in the North Atlantic Subtropical Gyre with monthly sampling over four years at the Bermuda Atlantic Time-series Study site. Water column structure was used to delineate seasonal stability periods more ecologically relevant than seasons defined by calendar dates. During winter mixing, tiny prasinophytes dominated by Class II comprise 46  ±  24% of eukaryotic algal (plastid-derived) 16S rRNA V1-V2 amplicons, specifically Ostreococcus Clade OII, Micromonas commoda, and Bathycoccus calidus. In contrast, Class VII are rare and Classes I and VI peak during warm stratified periods when surface eukaryotic phytoplankton abundances are low. Seasonality underpins a reservoir of genetic diversity from multiple prasinophyte classes during warm periods that harbor ephemeral taxa. Persistent Class II sub-species dominating the winter/spring bloom period retreat to the deep chlorophyll maximum in summer, poised to seed the mixed layer upon winter convection, exposing a mechanism for initiating high abundances at bloom onset. Comparisons to tropical oceans reveal broad distributions of the dominant sub-species herein. This unparalleled window into temporal and spatial niche partitioning of picoeukaryotic primary producers demonstrates how key prasinophytes prevail in warm oceans.

This paper reviews the effects of gut microbiota in regulating neurodegenerative diseases through controlling gut-brain axis. Specific microbial populations and their metabolites (short-chain fatty acids and tryptophan derivatives) regulate neuroinflammation, neurogenesis and neural barrier integrity. We then discuss ways by which these insights lead to possible interventions - probiotics, prebiotics, dietary modification, and fecal microbiota transplantation (FMT). We also describe what epidemiological and clinical studies have related certain microbiota profiles with the courses of neurodegenerative diseases and how these impact the establishment of microbiome-based diagnostics and individualized treatment options. We aim to guide microbial ecology research on this key link to neurodegenerative disorders and also to highlight collaborative approaches to manage neurological health by targeting microbiome-related factors. [ABSTRACT FROM AUTHOR]

Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases. [ABSTRACT FROM AUTHOR]

A river-lake system plays an important role in water management by providing long-term and frequent water diversions. However, hydrological connectivity in the system can have a profound effect on sediment microbial communities through pH, nutrient concentrations, and benthos invertebrates. Consequently, identifying the key environmental factors and their driving mechanisms is vital for microbial adaptation strategies to extreme environments. In this study, we analyzed the significant difference in sediment bacterial and fungal community structures and diversity indices among Dongting Lake and its tributary rivers, which worked as a typical river-connected lake ecosystem. There were significant differences in biotic and abiotic environments in the sediment habitats of Dongting Lake and its tributary rivers. Random forest analysis revealed that pH and Mollusca were found to be the most important abiotic and biotic variables for predicting both bacterial and fungal community structures, respectively. The beta diversity decomposition analyses showed that the bacterial and fungal community compositional dissimilarities among different sections were dominated by species replacement processes, with more than half of the OTUs in each section being unique. Notably, both biotic and abiotic factors affected the number and the relative abundance of these bacterial and fungal unique OTUs, leading to changes in community composition. Mollusca, pH, TP, NO3-N, and NH4-N were negatively related to the relative abundance of Actinobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes, and Ascomycota, while Annelida and ORP were positively related to the relative abundance of Actinobacteria and Gemmatimonadetes. Additionally, PICRUSt analysis revealed that the functional dissimilarity among lakes and rivers was strengthened in unique species compared to all species in bacterial and fungal communities, and the changes of functional types helped to improve the habitat environment in the main Dongting Lake and promote the process of microbial growth. From our results, the role of macrozoobenthos and physicochemical characteristics in driving the sediment microbial community spatial variations became clear, which contributed to further understanding of the river-lake ecosystem. [ABSTRACT FROM AUTHOR]

The editorial discusses the importance of microbial OMICS in advancing sustainability in agricultural and environmental microbiology. Microorganisms provide essential ecosystem services and play crucial roles in global ecosystems. The use of OMICS technologies has led to significant progress in sustainable agriculture and environmental management by elucidating microbial functions and interactions in diverse ecosystems. Studies highlighted in the editorial demonstrate how microbial OMICS can impact soil health, crop productivity, and the diversity of soil bacterial communities, offering potential solutions to challenges such as food scarcity and environmental protection. [Extracted from the article]

The mammalian gastrointestinal tract quickly becomes densely populated with foreign microorganisms shortly after birth, thereby establishing a lifelong presence of a microbial community. These commensal gut microbiota serve various functions, such as providing nutrients, processing ingested compounds, maintaining gut homeostasis, and shaping the intestinal structure in the host. Dysbiosis, which is characterized by an imbalance in the microbial community, is closely linked to numerous human ailments and has recently emerged as a key factor in health prognosis. Tuberculosis (TB), a highly contagious and potentially fatal disease, presents a pressing need for improved methods of prevention, diagnosis, and treatment strategies. Thus, we aim to explore the latest developments on how the host's immune defenses, inflammatory responses, metabolic pathways, and nutritional status collectively impact the host's susceptibility to or resilience against Mycobacterium tuberculosis infection. The review addresses how the fluctuations in the gut microbiota not only affect the equilibrium of these physiological processes but also indirectly influence the host's capacity to resist M. tuberculosis. This work highlights the central role of the gut microbiota in the host–microbe interactions and provides novel insights for the advancement of preventative and therapeutic approaches against tuberculosis. [ABSTRACT FROM AUTHOR]

Microbes play an important role in human and animal health, as well as animal productivity. The host microbial interactions within ruminants play a critical role in animal health and productivity and provide up to 70% of the animal's energy needs in the form of fermentation products. As such, many studies have investigated microbial community composition to understand the microbial community changes and factors that affect microbial colonization and persistence. Advances in next-generation sequencing technologies and the low cost of sequencing have led many studies to use 16S rDNA-based analysis tools for interrogation of microbiomes at a much finer scale than traditional culturing. However, methods that rely on single base pair differences for bacterial taxa clustering may inflate or underestimate diversity, leading to inaccurate identification of bacterial diversity. Therefore, in this study, we sequenced mock communities of known membership and abundance to establish filtration parameters to reduce the inflation of microbial diversity due to PCR and sequencing errors. Additionally, we evaluated the effect of the resulting filtering parameters proposed using established bioinformatic pipelines on a study consisting of Holstein and Jersey cattle to identify breed and treatment effects on the bacterial community composition and the impact of filtering on global microbial community structure analysis and results. Filtration resulted in a sharp reduction in bacterial taxa identified, yet retain most sequencing data (retaining >79% of sequencing reads) when analyzed using 3 different microbial analysis pipelines (DADA2, Mothur, USEARCH). After filtration, conclusions from α-diversity and β-diversity tests showed very similar results across all analysis methods. The mock community-based filtering parameters proposed in this study help provide a more realistic estimation of bacterial diversity. Additionally, filtration reduced the variation between microbiome analysis methods and helped to identify microbial community differences that could have been missed due to the large animal-to-animal variation observed in the unfiltered data. As such, we believe the new filtering parameters described in this study will help to obtain diversity estimates that are closer to realistic values, improve the ability to detecting microbial community differences, and help to better understand microbial community changes in 16S rDNA-based studies. The list of standard abbreviations for JDS is available at adsa.org/jds-abbreviations-24. Nonstandard abbreviations are available in the Notes. [ABSTRACT FROM AUTHOR]

