Distinct Microbial Communities Research Articles

Polyurethane foam degradation combining ozonization and mealworm biodegradation and its exploitation.

The biodegradation of polyurethane foam (PU foam) using a combination of oxidative pre-treatment (ozonization) and Tenebrio molitor (T. molitor) mealworms was conducted in this study. Different degrees of ozone oxidation (0%, 25%, and 50%) were applied to PU foam, which was subsequently fed to mealworms. The mealworms' survival and growth were then compared to mealworms receiving a normal diet (bran). Results showed that mealworms fed with non-oxidized PU foam (PUF0) exhibited a higher consumption rate (11.8%) than those fed with 25% (PUF25) and 50% (PUF50) oxidized PU foam (7.7% and 5.7%, respectively). The survival rate was similar across all the PU foam diets and the bran diet. Fourier transform infrared (FTIR) spectroscopy and differential scanning calorimetry (DSC) analyses revealed minor structural changes in the PU foam. The gut microbiota analysis showed a significant correlation between the PU foam and bran diets. Among the different oxidized PU, distinct microbial community profiles were also observed, with the genus Klebsiella consistently present across the PU foam diets. The ozone pre-treatment altered the palatability and degradation of the PU foam by mealworms, while the mealworm frass and chitin obtained could potentially be used as resources for agricultural and industrial applications that would close the circular bio-economy cycle.

Unveiling microbial succession dynamics on different plastic surfaces using WGCNA.

Over recent decades, marine microorganisms have increasingly adapted to plastic debris, forming distinct plastic-attached microbial communities. Despite this, the colonization and succession processes on plastic surfaces in marine environments remain poorly understood. To address this knowledge gap, we conducted a microbiome succession experiment using four common plastic polymers (PE, PP, PS, and PET), as well as glass and wood, in a temperature-controlled seawater system over a 2- to 90-day period. We employed long-read 16S rRNA metabarcoding to profile the prokaryotic microbiome's taxonomic composition at five time points throughout the experiment. By applying Weighted Gene Co-expression Network Analysis (WGCNA) to our 16S metabarcoding data, we identified unique succession signatures for 77 bacterial genera and observed polymer-specific enrichment in 39 genera. Our findings also revealed that the most significant variations in microbiome composition across surfaces occurred during the initial succession stages, with potential intra-genus relationships that are linked to surface preferences. This research advances our understanding of microbial succession dynamics on marine plastic debris and introduces a robust statistical approach for identifying succession signatures of specific bacterial taxa.

Effects of life history strategy on the diversity and composition of the coral holobiont communities of Sabah, Malaysia

Coral-associated microbes have essential roles in promoting and regulating host function and health. As climate change advances and other environmental perturbations increasingly impact corals, it is becoming ever more important that we understand the composition of the microbial communities hosted. Without this baseline it is impossible to assess the magnitude and direction of any future changes in microbial community structure. Here, we characterised both the bacterial and Symbiodiniaceae communities in four coral species (Diploastrea heliopora, Porites lutea, Pachyseris speciosa, and Pocillopora acuta) collected from Sabah, Malaysia. Our findings reveal distinct microbial communities associated with different coral species tending to reflect the varied life history strategies of their hosts. Microbial communities could be differentiated by collection site, with shifts in Symbiodiniaceae communities towards more stress tolerant types seen in samples collected on the shallow Sunda Shelf. Additionally, we identified a core microbiome within species and a more discrete core between all species. We show bacterial and Symbiodiniaceae communities are structured by host species and appear to be influenced by host life history characteristics. Furthermore, we identified a core microbiome for each species finding that several amplicon sequence variants were shared between hosts, this suggests a key role in coral health regardless of species identity. Given the paucity of work performed in megadiverse regions such as the Coral Triangle, this research takes on increased importance in our efforts to understand how the coral holobiont functions and how it could be altered as climate change advances.

