Microbiome Gene Research Articles

Lacticaseibacillus rhamnosus LRa05 in the treatment of acute diarrhea in children: a randomized controlled trial

IntroductionThe goal of this study is to assess the efficacy and safety of Lacticaseibacillus rhamnosus LRa05, as an adjunct to the treatment of acute watery diarrhea in children.MethodsEligible diarrheal children were randomized into intervention group (IG, n = 57) and control group (CG, n = 54), and given probiotics or placebo, respectively.ResultsThe total duration of diarrhea in the IG (121.4 ± 13.7 h) was significantly shorter than that in the CG (143.9 ± 19.8 h, p < 0.001). More children in the IG showed improvements in diarrhea than those in the CG for both per protocol analysis (70.2 vs. 46.3%, p = 0.01) and intention-to-treat analysis (66.7 vs. 41.7%, p = 0.003). The LL-37 levels in the IG was markedly higher than that in the CG after the intervention (4349.35 ± 1143.86 pg./g vs. 3682.49 ± 869.21 pg./g, p = 0.039). The intervention led to higher abundance of Bifidobacterium longum and lower abundance of Enterococcus faecium, Lactobacillus rhamnosus, and Bacteroides fragilis (p < 0.05). LRa05 treatment upregulated the functional genes of gut microbiota involving immunity regulation.DiscussionAdministration of the Lacticaseibacillus rhamnosus LRa05 at a dose of 5 × 109 CFU/day to children aged 0-3 years resulted in shorter duration of diarrhea, faster improvement in fecal consistency, and beneficial changes in gut microbiome composition and gene functions.Clinical trial registrationThe present study has been approved and registered in the Chinese Clinical Trial Registration Center with the registration number of ChiCTR2100053700 (https://www.chictr.org.cn/showproj.html?proj=141082).

Cultivar-dependent differences in plant bud microbiome and functional gene pathways in woody plants commonly used in urban green space.

Plant richness and microbiota have been associated with plant health; hardly any studies have investigated how plant taxa differs in microbiota in the context of human health. We investigated the microbial differences in buds of 83 woody plant taxa used in urban green spaces in hemiboreal climate, using 16S rRNA and whole metagenome shotgun sequencing. Bud microbial community was the richest in Cotoneaster Nanshan and C. integerrimus, and Malus domestica cultivars 'Sandra' and 'Lobo' and poorest in Ribes glandulosum. Metagenomic shotgun sequencing of two M. domestica and four Ribes varieties confirmed differences in taxa in bud microbiota and indicated higher siderophore synthesis in Malus. Microbial richness, including bacteria, archaea and viruses, and functional richness of gene pathways was higher in Malus compared to Ribes. The ten most abundant amplicon sequence units, often referred as species, belonged to the phylum Proteobacteria. The differences between plant taxa were evident in classes Alpha- and Gammaproteobacteria, known for potential human health-benefits. Since environmental microbiota contributes to human microbiota and immunoregulation, horticultural cultivars hosting rich microbiota may have human health benefits. Further studies are needed to confirm the effectiveness of microbially-oriented plant selection in optimizing human microbiota and planetary health.

CSIG-21. THE ROLE OF GUT MICROBIOTA IN GLIOBLASTOMA: INSIGHTS FROM MICROBIOME-GENE EXPRESSION INTERACTIONS

Abstract Glioblastoma, the most aggressive form of primary brain tumor, remains a formidable clinical challenge due to its invasiveness and resistance to therapy. Emerging evidence suggests that the gut microbiome plays a crucial role in modulating cancer progression through complex interactions with host physiology. In this study, we investigated the influence of gut microbiota and tumor gene expression by analyzing stool and tissue samples from glioblastoma patients. Utilizing 16S rRNA sequencing of stool samples and NanoString gene expression analysis of tumor tissue samples, we explored the relationship between gut microbiome taxa and gene expression levels in tissue. Pathway analysis using KEGG and Gene Ontology databases was employed to elucidate the functional implications of these interactions. Our findings reveal contrasting effects of specific gut microbiota taxa and gene expression, with Fusobacterium demonstrating a potential oncogenic role, while Bifidobacteriaceae and Akkermansiaceae display potential tumor-suppressive effects. Fusobacterium is associated with the upregulation of key oncogenes and pathways promoting cancer cell survival, growth, and metabolism, whereas Bifidobacteriaceae and Akkermansiaceae are linked to the downregulation of genes involved in pathways promoting cancer cell survival and proliferation, such as MAPK signaling and stress response pathways, potentially inhibiting cancer cell growth. These results highlight the intricate interplay between gut microbiota composition and cancer biology and underscore the potential of gut microbiota modulation as a therapeutic strategy in glioblastoma management.