Archaea continues to be one of the least investigated domains of life, and in recent years, the advent of metagenomics has led to the discovery of many new lineages at the phylum level. For the majority, only automatic genomic annotations can provide information regarding their metabolic potential and role in the environment. Here, genomic data from 2,978 archaeal genomes was used to perform automatic annotations using bioinformatics tools, alongside synteny analysis. These automatic classifications were done to assess how good these different tools perform in relation to archaeal data. Our study revealed that even with lowered cutoffs, several functional models do not capture the recently discovered archaeal diversity. Moreover, our investigation revealed that a significant portion of archaeal genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial genomes, a diverse range of unclassified proteins is obtained, with well-studied organisms like Escherichia coli having a substantially lower proportion of uncharacterized regions, ranging from <5 to 25%, and less studied lineages being comparable to archaea with the range of 35–40% of unclassified regions. Leveraging this analysis, we were able to identify metabolic protein markers, thereby providing insights into the metabolism of the archaea in our dataset. Our findings underscore a substantial gap between automatic classification tools and the comprehensive mapping of archaeal metabolism. Despite advances in computational approaches, a significant portion of archaeal genomes remains unexplored, highlighting the need for extensive experimental validation in this domain, as well as more refined annotation methods. This study contributes to a better understanding of archaeal metabolism and underscores the importance of further research in elucidating the functional potential of archaeal genomes. [ABSTRACT FROM AUTHOR]

Hatcheries nationwide suffer from unexplained acute production failures, termed crashes. The microbiota of oysters relates to larval health with previous studies showing that some bacterial species have positive and others negative effects on oyster health. To investigate microbial correlates of crashes, we collected samples from every batch of oyster larvae (Crassostrea virginica) produced by the Horn Point Laboratory Oyster Hatchery since 2021 and analyzed the microbiota of 15 of those batches over their duration in the hatchery, from age of 3 to 5 days until either harvest or complete die off of the batch. Across events, die-offs generally became evident at or after six days of age. We found that the microbiota of oyster larvae appears to respond to die-off events with crashed batches having fundamentally different microbiota than good batches at age 7 to 9 and 9 to 12 days. Crashed batches were often taken over by microeukaryotes and bacterial taxa from the Protobacteria and Bacteroidetes phyla. However, this presumably opportunistic community differed between batches. Observed Vibrio species level groups did not appear to be oyster pathogens and appeared to respond to, rather than precede, crashes. The microbiota of 3 to 5 day old larvae were statistically related to whether a die-off occurred later in the larval batches' life, only when the taxa were first agglomerated to family level. The detection of two microbial species not previously known to associate with oysters, along with an increased presence of Dinophyceae, predominantly the toxin-producing Gyrodinium jinhaense, in 3 to 5 day old oyster larvae was statistically linked with subsequent batch crashes. This study suggests that the health of larval oysters shapes their microbiome. Conversely, it provides hints that the microbiome of larvae, and perhaps harmful algae, may drive hatchery crashes. [ABSTRACT FROM AUTHOR]

Tumor microenvironment (TME) immune cells and gastric mucosal microbiome constitute two vital elements of tumor tissue. Increasing evidence has elucidated their clinicopathological significance in predicting outcomes and therapeutic efficacy. However, comprehensive characterization of immune cell-associated microbiome signatures in the TME is still in the early stages of development. Here, we characterized the gastric mucosa microbiome and its associations with immune-activated related transcripts (IATs) in 170 GC tumor tissues and matched non-tumor tissues using 16s rRNA gene sequencing and quantitative reverse transcription-PCR. Microbial diversity and richness were significantly higher in GC tumor tissues than in non-tumor tissues. Differences in microbial composition between the groups were evident, with Firmicutes, Proteobacteria, Bacteroidota, Campilobacterota, Actinobacteria, Fusobacteriota, Verrucomicrobiota, Acidobacteriota, and Cyanobacteria being the dominant phyla in the gastric mucosal microbiota. Microbial interaction network analysis revealed distinctive centralities of oral bacteria (such as Fusobacterium, Porphyromonas, Prevotella, etc.) in both tumor and normal mucosae networks, suggesting their significant influence on GC microbial ecology. Furthermore, we analyzed the expression of IATs (CXCL9, CXCL10, GZMA, GZMB, PRF1, CD8A, IFNG, TBX2, and TNF) and characterized IAT-relevant gastric microbiome signatures in GC patients. Our results showed that the expression of CXCL9, CXCL10, GZMA, GZMB, PRF1 and IFNG was significantly higher in tumor tissues than in adjacent normal tissues in GC patients. Notably, high expression of IATs in tumor tissues was associated with improved survival in GC patients and could serve as a powerful predictor for disease-free survival. Additionally, analysis of IAT levels and mucosal microbiota diversity revealed a correlation between higher IAT expression and increased microbiota richness and evenness in the IATs high group, suggesting potential interactions between mucosal microbiota and tumor immunopathology. Spearman correlation analysis showed positive associations between IAT expression and specific mucosal bacterial species. Notably, Akkermansia muciniphila demonstrated potential involvement in modulating GZMB expression in the GC mucosal microenvironment. These findings underscore the importance of mucosal microbiota alterations in GC and suggest potential therapeutic targets focusing on modulating the tumor microbiota for improved clinical outcomes. The detailed characterization of these elements has profound implications for both treatment and survival prediction in GC. We observed that microbial diversity and richness were significantly higher in GC tumor tissues compared to non-tumor tissues. These differences highlight the unique microbial landscape of GC tumors and suggest that the microbiome could influence tumor development and progression. Importantly, our study demonstrated that high expression levels of IATs in GC tumor tissues were associated with improved patient survival. This suggests that IATs not only reflect immune activation but also serve as valuable biomarkers for predicting disease-free survival. The potential of IATs as predictive markers underscores their utility in guiding therapeutic strategies and personalizing treatment approaches. Moreover, the correlation between higher IAT expression and increased microbiota richness and evenness suggests that a diverse and balanced microbiome may enhance immune responses and contribute to better clinical outcomes. These findings highlight the critical need to consider mucosal microbiota alterations in GC management. Targeting the tumor microbiota could emerge as a promising therapeutic strategy, potentially leading to more effective treatments and improved patient outcomes. Understanding and modulating the microbiome’s role in GC opens new avenues for innovative therapeutic interventions and personalized medicine. [ABSTRACT FROM AUTHOR]