Screening for Pathogens and Studying Bats’ Blood and Tissue Microbiome

Bats possess unique physiological adaptations, including thermophysiological flexibility, which enable them to tolerate and harbor diverse pathogens without overt disease. Their ability to sustain powered flight and enter torpor or hibernation contributes to their immune resilience, making them important reservoirs for zoonotic pathogens such as viruses (rabies, Ebola, coronaviruses) and bacteria (Leptospira, Salmonella, Bartonella, Rickettsia). Bats' dense social roosting and migratory behaviors facilitate pathogen transmission, underscoring the need for effective surveillance. This study examined the blood microbiomes of five bat species from the Vespertilionidae and Rhinolophidae families inhabiting three caves in northern Bulgaria (Devetashka, Orlova, and Parnicite). Using pooled blood samples (n=120) and two bat hearts, DNA was extracted for microbiome analysis via shotgun metagenomic sequencing, alongside PCR-based detection of human pathogens. Bacterial phyla and genera distribution varied significantly among bat species, with prominent genera including Bacillus, Mycoplasma, Pseudomonas, and Sphingobacterium. Alpha diversity, measured by the Simpson index, revealed slightly higher microbial diversity in Miniopterus schreibersii and Myotis myotis, with no significant differences among cave populations. Principal Coordinates Analysis (PCoA) highlighted distinct microbial community compositions between bat species and cave locations. PCR results identified Mycobacterium in 26 of 34 blood samples and in 1 of 2 heart tissue samples, suggesting its prevalence in bat populations. No samples tested positive for Mycobacterium tuberculosis, Brucella spp., Coxiella burnetii, or Toxoplasma gondii, indicating the absence of these pathogens in the sampled individuals. The detection of atypical Mycobacteria and Brucella sp. in the bats' blood emphasizes its potential role as an opportunistic pathogen and the need for further investigation into its zoonotic significance. These findings highlight the diversity and zoonotic potential of bat-associated microbiomes, supporting the need for continued pathogen surveillance in bat populations. All metagenomic shotgun sequencing data were published at NCBI Sequence Read Archive under the bioproject number PRJNA1215671.

The impact of wild-boar-derived microbiota transplantation on piglet microbiota, metabolite profile, and gut proinflammatory cytokine production differs from sow-derived microbiota.

Colonization of co-evolved, species-specific microbes in early life plays a crucial role in gastrointestinal development and immune function. This study hypothesized that modern pig production practices have resulted in the loss of co-evolved species and critical symbiotic host-microbe interactions. To test this, we reintroduced microbes from wild boars (WB) into conventional piglets to explore their colonization dynamics and effects on gut microbial communities, metabolite profiles, and immune responses. At postnatal day (PND) 21, 48 piglets were assigned to four treatment groups: (i) WB-derived mixed microbial community (MMC), (ii) sow-derived MMC, (iii) a combination of WB and sow MMC (Mix), or (iv) Control (PBS). Post-transplantation analyses at PND 48 revealed distinct microbial communities in WB-inoculated piglets compared with Controls, with trends toward differentiation from Sow but not Mix groups. WB-derived microbes were more successful in colonizing piglets, particularly in the Mix group, where they competed with Sow-derived microbes. WB group cecal digesta enriched with Lactobacillus helveticus, Lactobacillus mucosae, and Lactobacillus pontis. Cecal metabolite analysis showed that WB piglets were enriched in histamine, acetyl-ornithine, ornithine, citrulline, and other metabolites, with higher histamine levels linked to Lactobacillus abundance. WB piglets exhibited lower cecal IL-1β and IL-6 levels compared with Control and Sow groups, whereas the Mix group showed reduced IFN-γ, IL-2, and IL-6 compared with the Sow group. No differences in weight gain, fecal scores, or plasma cytokines were observed, indicating no adverse effects. These findings support that missing WB microbes effectively colonize domestic piglets and may positively impact metabolite production and immune responses.IMPORTANCEThis study addresses the growing concern over losing co-evolved, species-specific microbes in modern agricultural practices, particularly in pig production. The implementation of strict biosecurity measures and widespread antibiotic use in conventional farming systems may disrupt crucial host-microbe interactions that are essential for gastrointestinal development and immune function. Our research demonstrates that by reintroducing wild boar-derived microbes into domestic piglets, these microbes can successfully colonize the gut, influence microbial community composition, and alter metabolite profiles and immune responses without causing adverse effects. These findings also suggest that these native microbes can fill an intestinal niche, positively impacting immune activation. This research lays the groundwork for future strategies to enhance livestock health and performance by restoring natural microbial populations that produce immune-modulating metabolites.

Unraveling the shifts in the belowground microbiota and metabolome of Pinus pinaster trees affected by forest decline.