From nature to urbanity: exploring phyllosphere microbiome and functional gene responses to the Anthropocene.

The Anthropocene exerts various pressures and influences on the stability and function of the Earth's ecosystems. However, our understanding of how the microbiome responds in form and function to these disturbances is still limited, particularly when considering the phyllosphere, which represents one of the largest microbial reservoirs in the terrestrial ecosystem. In this study, we comprehensively characterized tree phyllosphere bacteria and associated nutrient-cycling genes in natural, rural, suburban, and urban habitats in China. Results revealed that phyllosphere bacterial community diversity, richness, stability, and composition heterogeneity were greatest at the most disturbed sites. Stochastic processes primarily governed the assembly of phyllosphere bacterial communities, although the role of deterministic processes (environmental selection) in shaping these communities gradually increased as we moved from rural to urban sites. Our findings also suggest that human disturbance is associated with the reduced influence of drift as increasingly layered environmental filters deterministically constrain phyllosphere bacterial communities. The intensification of human activity was mirrored in changes in functional gene expression within the phyllosphere microbiome, resulting in enhanced gene abundance, diversity, and compositional variation in highly human-driven disturbed environments. Furthermore, we found that while the relative proportion of core microbial taxa decreased in disturbed habitats, a core set of microbial taxa shaped the distributional characteristics of both microbiomes and functional genes at all levels of disturbance. In sum, this study offers valuable insights into how anthropogenic disturbance may influence phyllosphere microbial dynamics and improves our understanding of the intricate relationship between environmental stressors, microbial communities, and plant function within the Anthropocene.

The gut microbiome and resistome of yellow perch (Perca flavescens) living in Minnesota lakes under varying anthropogenic pressure

Anthropogenic activities can significantly impact wildlife in natural water bodies, affecting not only the host's physiology but also its microbiome. This study aimed to analyze the gut microbiome and antimicrobial resistance gene profile (i.e., the resistome) of yellow perch living in lakes subjected to different levels of anthropogenic pressure: wastewater effluent-impacted lakes and undeveloped lakes. Total DNA and RNA from gut content samples were extracted and sequenced for analysis. Results indicate that the gut resistome and microbiome of yellow perch differ between lakes, perhaps due to varying anthropogenic pressure. The resistome was predominated by macrolide resistance genes, particularly the MLS23S group, making up 53 % of resistome sequences from effluent-impacted lakes and 73 % from undeveloped lakes. The colistin resistance gene group (mcr) was detected in numerous samples, including variants associated with Aeromonas and the family Enterobacteriaceae. The gut microbiome across all samples was dominated by the phyla Proteobacteria, Firmicutes, and Actinobacteria, with the opportunistic pathogens Plesiomonas shigelloides and Aeromonas veronii more abundant in effluent-impacted lakes. Metagenomic analysis of wild fish samples offers valuable insights into the effects of anthropogenic pressures on microbial communities, including antimicrobial resistance genes, in water bodies.

Integration of host gene regulation and oral microbiome reveals the influences of smoking during the development of oral squamous cell carcinoma.

This study aims to investigate the regulation of host gene transcription and microbial changes during the development of oral squamous cell carcinoma (OSCC) associated with smoking. The OSCC mouse model and smoking mouse model were established using 200 μg/mL 4-nitroquinoline-1-oxide (4NQO) in drinking water and exposure to cigarette smoke (four cigarettes per session, once a day, 5 days a week). Tongue tissues were harvested at 4 weeks and 16 weeks. Histopathological changes were evaluated using hematoxylin and eosin staining and Ki67 staining. RNA sequencing was performed on the mouse tongue tissues to identify differentially expressed genes (DEGs), and the results were validated by RT-PCR and immunohistochemistry. 16S rDNA sequencing was used to analyze changes in the oral microbiota during the early development of OSCC, identifying differentially abundant taxa associated with smoking. Finally, associations between the relative abundances of the oral microbiome and host gene expression were modeled using the Origin software. DEGs associated with smoking during the development of OSCC were identified. There were 12 upregulated genes, including NR4A3 and PPP1R3C, and 23 downregulated genes, including CD74 and ANKRD1. These genes were enriched in functions related to the signal transduction of cellular processes such as inflammation, differentiation, immunity, and PI3K/AKT, NF-κB signaling pathways. 4NQO and smoking treatment decreased oral microbial diversity and reduced the abundance of Bacteroidetes, Proteobacteria, and Lactobacillus but increased the abundance of Staphylococcus. Integrative analysis showed that the expression of CD74 was positively correlated with the relative abundance of Lactobacillus, while PPP1R3C was negatively correlated with Bacteroidota. In addition to characterizing host gene expression and the oral microbiome, our study explored the potential role of host-microbiome interactions in the development of OSCC. These findings enhance our understanding of smoking-related OSCC occurrence and development, providing new insights for its prevention.