Bacterial communities are ubiquitous, found in natural ecosystems, such as soil, and within living organisms, like the human microbiome. The dynamics of these communities in diverse environments depend on factors such as spatial features of the microbial niche, biochemical kinetics, and interactions among bacteria. Moreover, in many systems, bacterial communities are influenced by multiple physical mechanisms, such as mass transport and detachment forces. One example is gut mucosal communities, where dense, closely packed communities develop under the concurrent influence of nutrient transport from the lumen and fluid-mediated detachment of bacteria. In this study, we model a mucosal niche through a coupled agent-based and finite-volume modeling approach. This methodology enables us to model bacterial interactions affected by nutrient release from various sources while adjusting individual bacterial kinetics. We explored how the dispersion and abundance of bacteria are influenced by biochemical kinetics in different types of metabolic interactions, with a particular focus on the trade-off between growth rate and yield. Our findings demonstrate that in competitive scenarios, higher growth rates result in a larger share of the niche space. In contrast, growth yield plays a critical role in neutralism, commensalism, and mutualism interactions. When bacteria are introduced sequentially, they cause distinct spatiotemporal effects, such as deeper niche colonization in commensalism and mutualism scenarios driven by species intermixing effects, which are enhanced by high growth yields. Moreover, sub-ecosystem interactions dictate the dynamics of three-species communities, sometimes yielding unexpected outcomes. Competitive, fast-growing bacteria demonstrate robust colonization abilities, yet they face challenges in displacing established mutualistic systems. Bacteria that develop a cooperative relationship with existing species typically obtain niche residence, regardless of their growth rates, although higher growth yields significantly enhance their abundance. Our results underscore the importance of bacterial niche dynamics in shaping community properties and succession, highlighting a new approach to manipulating microbial systems. [ABSTRACT FROM AUTHOR]

Among salmonids, brook charr, Salvelinus fontinalis has been gaining popularity in aquaculture. However, major limitations associated with opportunistic diseases that result from unstable egg and fry‐rearing conditions are experienced under intensive rearing conditions. Great losses in brook charr culture result from viral (e.g., infectious pancreatic necrosis, viral hemorrhagic septicemia virus), fungal (e.g., saprolegniosis), and bacterial (e.g., furunculosis, cold water disease, columnaris) diseases. Unfortunately, there is no effective treatment for viral diseases for brook charr, and the chemical disinfectants and antibiotics commonly used against bacterial and fungal infections are reaching their limits (pathogen resistance, microbial community disruption), making alternative and more sustainable rearing approaches essential to bolster aquaculture. In this regard, recent studies show that many microbial species (bacteria, archaea, viruses, eukaryotes‐like protozoa, and unicellular fungi) are essential from the earliest life stages for the proper development and growth of fish. Based on ecological theory and work on marine fish, it has been hypothesized that current aquaculture practices favor r‐strategic, opportunistic microbes that are detrimental to fish health and development. Consequently, to ensure the success and sustainability of brook charr farming, a new aquaculture paradigm involving recirculating aquaculture systems (RAS) that select a K‐enriched, specialized microbial community as a preventive measure against those microbial diseases is a very promising avenue. In this review, after introducing brook charr biology, the role of microbes in brook charr rearing and the general problems of disease and low fry survival due to an imbalance in the microbial community will be discussed. Various curative and prophylactic treatment methods currently used to control these diseases and their impact on microbial ecology will be covered, and we will conclude with the rationale of microbial ecology management and its effectiveness in promoting fry survival through disease prevention. To our knowledge, this is the first literature review addressing the promises of managing microbial ecology in a sustainable way in the brook char industry. [ABSTRACT FROM AUTHOR]

The editorial "Microbiome and machine learning, volume II" published in Frontiers in Microbiology on October 15, 2024, explores the intersection of microbiomes and machine learning. It highlights the importance of understanding microbial communities for human health, biodiversity, and food production. The editorial discusses the challenges and benefits of using machine learning techniques, such as neural networks, in microbiome research. It also emphasizes the ethical considerations and practical applications of machine learning in various fields, including clinical diagnostics and food safety. [Extracted from the article]

Objective: Bacterial vaginosis is a disease caused by vaginal microecology disorder, which seriously affects female health. At present, there are many drugs to treat BV, and this study aims to compare the efficacy and safety of multiple drugs for BV through a network meta-analysis (NMA). Methods: All studies were sourced from PubMed and Embase databases from the establishment date to April 13, 2023. We evaluated the clinical cure success rate and adverse effects (abnormal increase in vaginal discharge, external genital irritation, and vulvar itching) and performed subgroup analyses of the clinical cure success rate for different modes of administration. All statistical analyses were performed using R and STATA 14.0 software for network meta-analysis. Results: Weincluded42studies thatmetthecriteria, involving a total of8382patients. Network meta-analysis results showed that metronidazole and secnidazole had a higher rate of adverse reactions than placebo (RR 7.06; 95%-CI 2.61-19.10, RR 4.03; 95%-CI1.63-9.98), theadverse reaction rateofprobioticsgroupwaslowerthanthat of metronidazole group (RR 0.44; 95%-CI 0.21-0.93). The clinical cure rate of oral ornidazole was better than clindamycin (RR 16.08; 95%-CI 1.72-150.47), Secnidazole (RR 8.17; 95%-CI 1.66-40.25) and probiotics. Directmeta-analysis results showed that ornidazole had a better clinical cure rate than Secnidazole (RR1.22; 95%-CI 1.10-1.34), oral ornidazole had a better clinical cure rate than Secnidazole (RR 1.23; 95%-CI 1.11-1.36). The clinical cure rate of vaginal application of sucrose was better than metronidazole (RR 1.12; 95%-CI 1.03-1.21) and metronidazole had a lower clinical cure rate than probiotics (RR 0.68; 95%-CI 0.52-0.88). Conclusions: The results of this systematic review and network meta-analysis suggest that ornidazole may be an effective alternative for the treatment of BV, and that sucrose and probiotics are potential BV treatments that need to be validated by more high-quality clinical studies in the future. [ABSTRACT FROM AUTHOR]