Pinus pinaster Aiton (maritime pine) stands are suffering a generalized deterioration due to different decline episodes throughout all its distribution area. It is well known that external disturbances can alter the plant associated microbiota and metabolome, which ultimately can entail the disruption of the normal growth of the hosts. Notwithstanding, very little is known about the shifts in the microbiota and the metabolome in pine trees affected by decline. The aim of our work was to unravel whether bacterial and fungal communities inhabiting the rhizosphere and root endosphere of P. pinaster trees with symptoms of decline and affected by Matsucoccus feytaudi in the National Park of Sierra Nevada (Granada, Spain) showed alterations in the structure, taxonomical profiles and associative patterns. We also aimed at deciphering potential changes in the rhizosphere and root metabolome. Trees infected by M. feytaudi and healthy individual harbored distinct microbial communities at both compositional and associative patterns. Unhealthy trees were enriched selectively in certain plant growth promoting microorganisms such as several ectomycorrhizal fungi (Clavulina) and Streptomyces, while other beneficial microorganisms (Micromonospora) were more abundant in unaffected pines. The rhizosphere of unhealthy trees was richer in secondary metabolites involved in plant defense than healthy pines, while the opposite trend was detected in root samples. The abundance of certain microorganisms was significantly correlated with several antimicrobial metabolites, thus, being all of them worthy of further isolation and study of their role in forest decline.

Differential mediation of biogeochemical processes through bioturbation by fiddler and sesarmid mangrove crabs.

Macrobenthic bioturbation is vital to facilitate nutrient turnover in estuarine ecosystems and drives spatial heterogeneity in the sediment matrix. In this study, we compared the sediment physico-chemical properties, microbial community structure and functional genes in vertically-stratified sediment samples from bioturbated (burrows of Parasesarma bidens and Tubuca arcuata) and non-bioturbated area in mangrove ecosystems (the Hanjiang River Estuary, Southern China). The result indicated that bioturbation by P. bidens and T. arcuata had significantly different effects on sediment properties, with the action of P. bidens enhancing nutrient accumulation while T. arcuata promoted N2O emission. Burrow microhabitats harbored distinctive microbial communities although the dominant phylum and genera shared considerable similarity with the control sediment surface with Woeseia dominating in vertical profiles across different habitats. Co-occurrence network analysis revealed that crab bioturbation promoted formation of less complex but more functionally-specialized microbial communities. Crab bioturbation enhanced nutrient metabolism and separated clusters in dendrogram demonstrated the species-specific effect between P. bidens and T. arcuata. Our work verified the significance of bioturbators in regulating biogeochemical processes and highlighted the species-specific bioturbation effect between two dominant mangrove crabs (P. bidens vs. T. arcuata).

Sulfate and Dissolved Organic Carbon Concentrations Drive Distinct Microbial Community Patterns in Prairie Wetland Ponds.

Prairie wetland ponds on the Great Plains of North America offer a diverse array of geochemical scenarios that can be informative about their impact on microbial communities. These ecosystems offer invaluable ecological services while experiencing significant stressors, primarily through drainage and climate change. In this first study systematically combining environmental conditions with microbial community composition to identify various niches in prairie wetland ponds, sediments had higher microbial abundance but lower phylogenetic diversity in ponds with lower concentrations of dissolved organic carbon ([DOC]; 10-18 mg/L) and sulfate ([SO4 2-]; 37-58 mg/L) in water. As [DOC] and [SO4 2-] increased, there was an initial decline in abundance but not phylogenetic diversity. Maximum values of both abundance and phylogenetic diversity occurred between 56 and 115 mg/L [DOC] and 5,000-6,000 mg/L [SO4 2-] and decreased thereafter in ponds with 150-180 mg/L and 8,000-14,000 mg/L [DOC] and [SO4 2-], respectively. These findings confirm that environmental variables shape the microbial communities and that key microbial taxa involved in sulfur and carbon cycling dominated these ponds potentially impacting vital biogeochemical processes such as bioavailability of heavy metals, carbon sequestration, and methane emissions.

Rebuilding microbiomes: Facilitating animal-microbe interactions through ecological restoration and rewilding.

Restoring degraded ecosystems is a complex process that involves rebuilding myriad species interactions that make a functioning ecological community. Microorganisms are key to robust ecological restoration - their mutualisms with above-ground communities drive community assembly and increase host fitness. However, microbes are largely ignored during restoration and there is a significant knowledge gap regarding how to restore their interactions with above-ground communities. Here, we tested whether we could enhance interactions between microbes and their invertebrate hosts by reintroducing, or 'rewilding', leaf litter and soil from remnant sites containing species-rich microbial communities, into species poor and geographically isolated revegetated farmland sites. We sequenced both the soil microbiome and the gut microbiome of two dominant invertebrates: native Ecnolagria grandis beetles and introduced Ommatoiulus moreleti millipedes. We sampled 35 months after the initial reintroduction event in remnant (conservation area and source of litter and soil transplant), rewilding transplant (revegetation site with transplant), and control sites (revegetation with no transplant). We found that even ∼20 years after revegetation, restoration sites had distinct microbial communities compared to remnant areas. Although litter and soil transplants failed to increase soil microbial community similarity towards remnant sites, we found marked increases in the diversity and richness of E. grandis microbiomes and a greater degree of overlap with soil microbiomes within rewilding transplant sites relative to control sites. In contrast, there were few changes in O. moreleti microbiomes. Overall, our results suggest rewilding can recover some species interactions during restoration but may not influence all host-microbe systems.