Fungi and bacteria can be found coexisting in a wide variety of environments. The combination of their physical and molecular interactions can result in a broad range of outcomes for each partner, from competition to cooperative relationships. Most of these interactions can also be found in the human gastrointestinal tract. The gut microbiota is essential for humans, helping the assimilation of food components as well as the prevention of pathogen invasions through host immune system modulation and the production of beneficial metabolites such as short-chain fatty acids (SCFAs). Several factors, including changes in diet habits due to the progressive Westernization of the lifestyle, are linked to the onset of dysbiosis statuses that impair the correct balance of the gut environment. It is therefore crucial to explore the interactions between commensal and diet-derived microorganisms and their influence on host health. Investigating these interactions through co-cultures between humanand fermented food-derived lactobacilli and yeasts led us to understand how the strains' growth yield and their metabolic products rely on the nature and concentration of the species involved, producing either cooperative or competitive dynamics. Moreover, single cultures of yeasts and lactobacilli proved to be ideal candidates for developing immune-enhancing products, given their ability to induce trained immunity in blood-derived human monocytes in vitro. Conversely, co-cultures as well as mixtures of yeasts and lactobacilli have been shown to induce an anti-inflammatory response on the same immune cells in terms of cytokine profiles and activation surface markers, opening new possibilities in the design of probiotic and dietary therapies. [ABSTRACT FROM AUTHOR]

Background: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs. Results: The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs. Conclusions: This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Bh9ATT9ssZEtNaJHv1wg7G Video Abstract [ABSTRACT FROM AUTHOR]

The use of potentially beneficial microorganisms in agriculture (microbial inoculants) has rapidly accelerated in recent years. For microbial inoculants to be effective as agricultural tools, these organisms must be able to survive and persist in novel environments while not destabilizing the resident community or spilling over into adjacent natural ecosystems. Despite the importance of propagule pressure to species introductions, few tools exist in microbial ecology to predict the outcomes of agricultural microbial introductions. Here, we adapt a macroecological propagule pressure model to a microbial scale and present an experimental approach for testing the role of propagule pressure in microbial inoculant introductions. We experimentally determined the riskrelease relationship for an IAA-expressing Pseudomonas simiae inoculant in a model monocot system. We then used this relationship to simulate establishment outcomes under a range of application frequencies (propagule number) and inoculant concentrations (propagule size). Our simulations show that repeated inoculant applications may increase establishment, even when increased inoculant concentration does not alter establishment probabilities. Applying ecological modeling approaches like those presented here to microbial inoculants may aid their sustainable use and provide a monitoring tool for microbial inoculants. [ABSTRACT FROM AUTHOR]

Cave microbiota knowledge has greatly expanded in the past decades, driven by the development of molecular techniques, which allow an in-depth characterization of diversity and its metabolic potential. This review focuses on the contribution of DNA sequencing technologies to depict the cave microbiome for the three domains of life (Bacteria, Archaea, and Microeukaryotes), assessing their advantages and limits. Cultural methods do not provide a representative view of cave microbial diversity but do offer, subsequently, the possibility to genomically characterize the strains isolated from caves. Next-generation DNA sequencing permits an exhaustive description of microbial biodiversity in caves, using metabarcoding (for taxonomic assessment) or metagenomics (for taxonomic and functional assessments). It proved useful to compare caves, different rooms, or substrata (water, soil, bedrock, etc.) within a cave, or the effect of cave disturbance in Lascaux and elsewhere. The integration of next-generation DNA sequencing with cultivation techniques, physico-chemical characterization, and other complementary approaches is important to understand the global functioning of caves and to provide key information to guide cave conservation strategies. [ABSTRACT FROM AUTHOR]

Persistent human papillomavirus (HPV) infection is associated with the grading of cervical intraepithelial neoplasia (CIN), high-risk HPV infection, multiple HPV infections, high HPV load, HPV infection of surgical margin, and age in CIN after conization. The immune mechanism is complex and is primarily related to vaginal microecology disorders, immune escape, immune response impairment, and the release of regulatory cytokines. Currently, the treatment methods for postoperative persistent HPV infection include surgical treatment, antiviral treatment, vaccination, and other approaches. [ABSTRACT FROM AUTHOR]

Clostridium perfringens type F isolates utilize C. perfringens enterotoxin (CPE) to cause food poisoning (FP) and nonfoodborne gastrointestinal diseases. The enterotoxin gene (cpe) can be located on either the chromosome or plasmids, but most FP isolates carry a chromosomal cpe (c-cpe) gene. Our 2000 article in Applied and Environmental Microbiology (66:3234-3240, 2000, https://doi.org/10.1128/aem.66.8.3234-3240.2000https://doi.org/10.1128/AEM.66.8.3234-3240.2000) determined that vegetative cells and spores of c-cpe isolates are more heat resistant than those of plasmid cpe (p-cpe) isolates, which is favorable for their survival in improperly cooked or held food. However, that 2000 article was recently retracted (90:e00249-24, 2024, https://doi.org/10.1128/aem.00249-24). To our knowledge, the 2000 article remains the only study reporting that heat resistance differences are common between both vegetative cells and spores of type F c-cpe isolates vs type F p-cpe isolates. To confirm and preserve this information in the literature, the heat resistance portion of the 2000 study has been repeated. The 2024 results reproduced the 2000 results by indicating that, relative to the surveyed type F p-cpe isolates, the vegetative cells of surveyed type F c-cpe isolates are ~2-fold more heat resistant and the spores of most surveyed c-cpe isolates are ~30-fold more heat resistant. However, consistent with several reports since our 2000 paper, one surveyed type F c-cpe isolate (which did not appreciably sporulate in 2000 but sporulated in 2024) produced spores with intermediate heat sensitivity, confirming that spores of some type F c-cpe isolates lack exceptional heat resistance. IMPORTANCE Clostridium perfringens type F food poisoning (FP), which is the second most common bacterial cause of FP, involves the production of C. perfringens enterotoxin. While the enterotoxin gene (cpe) can be located on either the chromosome or plasmids in type F isolates, most FP cases are caused by chromosomal cpe isolates. The current results support the conclusion that the vegetative cells and spores of type F chromosomal cpe isolates are often more heat resistant than vegetative cells and spores of type F plasmid cpe isolates. Greater heat resistance should favor the survival of the spores and vegetative cells of those chromosomal cpe isolates in temperature-abused food, which may help explain the strong association of type F chromosomal cpe strains with FP. [ABSTRACT FROM AUTHOR]

The coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a palm tree pest capable of rapidly expanding its population in new territories. Previous studies identified a digestive symbiosis between CRB and its gut microbes. However, no research compared the genetic variation of CRBs with their hindgut microbiota on a global scale. This study aims to investigate the genetic divergence of CRB and the compositional variation of CRB's microbiota across different geographical locations, and explore the association between them and their predicted functional profiles and environmental data. The research reveals a distinct and consistent microbial community within local populations, but it varies across different geographical populations. The microbial functional profiles linked to the production of digestive enzymes, including cellulases and ligninases, are nonetheless globally conserved. This suggests that CRBs employ specific mechanisms to select and maintain microbes with functional benefits, contributing to host adaptability, stress tolerance, and fitness. The CRB microbial communities did not appear to recapitulate the genetic variation of their hosts. Rather than depend on obligate symbionts, CRBs seem to establish similar digestive associations with whatever environmentally acquired microbes are available wherever they are, aiding them in successfully establishing after invading a new location. IMPORTANCE Coconut rhinoceros beetles (CRBs) are notorious pests on Arecaceae plants, posing destructive threats to countries highly reliant on coconut, oil palm, and date palm as economic crops. In the last century, CRBs have rapidly expanded their presence to territories that were once free of these beetles. The United States, for instance, has officially designated CRBs as invasive and alien pests. Given their remarkable ability to swiftly adapt to new environments, their gut microbes may play a crucial role in this process. While the microbiota of CRBs vary depending on geographical location, these beetles consistently exhibit a functionally identical digestive association with locally acquired microbes. This underscores the significance of CRB-microbe association in shaping the adaptive strategies of this agricultural pest. [ABSTRACT FROM AUTHOR]

This study investigates airborne bacterial and fungal communities in south-eastern Italy and Albania using advanced DNA-based techniques and compositional data analysis (CoDa). We assess the significance of airborne microbial communities, detailing our methodologies for site selection, sample collection, DNA extraction, and data analysis. Our results reveal distinct differences in microbial composition between the two regions, driven by local environmental factors. Specifically, Albanian samples showed higher abundances of bacterial species such as Rubellimicrobium roseum and Sphingomonas cynarae, while Italian samples were characterized by a prevalence of Truepera radiovictrix and Rubrobacter radiotolerans. In terms of fungi, Albanian sites exhibited greater abundance of Mycosphaerella tassiana, Aureobasidium pullulans, and Ascochyta herbicola. Aitchison distance-based dendrograms and principal component analysis (PCA) biplots, utilizing singular value decomposition, clearly delineated a geographical separation of microbial communities, underscoring the impact of regional atmospheric conditions on microbial composition. In the discussion, we interpret these findings in the context of regional environmental factors, highlighting their implications for understanding regional differences in airborne microbial communities. The conclusion emphasizes the effectiveness of advanced DNA techniques and CoDa in environmental microbiology, offering insights into how local environmental conditions shape microbial communities and suggesting directions for future research and public health considerations. [ABSTRACT FROM AUTHOR]

Disturbance response and recovery are increasingly important in microbial ecology, as microbes may recover from disturbances differently than macro communities. Past disturbances can alter microbial community structure and their response to subsequent disturbance events, but it remains unclear if the same recovery patterns persist after long‐term exposure to stress. Here, we compare bacterial community composition in a community that experienced 2 years of monthly salinity addition disturbances with a community that has not experienced salinity additions. We then track the response and recovery to an additional salinity addition based on past disturbance exposure. We tested the following hypotheses: first, communities with a repeated disturbance history will have a different community composition than communities without a disturbance history; second, communities exposed to repeated disturbances will undergo a different recovery trajectory than communities experiencing a novel disturbance. We find that repeated disturbances alter community composition and affect community response and recovery to a subsequent disturbance after 2 years, primarily through increased resistance. This work enhances our understanding of microbial temporal dynamics and suggests that novel disturbances may pose a threat to microbial community structure and function. [ABSTRACT FROM AUTHOR]

As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as "characteristic communities of microorganisms" found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns. [ABSTRACT FROM AUTHOR]

Oral mucositis is a common and debilitating oral complication in head and neck cancer patients undergoing radiotherapy, resulting in diminished quality of life and potential treatment disruptions. Oral microbiota has long been recognized as a contributing factor in the initiation and progression of radiation-induced oral mucositis (RIOM). Numerous studies have indicated that the radiation-induced oral microbial dysbiosis promotes the occurrence and severity of oral mucositis. Therefore, approaches that modulate oral microbial ecology are promising for the management of RIOM. Probiotics as a relatively predicable and safe measure that modulates microecology have garnered significant interest. In this review, we discussed the correlation between RIOM and oral microbiota, with a particular focus on the efficacy of probiotics in the control of RIOM, in order to provide novel paradigm for the management of this disease. [ABSTRACT FROM AUTHOR]

Filamentous bacteria are one of the main components of activated sludge microorganisms, which not only support flocculent bacteria in forming sludge flocs but also easily lead to sludge bulking. This article summarizes the high-throughput sequencing technology and database construction that integrates the FISH probe and 16s rRNA gene of filamentous bacteria. The detection frequency and abundance were statistically analyzed to determine the core filamentous bacteria. The filamentous bacteria searchable in the NCBI database belong to six phyla and 42 genera, with a total of 94 species. The core filamentous bacteria in the expanded activated sludge include Microthrix parvicella (M. parvicella), type 0092, Mycobacterium fortuitum, etc. The physiological ecology of the core filamentous bacteria is discussed in detail, aiming to establish targeted sludge expansion control strategies, reduce the incidence and harm of sludge expansion, and propose that future research needs to promote further development in the field of environmental microbiology. [ABSTRACT FROM AUTHOR]

Archival DNA samples collected and analysed for a range of research and applied questions have accumulated in the laboratories of universities, government agencies and commercial service providers for decades. These DNA archives represent a valuable, yet largely un‐tapped repository of genomic information. With lowering costs of, and increasing access to, high‐throughput sequencing, we predict an increase in retrospective research to explore the wealth of information that resides in these archival samples. However, for this to occur, we need confidence in the integrity of the DNA samples, often stored under suboptimal conditions and their fitness of purpose for downstream genomic analysis.Here, we borrow from a well‐established concept in ancient DNA to evaluate sample integrity, defined as loss of information content in recovered amplicons, of frozen DNA samples and based on the ratio of ⍺‐diversity of short‐ and long‐read 16S rRNA gene sequences.The 16S rRNA variable region of 87 stored DNA samples, extracted from soil, collected from western and southern agricultural regions of Australia between 2001 and 2021 were sequenced using both PacBio full length reads (V1–V9, 1.5 kbp) and Illumina short‐reads (V3–V4, 200–450 bp). When ⍺‐diversity ratios were calculated between the long and short reads to assess DNA degradation, the ratio of ⍺‐diversity did not decrease in older samples versus younger samples.We suggest this as a novel method to confirm integrity of DNA before embarking on large‐scale diversity profiling projects using archival DNA. [ABSTRACT FROM AUTHOR]

Recent advancements in next-generation sequencing have revolutionized our understanding of the human microbiome. Despite this progress, challenges persist in comprehending the microbiome's influence on disease, hindered by technical complexities in species classification, abundance estimation, and data compositionality. At the same time, the existence of macroecological laws describing the variation and diversity in microbial communities irrespective of their environment has been recently proposed using 16s data and explained by a simple phenomenological model of population dynamics. We here investigate the relationship between dysbiosis, i.e. in unhealthy individuals there are deviations from the "regular" composition of the gut microbial community, and the existence of macro-ecological emergent law in microbial communities. We first quantitatively reconstruct these patterns at the species level using shotgun data, and addressing the consequences of sampling effects and statistical errors on ecological patterns. We then ask if such patterns can discriminate between healthy and unhealthy cohorts. Concomitantly, we evaluate the efficacy of different statistical generative models, which incorporate sampling and population dynamics, to describe such patterns and distinguish which are expected by chance, versus those that are potentially informative about disease states or other biological drivers. A critical aspect of our analysis is understanding the relationship between model parameters, which have clear ecological interpretations, and the state of the gut microbiome, thereby enabling the generation of synthetic compositional data that distinctively represent healthy and unhealthy individuals. Our approach, grounded in theoretical ecology and statistical physics, allows for a robust comparison of these models with empirical data, enhancing our understanding of the strengths and limitations of simple microbial models of population dynamics. Author summary: In this study, we explore emerging ecological properties in gut microbiomes. Our aim here is to determine whether these patterns can be informative of the gut microbiome (healthy or diseased) and unveil essential ingredients driving its population dynamics. Leveraging on metagenomic data and interpretable statistical models based on ecological processes, we show that not all ecological patterns are informative to characterize its states, while few are (e.g., species diversity). Eventually, thanks to the ecological interpretability of the inferred models' parameters, our analysis provides insights into the role of environmental fluctuations and carrying capacities of the gut microbiomes in both health and disease. This study offers valuable knowledge, bridging theoretical concepts with practical implications for human health. [ABSTRACT FROM AUTHOR]

Introduction: Gut microbiome plays a crucial role in the health of wild animals. Their structural and functional properties not only reflect the host's dietary habits and habitat conditions but also provide essential support for ecological adaptation in various environments. Methods: This study investigated the gut microbiome of Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita) across different geographic regions using 16S rRNA gene and metagenomic sequencing. Results: Results showed distinct clustering patterns in gut microbiota based on geographic location. Soil had an insignificant impact on host gut microbiome. Himalayan langurs from mid-altitude regions exhibited higher levels of antibiotic resistance genes associated with multidrug resistance, while Xizang macaques from high-altitude regions showed a broader range of resistance genes. Variations in carbohydrate-active enzymes and KEGG pathways indicated unique metabolic adaptations to different environments. Discussion: These findings provide valuable insights into the health and conservation of these primates and the broader implications of microbial ecology and functional adaptations in extreme conditions. [ABSTRACT FROM AUTHOR]

Objective: To investigate the effects of berberine (BBR) as a treatment on intestinal microecological alterations and enteritis in mice produced by TNBS. Methods: There were seven mice per group: seven in the healthy group (Ctrl), seven in the TNBS-induced enteritis group (TNBS), and seven in the berberine treatment group (BBR). The mice were weighed, slaughtered after 7 days, and subjected to high-throughput intestinal microecological analysis by Illumina, as well as haematological detection and imaging evaluation of colon pathology. Results: The alterations in colon length, immune cell subpopulations, inflammatory factors, and intestinal microecology of mice induced by BBR were refined using a battery of experiments and observations. According to intestinal microecological studies, BBR can increase the number of bacteria, including Lactobacillus, Verrucomicrobia, Bacteroides, and Akkermansia muciniphila. Conclusion: BBR has a therapeutic effect on TNBS-induced colitis in mice, which is associated with modifications in immune cell subpopulations and intestinal microecology. It also offers a viable approach as a prospective probiotic (like Akkermansia muciniphila) to IBD therapy in clinical settings. [ABSTRACT FROM AUTHOR]

In recent years, there has been an increasing focus on microbial ecology and its possible impact on agricultural production, owing to its eco-friendly nature and sustainable use. The current study employs metabolomics technologies and bioinformatics approaches to identify changes in the exometabolome of Streptomyces albidoflavus B24. This research aims to shed light on the mechanisms and metabolites responsible for the antifungal and growth promotion strategies, with potential applications in sustainable agriculture. Metabolomic analysis was conducted using Q Exactive UPLC-MS/MS. Our findings indicate that a total of 3,840 metabolites were identified, with 137 metabolites exhibiting significant differences divided into 61 up and 75 downregulated metabolites based on VIP >1, |FC| >1, and p < 0.01. The interaction of S. albidoflavus B24 monoculture with the co-culture demonstrated a stronger correlation coefficient. The Principal Component Analysis (PCA) demonstrates that PCA1 accounted for 23.36%, while PCA2 accounted for 20.28% distinction. OPLS-DA score plots indicate significant separation among different groups representing (t1) 24% as the predicted component (to1) depicts 14% as the orthogonal component. According to the findings of this comprehensive study, crude extracts from S. albidoflavus demonstrated varying abilities to impede phytopathogen growth and enhance root and shoot length in tested plants. Through untargeted metabolomics, we discovered numerous potential molecules with antagonistic activity against fungal phytopathogens among the top 10 significant metabolites with the highest absolute log2FC values. These include Tetrangulol, 4-Hydroxybenzaldehyde, and Cyclohexane. Additionally, we identified plant growth-regulating metabolites such as N-Succinyl-L-glutamate, Nicotinic acid, L-Aspartate, and Indole-3-acetamide. The KEGG pathway analysis has highlighted these compounds as potential sources of antimicrobial properties The inhibitory effect of S. albidoflavus crude extracts on pathogen growth is primarily attributed to the presence of specific gene clusters responsible for producing cyclic peptides such as ansamycins, porphyrin, alkaloid derivatives, and neomycin. Overall, it is apparent that crude extracts from S. albidoflavus exhibited varying abilities to inhibit the growth of three phytopathogens and enhancement in both root and shoot length of tested plants. This research enhances our understanding of how secondary metabolites contribute to growth promotion and biocontrol, supporting ecosystem sustainability and resilience while boosting productivity in sustainable agriculture. [ABSTRACT FROM AUTHOR]