Microbial communities in biosolids-amended soils: A critical review of high-throughput sequencing approaches.

Sustainable reuse of treated wastewater sludge or biosolids in agricultural production requires comprehensive understanding of their risks and benefits. Microbes are central mediators of many biosolids-associated risks and benefits, however understanding of their responses to biosolids remains minimal. Application of biosolids to soils amounts to a coalescence of two distinct microbial communities adapted to vastly different matrices. High-throughput DNA and RNA sequencing (HTS) approaches are required to accurately describe the compositional and functional outcomes of this process as they currently provide the highest possible resolution to deal with complex community-scale phenomena. Furthermore, linkage of HTS data to physicochemical and functional data can reveal biotic and abiotic drivers of coalescence, impacts of biosolids-borne contaminants and the collective downstream implications for soil and plant health. Here we review the current body of literature examining microbial communities in biosolids-amended soils using HTS of total community DNA and RNA. We provide a critical synthesis of soil microbial community composition and functional responses, the physical, chemical and biological drivers of these responses, and the influence of three major biosolids-borne anthropogenic contaminants of concern; antimicrobials and antimicrobial resistance genes, plastics, and per- and polyfluoroalkyl substances (PFAS). Finally, we identify methodological limitations and outstanding research questions precluding a holistic understanding of microbial responses in biosolids-amended soils and envision future research whereby sequence-based microbial ecology is integrated with soil, plant, and contaminant data to preserve soil health, support plant productivity, and remediate contaminants.

In vitro dynamics of rumen microbiota and fermentation profiles with Antler growth of Sika deer.

The rumen microbiota plays a vital role in the nutrient metabolism affecting the growth of velvet antler. However, the fermentation patterns and dynamics of the rumen microbiota across growth stages of velvet antler remain largely unexplored. Here, we employed an in vitro fermentation approach to assess fermentation parameters and microbial composition in the rumen liquid of sika deer during the early growth (EG), metaphase growth (MG), and fast growth (FG) phases . Our findings indicated that the levels of short-chain fatty acids (SCFAs), ammonia nitrogen, and gas production increased over fermentation time in all three groups. The concentrations of total SCFAs, ammonia nitrogen, and gas production, along with the proportions of butyrate, isobutyrate, and isovalerate, were markedly higher in the MG and FG groups compared with the EG group. Principal coordinate analysis highlighted significant variations in microbial communities among the EG, MG, and FG groups during the fermentation process. The abundances of Stomatobaculum and Blautia across the three groups increased over fermentation time, whereas Bacteroides, Lawsonibacter, Sporobacter, Papillibacter, Butyricicoccus, and Succiniclasticum exhibited higher abundances in MG or FG groups than in the EG group after 24 hours of fermentation. Co-occurrence network analysis uncovered positive correlations between butyrate levels and butyrate-producing bacteria (Stomatobaculum, Butyrivibrio) in the MG and FG groups. Additionally, there were positive correlations between proteolytic bacteria (Clostridium and Roseburia) and branched-chain volatile fatty acids in the FG group. These findings shed light on the fermentation patterns and microbial dynamics within the rumen of sika deer during different growth periods of velvet antler.IMPORTANCEVelvet antlers are distinctive and rapidly growing organs that hold significant value in traditional medicine. Through in vitro analysis, our study characterized the dynamics of microbiota and metabolites within the rumen liquid fermentation of sika deer throughout the different antler growth phase. We identified distinct microbial communities at various fermentation time points and observed shifts in fermentation patterns that paralleled antler development. These findings suggest a potentially pivotal role for these microbial dynamics in facilitating the growth process of velvet antlers.

Machine learning models reveal microbial signatures in healthy human tissues, challenging the sterility of human organs

BackgroundThe presence of microbes within healthy human internal organs still remains under question. Our study endeavors to discern microbial signatures within normal human internal tissues using data from the Genotype-Tissue Expression (GTEx) consortium. Machine learning (ML) models were developed to classify each tissue type based solely on microbial profiles, with the identification of tissue-specific microbial signatures suggesting the presence of distinct microbial communities inside tissues.MethodsWe analyzed 13,871 normal RNA-seq samples from 28 tissues obtained from the GTEx consortium. Unaligned sequencing reads with the human genome were processed using AGAMEMNON, an algorithm for metagenomic microbial quantification, with a reference database comprising bacterial, archaeal, and viral genomes, alongside fungal transcriptomes. Gradient-boosting ML models were trained to classify each tissue against all others based on its microbial profile. To validate the findings, we analyzed 38 healthy living tissue samples (samples from healthy tissues obtained from living individuals, not deceased) from an independent study, as the GTEx samples were derived from post-mortem biopsies.ResultsTissue-specific microbial signatures were identified in 11 out of the 28 tissues while the signatures for 8 tissues (Muscle, Heart, Stomach, Colon tissue, Testis, Blood, Liver, and Bladder tissue) demonstrated resilience to in silico contamination. The models for Heart, Colon tissue, and Liver displayed high discriminatory performance also in the living dataset, suggesting the presence of a tissue-specific microbiome for these tissues even in a living state. Notably, the most crucial features were the fungus Sporisorium graminicola for the heart, the gram-positive bacterium Flavonifractor plautii for the colon tissue, and the gram-negative bacterium Bartonella machadoae for the liver.ConclusionThe presence of tissue-specific microbial signatures in certain tissues suggests that these organs are not devoid of microorganisms even in healthy conditions and probably they harbor low-biomass microbial communities unique to each tissue. The discoveries presented here confront the enduring dogma positing the sterility of internal tissues, yet further validation through controlled laboratory experiments is imperative to substantiate this hypothesis. Exploring the microbiome of internal tissues holds promise for elucidating the pathophysiology underlying both health and a spectrum of diseases, including sepsis, inflammation, and cancer.

Evaluation of the biological treatment of a real contaminated groundwater through reductive dechlorination biostimulation

Chlorinated aliphatic hydrocarbons (CAHs) are common groundwater contaminants due to improper utilization in past industrial activity. Anaerobic reductive dechlorination, where bacteria use CAHs as electron acceptors, is crucial for bioremediation. Environmental conditions, such as nutrient availability and electron donors (i.e., molecular hydrogen), can influence the effectiveness of bioremediation processes. Also, bioremediation strategies like bioaugmentation (i.e., the supply of the enriched dechlorinating consortium) and bio-stimulation (i.e., the supply of electron donor) can improve CAHs removal performances. Here, a microcosm study is presented to assess the effectiveness of bioaugmentation with an enriched dechlorinating consortium for groundwater remediation. Target contaminants used were tetrachloroethane (TeCA), trichloroethylene (TCE) and sulphate ion. Various conditions, including biostimulation and bioaugmentation approaches were tested to evaluate the feasibility of biological treatment. Operating conditions, i.e., mineral medium and lactate, facilitated the dechlorination of TCE into ETH, leading to an increase in the dechlorinating population (Dehalococcoides mccartyi) to 67% of the total bacteria, with reductive dechlorination (RD) rates up to 7 µeq/Ld. Conversely, the RD performance of microcosms with real contaminated groundwater was negatively affected by the combined presence of TeCA and sulphate, indicated by a low abundance of D. mccartyi (<3%) and low RD rates (up to 0.39 µeq/Ld), suggesting that the native microbial population lacked the capacity for effective dechlorination. Moreover, the principal component analysis plot highlighted distinct groupings based on microbial community across different microcosm conditions, indeed, microbial community structures dominated by D. McCarty were associated with higher reductive dechlorination rates while non-augmented and non-stimulated microcosms reflected distinct microbial communities dominated by non-dechlorinating taxa. Additionally, RD decreased (48, 23, 22, and 14 µeq/Ld) with increasing sulphate concentrations (0, 150, 225, and 450 mgSO4 -2/L), further demonstrating the inhibitory effect of sulphate in the treated contaminated groundwater. Overall, this study highlights the complex interplay between environmental conditions, treatment strategies, and microbial communities in driving dechlorination processes. Specifically, the effectiveness of reductive dechlorination is heavily influenced by the availability of electron donors and the composition of the medium or groundwater, which can drive significant shifts in microbial community dynamics, either supporting or hindering the reductive dechlorination process.