Milk residue and the accompanying biofilm accumulation in milking systems can compromise the microbial quality of milk and the downstream processes of cheese production. Over a six-month study, the microbial ecosystems of milk (n = 24), tap water (n = 24) and environmental swabs (n = 384) were cultured by plating decimal dilutions to obtain viable counts of total aerobic mesophilic lactose-utilizing bacteria (lactose-M17), lactic acid bacteria (MRS), yeasts and molds (Yeast, Glucose, Chloramphenicol (YGC) medium). Viable aerobic lactose-M17 plate counts of milk remained well below 4.7 log CFU/ml over five of the months, except for 1 week in November where milk at the facility exceeded 5 log CFU/ml. Swab samples of the farm milking equipment showed consistent viable counts after sanitation, while the bulk tank swabs contained the lowest counts. Viable counts from swabs of the facility were generally below the detection limit in the majority of samples with occasional residual contamination on some food contact surfaces. Extracted DNA was amplified using primers targeting the V3-V4 region of the 16S rRNA gene, and the amplicons were sequenced by MiSeq to determine the shared microbiota between the farm and the processing facility (8 genera). Culture independent analysis of bacterial taxa in milk, water and residual contamination after sanitation with swab samples revealed the shared and distinct microbiota between the sample types of both facilities. Amplicon sequence variants (ASVs) of the V3-V4 region of the 16S rRNA gene revealed that the microbiota of milk samples had lower diversity than water or environmental swabs (279 ASVs compared to 3,444 in water and 8,747 in environmental swabs). Brevibacterium and Yaniella (both Actinomycetota) were observed in all sampling types. Further studies will include whole genome sequencing of Brevibacterium spp. isolates to determine their functionality and diversity within the system. [ABSTRACT FROM AUTHOR]

Gut microecology, the complex community consisting of microorganisms and their microenvironments in the gastrointestinal tract, plays a vital role in maintaining overall health and regulating various physiological and pathological processes. Recent studies have highlighted the significant impact of gut microecology on the regulation of uric acid metabolism. Natural products, including monomers, extracts, and traditional Chinese medicine formulations derived from natural sources such as plants, animals, and microorganisms, have also been investigated for their potential role in modulating uric acid metabolism. According to research, The stability of gut microecology is a crucial link for natural products to maintain healthy uric acid metabolism and reduce hyperuricemia-related diseases. Herein, we review the recent advanced evidence revealing the bidirectional regulation between gut microecology and uric acid metabolism. And separately summarize the key evidence of natural extracts and herbal formulations in regulating both aspects. In addition, we elucidated the important mechanisms of natural products in regulating uric acid metabolism and secondary diseases through gut microecology, especially by modulating the composition of gut microbiota, gut mucosal barrier, inflammatory response, purine catalyzation, and associated transporters. This review may offer a novel insight into uric acid and its associated disorders management and highlight a perspective for exploring its potential therapeutic drugs from natural products. [ABSTRACT FROM AUTHOR]

Background: In this study, individual methanogenic (anaerobic), granular biofilms were used as true community replicates to assess whole-microbial-community responses to environmental cues. The aggregates were sourced from a lab-scale, engineered, biological wastewater treatment system, were size-separated, and the largest granules were individually subjected to controlled environmental cues in micro-batch reactors (μBRs). Results: Individual granules were identical with respect to the structure of the active community based on cDNA analysis. Additionally, it was observed that the active microbial community of individual granules, at the depth of 16S rRNA gene sequencing, produced reproducible responses to environmental changes in pH, temperature, substrate, and trace-metal supplementation. We identified resilient and susceptible taxa associated with each environmental condition tested, as well as selected specialists, whose niche preferences span the entire trophic chain required for the complete anaerobic degradation of organic matter. Conclusions: We found that single anaerobic granules can be considered highly-replicated whole-ecosystems with potential usefulness for the field of microbial ecology. Additionally, they act as the smallest whole-community unit within the meta-community of an engineered bioreactor. When subjected to various environmental cues, anaerobic granules responded reproducibly allowing for rare or unique opportunities for high-throughput studies testing whole-community responses to a wide range of environmental conditions. [ABSTRACT FROM AUTHOR]

Acanthamoeba, are ubiquitous eukaryotic microorganisms, that play a pivotal role in recognizing and engulfing various microbes during predation, offering insights into microbial dynamics and immune responses. An intriguing observation lies in the apparent preference of Acanthamoeba for Gram-negative over Gram-positive bacteria, suggesting potential differences in the recognition and response mechanisms to bacterial prey. Here, we comprehensively review pattern recognition receptors (PRRs) and microbe associated molecular patterns (MAMPs) that influence Acanthamoeba interactions with bacteria. We analyze the molecular mechanisms underlying these interactions, and the key finding of this review is that Acanthamoeba exhibits an affinity for bacterial cell surface appendages that are decorated with carbohydrates. Notably, this parallels warm-blooded immune cells, underscoring a conserved evolutionary strategy in microbial recognition. This review aims to serve as a foundation for exploring PRRs and MAMPs. These insights enhance our understanding of ecological and evolutionary dynamics in microbial interactions and shed light on fundamental principles governing immune responses. Leveraging Acanthamoeba as a model organism, provides a bridge between ecological interactions and immunology, offering valuable perspectives for future research. [ABSTRACT FROM AUTHOR]

Genetically lean and obese individuals have distinct intestinal microbiota and function. However, the underlying mechanisms of the microbiome heterogeneity and its regulation on epithelial function such as intestinal stem cell (ISC) fate remain unclear. Employing pigs of genetically distinct breeds (obese Meishan and lean Yorkshire), this study reveals transcriptome‐wide variations in microbial ecology of the jejunum, characterized by enrichment of active Lactobacillus species, notably the predominant Lactobacillus amylovorus (L. amylovorus), and lactate metabolism network in obese breeds. The L. amylovorus‐dominant heterogeneity is paralleled with epithelial functionality difference as reflected by highly expressed GPR81, more proliferative ISCs and activated Wnt/β‐catenin signaling. Experiments using in‐house developed porcine jejunal organoids prove that live L. amylovorus and its metabolite lactate promote intestinal organoid growth. Mechanistically, L. amylovorus and lactate activate Wnt/β‐catenin signaling in a GPR81‐dependent manner to promote ISC‐mediated epithelial proliferation. However, heat‐killed L. amylovorus fail to cause these changes. These findings uncover a previously underrepresented role of L. amylovorus in regulating jejunal stem cells via Lactobacillus‐lactate‐GPR81 axis, a key mechanism bridging breed‐driven intestinal microbiome heterogeneity with ISC fate. Thus, results from this study provide new insights into the role of gut microbiome and stem cell interactions in maintaining intestinal homeostasis. [ABSTRACT FROM AUTHOR]