OP18 Multi-analytical Approaches Reveal Robust Gut Microbial Biomarkers for Inflammatory Bowel Disease Diagnosis: A Large-scale Cohort Study

Abstract Background Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is strongly associated with gut microbiota dysbiosis. While numerous association studies have identified potential diagnostic gut microbial markers, their clinical utility remains limited due to substantial variability across studies and lack of robust validation. Furthermore, despite the availability of multiple analytical approaches for identifying microbial biomarkers, their relative effectiveness remains unclear, and definitive biomarkers for IBD diagnosis are still lacking. This study aims to identify robust gut microbial biomarkers for IBD diagnosis through multiple analytical approaches. Methods We analysed 3,762 participants, including healthy controls (HC, n = 2,467) and patients with IBD (n = 1,293), stratified into CD (n = 879) and UC (n = 414). Gut microbiota profiles were analysed from stool samples using 16S rRNA gene sequencing. Four analytical approaches were employed: (1) differential abundance analyses (DA: LEfSe, ANCOM-BC, and MaAsLin2), (2) supervised random forest machine learning (ML), (3) unsupervised network analysis (NW), and (4) literature-based curation (LC). Biomarker candidates generated by these methods were compared for diagnostic performance using an ensemble ML model. Results Diversity analysis revealed distinct gut microbial community structures among HC, UC, and CD groups (unweighted UniFrac distance, PERMANOVA, p < 0.001, Fig. 1A). Dysbiosis scores, calculated based on these structural differences, were significantly higher in IBD groups compared to HC (Fig. 1B). Each analytical approach identified distinct microbial biomarkers associated with IBD and its subtypes. Supervised ML produced the most effective biomarker sets, achieving the highest diagnostic performance for distinguishing IBD from HC (AUC = 0.971), surpassing LC (AUC = 0.938), DA (AUC = 0.928), and NW (AUC = 0.912), Fig. 2. ML biomarker sets also demonstrated superior accuracy in distinguishing CD from HC (AUC = 0.933) and UC from CD (AUC = 0.892). These results highlight the superiority of ML in selecting robust biomarkers for IBD diagnostics across multiple classification tasks. Conclusion This study identifies robust gut microbial biomarkers for IBD diagnosis through multiple analytical approaches. The biomarker panel demonstrates high diagnostic accuracy in distinguishing both IBD from healthy controls and CD from UC. External validation of these findings is currently ongoing in an independent cohort. These findings provide a foundation for developing reliable microbiome-based diagnostic tools for IBD, potentially enabling more precise disease diagnosis and improved patient care.

Exploring animal food microbiomes and resistomes via 16S rRNA gene amplicon sequencing and shotgun metagenomics.

As a diverse and complex food matrix, the animal food microbiota and repertoire of antimicrobial resistance (AMR) genes remain to be better understood. In this study, 16S rRNA gene amplicon sequencing and shotgun metagenomics were applied to three types of animal food samples (cattle feed, dry dog food, and poultry feed). ZymoBIOMICS mock microbial community was used for workflow optimization including DNA extraction kits and bead-beating conditions. The four DNA extraction kits (AllPrep PowerViral DNA/RNA Kit, DNeasy Blood & Tissue Kit, DNeasy PowerSoil Kit, and ZymoBIOMICS DNA Miniprep Kit) were compared in animal food as well as the use of peptide nucleic acid blockers for 16S rRNA gene amplicon sequencing. Distinct microbial community profiles were generated, which varied by animal food type and DNA extraction kit. Employing peptide nucleic acid blockers prior to 16S rRNA gene amplicon sequencing was comparable with post-sequencing in silico filtering at removing chloroplast and mitochondrial sequences. There was a good agreement between 16S rRNA gene amplicon sequencing and shotgun metagenomics on community profiles in animal feed data sets; however, they differed in taxonomic resolution, with the latter superior at resolving at the species level. Although the overall prevalence of AMR genes was low, resistome analysis of animal feed data sets by shotgun metagenomics revealed 10 AMR gene/protein families, including beta-lactamases, erythromycin/lincomycin/pristinamycin/tylosin, fosfomycin, phenicol, and quinolone. Future expansion of microbiome and resistome profiling in animal food will help better understand the bacterial and AMR gene diversity in these commodities and help guide pathogen control and AMR prevention efforts.IMPORTANCEWith the growing interest and application of metagenomics in understanding the structure/composition and function of diverse microbial communities along the One Health continuum, this study represents one of the first attempts to employ these advanced sequencing technologies to characterize the microbiota and AMR genes in animal food. We unraveled the effects of DNA extraction kits on sample analysis by 16S rRNA gene amplicon sequencing and showed similar efficacies of two strategies at removing chloroplast and mitochondrial reads. The in-depth analysis using shotgun metagenomics shed light on the community compositions and the presence of an array of AMR genes in animal food. This exploration of microbiomes and resistomes in representative animal food samples by both sequencing approaches laid important groundwork for future metagenomic investigations to gain a better understanding of the baseline/core microbiomes and associated AMR functions in these diverse commodities and help guide pathogen control and AMR prevention efforts.

Dynamics of Bacterial and Viral Transmission in Experimental Microbiota Transplantation.

Mouse models are vital tools for discerning the relative contributions of host and microbial genetics to disease, often requiring the transplantation of microbiota between different mouse strains. Transfer methods include antibiotic treatment of recipients and colonization using either co-housing with donors or the transplantation of fecal or cecal donor material. However, the efficiency and dynamics of these methods in reconstituting recipients with donor microbes is not well understood. We thus directly compared co-housing, fecal transplantation, and cecal transplantation methods. Donor mice from Taconic Biosciences, possessing distinct microbial communities, served as the microbial source for recipient mice from Jackson Laboratories, which were treated with antibiotics to disrupt their native microbiota. We monitored microbial populations longitudinally over the course of antibiotics treatment and reconstitution using 16S rRNA gene sequencing, quantitative PCR, and shotgun sequencing of viral-like particles. As expected, antibiotic treatment rapidly depleted microbial biomass and diversity, with slow and incomplete natural recovery of the microbiota in non-transplanted control mice. While all transfer methods reconstituted recipient mice with donor microbiota, co-housing achieved this more rapidly for both bacterial and viral communities. This study provides valuable insights into microbial transfer methods, enhancing reproducibility and informing best practices for microbiota transplantation in mouse models.

Influence of light quality on the profiling of metabolites and the status of Lactobacillus community in the phyllosphere of hydroponically grown ginseng

BackgroundThe microbial community within the phyllosphere plays a critical role in plant health and growth by facilitating nutrient uptake, inducing resistance and enhancing tolrance to stress. Environmental factors, such as light intensity and quality, are known to influence the composition and function of phyllosphere microbiota. In hydroponic systems, these interactions are particularly relevant, as they can significantly affect plant growth and yield. Based on the potential of controlled environments to shape both plant and microbial responses, the impact of different light conditions on the phyllosphere microbiota is crucial for plant health and productivity.MethodsThis study evaluated two Korean ginseng varieties exposed to different LED light treatments in a hydroponic system. Metabolite profiling and ginsenoside content were analysed, while bacterial abundance in the phyllosphere was quantified. Detailed insights into the microbial community were obtained through 16S rRNA sequencing. A multivariate analysis was performed to distinguish the effects of different LED treatments of the phyllosphere microbiota.ResultsCarbohydrates were most abundant in treatments with flouresence light (FL), blue light (BL), and red light (RD), while treatments with dark (DK), infrared (IR), and ultraviolet (UV) light exhibited higher levels of amino acids and organic acids. Minor ginsenoside content was significantly higher in Gumpoong (V2) variety compared to the Yunpoong (V1). Light intensity had a direct impact on the composition of the phyllosphere microbiota, with specific microorganisms being associated with each ginseng variety under different LED light exposures. Organic acids and amino acids positively influenced the abundance of Proteobacteria, Actinobacteria, Chloroflexi, and Ni-trospirae, while Firmicutes, Acidobacteria, Planctomycetes, and Cyanobacteria correlated significantly with carbohydrate levels. Proteobacteria remained stable under IR treatment, constituting over 80% in V2 and 60% in V1, while UV light promoted microbial stability in V2 and fostered more diverse ecosystems in V1, both characterized by richness in organic acids and amino acids. Lactiplantibacillus plantarum was the only lactic acid bacterium detected in both varieties, with higher abundance in V2, indicating its potential ubiquity across different ginseng types.ConclusionsCurrent findings showed that LED light treatments significantly influenced the metabolite profiles and phyllosphere microbiota of hydroponically grown Korean ginseng. Specific light conditions, such as blue, red, and infrared, promoted distinct microbial communities and enhanced the production of key metabolites, including carbohydrates, amino acids, and ginsenosides. The presence L. plantarum, highlights the potential of ginseng as a functional food with probiotic properties. This study provides valuable insights into optimizing ginseng cultivation for both enhanced metabolite production and microbiome health.Graphical