hermodynamics has predicted many different kinds of microbial metabolism by determining which pairs of electron acceptors and donors will react to produce an exergonic reaction (a negative net change in Gibbs free energy). In energy-limited environments, such as the deep subsurface, such an approach can reveal the potential for unexpected or counter-intuitive energy sources for microbial metabolism. Up until recently, these thermodynamic calculations have been carried out with the assumption that chemical species appearing on the reactant and product side of a reaction formula have a constant concentration, and thus do not count towards net concentration changes and the overall direction of the reaction. This assumption is reasonable considering microorganisms are too small (~1 μm) for any significant differences in concentration to overcome diffusion. However, recent discoveries have demonstrated that the reductive and oxidative halves of reactions can be separated by much larger distances, from millimetres to centimetres via conductive filamentous bacteria, mineral conductivity, and biofilm conductivity. This means that the concentrations of reactants and products can indeed be different, and that concentration differences can contribute to the net negative change in Gibbs free energy. It even means that the same redox reaction, simultaneously running in forward and reverse, can drive energy conservation, in an ElectroMicrobiological Concentration Cell (EMCC). This paper presents a model to investigate this phenomenon and predict under which circumstances such concentration-driven metabolism might take place. The specific cases of oxygen concentration cells, sulfide concentration cells, and hydrogen concentration cells are examined in more detail. [ABSTRACT FROM AUTHOR]

Hypersalinity is common in coastal wetlands throughout warm, tropical, and arid regions. Climate‐induced changes in rainfall, sea level, and anthropogenic modification to basins and coastlines are likely to further increase salinization in these ecosystems. Yet, carbon cycling in hypersaline coastal wetlands is not well understood, and poorly constrained in climate models. In the Coorong, a eutrophic, hypersaline coastal lagoon, recognized as internationally important under the Ramsar convention, organic matter rapidly accumulates in deeper areas of the lagoon, through the settling of fine detrital particles, phytoplankton and suspended sediments. During initial surveys, elevated surface water methane (CH4) concentrations were observed above these fine depositional sediments. To identify the drivers of CH4 production, organic matter and sediment characteristics were assessed in surface sediments. Genetic markers (i.e., 16rDNA and the mcrA functional gene) were used to characterize microbial communities. With multiple lines of evidence, this study identifies organic matter, methanogen abundance, and salinity as important drivers of CH4 production, which is concentrated in depositional zones. Archaea were also more abundant in depositional zones, including methylotrophic methanogens: Methanofastidiosales, Methanomasiliicoccales, Methermicoccaceae, and Methanococcoides. These methanogens were highly correlated to CH4 in porewater, suggesting an influence of methylotrophic methanogenesis. To investigate further, metabolic genes were predicted from 16S rRNA with PICRUSt2. This represents the first effort to analyze CH4 dynamics in the Coorong, underscoring the need to integrate these unique ecosystems into global climate models to enhance our understanding of greenhouse gas dynamics and emissions in a changing climate. [ABSTRACT FROM AUTHOR]

Methicillin‐resistant Staphylococcus aureus (MRSA) can be transmitted between pigs and humans on farms. Hence, the reduction of MRSA carriage in pigs could decrease the risk of zoonotic transmission. Recently, straw bedding has been found to significantly reduce MRSA carriage in pigs. The mechanisms behind this effect remain unclear but changes in the nasal microbiome may play a role. In this exploratory study, the nasal microbiota of pigs kept on straw was examined using V1/V2 16S rRNA gene sequencing. Nasal swabs were collected from 13 pigs at six different time points during the course of a full fattening cycle resulting in 74 porcine samples. In addition, straw samples were collected at each time point. Eleven out of 13 pigs were MRSA positive at housing‐in. We found a strong temporal pattern in the microbial communities. Both microbial diversity and abundance of Staphylococcus species peaked in week 5 after introduction to the straw stable decreased in week 10, when all pigs turned MRSA‐negative, and increased again toward the end of the fattening period. These findings show that the introduction of pigs into a new environment has a huge impact on their nasal microbiota, which might lead to unfavorable conditions for MRSA. Moreover, other Staphylococcus species may play a role in eliminating MRSA carriage. We designed a follow‐up study including two different husbandry systems to further assess these effects. [ABSTRACT FROM AUTHOR]

We report the relationship between enrichment of adapted populations and enhancement of community functional resilience in methanogenic bioreactors. Although previous studies have shown the positive effects of acclimation, this work directly investigated the relationships between microbiome dynamics and performance of anaerobic co-digesting reactors in response to different levels of an environmental perturbation (loading of grease interceptor waste [GIW]). Using the methanogenic microbiome from a full-scale digester, we developed eight sets of microbial communities in triplicate using different feed sources. These substrate-specific microbiomes were then exposed to three independent disturbance events of low-, mid- and high-GIW loading rates. This approach allowed us to directly attribute differences in community responses to differences in community composition. Despite identical inocula, environment (digester operation, substrate loading rate, and feeding patterns) and general whole-community function (methane production and effluent quality) during the cultivation period, different substrates led to different microbial community assemblies. Lipid pre-acclimation led to enrichment of a pool of specialized populations, along with thriving of sub-dominant communities. The enrichment of these populations improved functional resilience and process performance when exposed to a low level of lipid-rich perturbation compared with less-acclimated communities. At higher levels of perturbation, the communities were not able to recover methanogenesis, indicating a loading limit to the resilience response. This study extends our current understanding of environmental perturbations, feed-specific adaptation, and functional resilience in methanogenic bioreactors. [ABSTRACT FROM AUTHOR]

The microbial ecology of raw milk cheeses is determined by bacteria originating from milk and milk-producing animals. Recently, it has been shown that members of the Bifidobacterium mongoliense species may become transmitted along the Parmigiano Reggiano cheese production chain and ultimately may colonize the consumer intestine. However, there is a lack of knowledge regarding the molecular mechanisms that mediate the interaction between B. mongoliense and the human gut. Based on 128 raw milk cheeses collected from different Italian regions, we isolated and characterized 10 B. mongoliense strains. Comparative genomics allowed us to unveil the presence of enzymes required for the degradation of sialylated host-glycans in B. mongoliense, corroborating the appreciable growth on de Man-Rogosa-Sharpe (MRS) medium supplemented with 3'-sialyllactose (3'-SL) or 6'-sialyllactose (6'-SL). The B. mongoliense BMONG18 was chosen, due to its superior ability to utilize 3'-SL and mucin as representative strain, to investigate its behavior when co-inoculated with other bifidobacterial species. Conversely, members of other bifidobacterial species did not appear to benefit from the presence of BMONG18, highlighting a competitive scenario for nutrient acquisition. Transcriptomic data of BMONG18 reveal no significant differences in gene expression when cultivated in a gut simulating medium (GSM), regardless of whether cheese was included or not. Furthermore, BMONG18 was shown to exhibit high adhesion capabilities to HT29-MTX human cells, in line with its colonization ability of a human host. [ABSTRACT FROM AUTHOR]