Supporting wild bee development with a bacterial symbiont

Abstract Aims Wild bees foster diverse microbiota that may determine survival success of developing larvae. Here, we compare survivorship and microbial communities of Ceratina calcarata small carpenter bees reared from eggs across three treatments: maternally collected control provisions with diverse microbiota, sterile provisions, and probiotic provisions supplemented with a beneficial symbiont, Apilactobacillus kunkeei. Methods and results Survival probability and adult masses differed across treatments, with the probiotic treatment resulting in highest survivorship and masses. By comparing the bacterial (16S rRNA), fungal (ITS), and plant (rbcL) communities of adults reared across treatments, we characterized distinct microbial communities across each that suggest the microbiome may be sensitive to microbial succession and competition. Conclusions We describe positive implications for the usage of probiotics on wild bees. Furthermore, the sensitivity of bee microbiota’s relationships to their host, floral resources, and the environment suggests that holistic approaches best encapsulate the complex network of interactions between bees and their microbes.

Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs

Transgenic expression of a double-stranded RNA in plants can induce silencing of homologous mRNAs in fungal pathogens. Although such host-induced gene silencing is well documented, the molecular mechanisms by which RNAs can move from the cytoplasm of plant cells across the plasma membrane of both the host cell and fungal cell are poorly understood. Indirect evidence suggests that this RNA transfer may occur at a very early stage of the infection process, prior to breach of the host cell wall, suggesting that silencing RNAs might be secreted onto leaf surfaces. To assess whether Arabidopsis plants possess a mechanism for secreting RNA onto leaf surfaces, we developed a protocol for isolating leaf surface RNA separately from intercellular (apoplastic) RNA. This protocol yielded abundant leaf surface RNA that displayed an RNA banding pattern distinct from apoplastic RNA, suggesting that it may be secreted directly onto the leaf surface rather than exuded through stomata or hydathodes. Notably, this RNA was not associated with either extracellular vesicles or protein complexes; however, RNA species longer than 100 nucleotides could be pelleted by ultracentrifugation. Furthermore, pelleting was inhibited by the divalent cation chelator EGTA, suggesting that these RNAs may form condensates on the leaf surface. These leaf surface RNAs are derived almost exclusively from Arabidopsis, but come from diverse genomic sources, including rRNA, tRNA, mRNA, intergenic RNA, microRNAs, and small interfering RNAs, with tRNAs especially enriched. We speculate that endogenous leaf surface RNA plays an important role in the assembly of distinct microbial communities on leaf surfaces.

Shaping rhizocompartments and phyllosphere microbiomes and antibiotic resistance genes: The influence of different fertilizer regimes and biochar application.

Understanding the impact of different soil amendments on microbial communities and antibiotic resistance genes (ARGs) dissemination is crucial for optimizing agricultural practices and mitigating environmental risks. This study investigated the effects of different fertilizer regimes and biochar on plant-associated bacterial communities and ARGs dissemination. The biochar's structural and chemical characteristics were characterized using scanning electron microscopy (SEM) and Fourier-transform infrared (FTIR) spectroscopy, revealing a porous architecture with diverse functional groups. The presence of ARGs varied significantly across groups, with manure-treated samples exhibiting the greatest diversity and abundance, raising concerns about ARGs dissemination. Soil enzyme activities responded differently to treatments; manure significantly enhanced catalase, acid phosphatase, and urease activities, whereas saccharase was most responsive to chemical fertilizer. These differences are possibly responsible for the distinct microbiome structure associated with the plant's root system. The analysis of bacterial diversity and richness across rhizocompartments and the phyllosphere highlighted that manure-treated rhizospheres and phyllospheres displayed the highest species richness and diversity. Notably, Proteobacteria dominated across most treatments, with distinct shifts in bacterial phyla and genera influenced by manure and biochar applications. The LEfSe analysis identified key indicator genera specific to each group, indicating that both fertilizer type and biochar application significantly shape microbial community composition. Co-occurrence network analysis further demonstrated that manure and biochar treatments created unique microbial networks in the rhizosphere, rhizoplane, phyllosphere, and endosphere, highlighting the role of these amendments in modulating microbial interactions in plant-associated environments. These findings suggest that manure, while enhancing microbial diversity and soil enzyme activities, also increases ARGs, whereas biochar may not contribute to the spread of ARGs and fosters distinct microbial communities, offering valuable insights for sustainable agricultural practices.