Female reproductive tract microbiota varies with MHC profile.

Numerous studies have shown that a healthy reproductive tract microbiota is crucial for successful reproduction and that its composition is influenced by various environmental and host factors. However, it is not known whether the reproductive microbiota is also shaped by the major histocompatibility complex (MHC), a family of genes essential to differentiate 'self' from 'non-self' peptides to initiate an adaptive immune response. We tested the association between the follicular fluid microbiome and MHC genes in 27 women. Women with higher MHC diversity had a higher microbiome diversity, characterized by bacteria commonly associated with vaginal dysbiosis. Women with similar MHC genes were also similar in their microbiome composition, indicating that MHC composition may be a key factor in determining the bacterial assemblage in the reproductive tract. Finally, the composition of the follicular fluid microbiome was similar to the vaginal microbiome, suggesting that numerous bacteria of the vagina are true inhabitants of the follicular fluid or that vaginal microbiota contaminated the follicular fluid microbiota during transvaginal collection. Collectively, our results demonstrate the importance of host genetic factors in shaping women's reproductive microbiota and they open the door for further research on the role of microbiota in mediating MHC-related variation in reproductive success.

Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.

The precise microbial determinants driving clinical outcomes in severe pneumonia are unknown. Competing ecological forces produce dynamic microbiota states in health; infection and treatment effects on microbiota state must be defined to improve pneumonia therapy. Here, we leverage our unique clinical setting, which includes systematic and serial bronchoscopic sampling in patients with suspected pneumonia, to determine lung microbial ecosystem dynamics throughout pneumonia therapy. We combine 16S rRNA gene amplicon, metagenomic, and transcriptomic sequencing with bacterial load quantification to reveal clinically-relevant pneumonia progression drivers. Microbiota states are predictive of pneumonia category and exhibit differential stability and pneumonia therapy response. Disruptive forces, like aspiration, associate with cohesive changes in gene expression and microbial community structure. In summary, we show that host and microbiota landscapes change in unison with clinical phenotypes and that microbiota state dynamics reflect pneumonia progression. We suggest that distinct pathways of lung microbial community succession mediate pneumonia progression.

Exploring microbial diversity and function in companion planting systems of white clover and orchard grass

Companion planting of white clover (Trifolium repens L.) with orchard grass (Dactylis glomerata L.), a famous hay grass, improves the forage quality of orchard grass. Microbiome profiling techniques can reveal the specific role of white clover companion planting with orchard grass. This study aimed to explore the microbiome distribution and gene functions of rhizosphere and non-rhizosphere soil via companion planting systems of white clover and orchard grass. From metagenomics sequencing analysis, we confirmed the significant role of white clover on soil environment modeling during companion planting with orchard grass. Twenty-eight biomarkers of rhizosphere soil organisms were identified during companion planting, including Proteobacteria, Betaproteobacteria, Flavobacteriia, and Caulobacterales. The number of gene functions of nitrogen and carbon fixation in companion planting was higher than that in single plants, indicating new functional flora for companion planting. We characterized specific rhizosphere effects, typical biomarker flora, and potential regulatory mechanisms for white clover-related companion planting by metagenomics analyses.

Effects of plastic aging on biodegradation of polystyrene by Tenebrio molitor larvae: Insights into gut microbiome and bacterial metabolism

Plastics aging reduces resistance to microbial degradation. Plastivore Tenebrio molitor rapidly biodegrades polystyrene (PS, size: < 80 μm), but the effects of aging on PS biodegradation by T. molitor remain uncharacterized. This study examined PS biodegradation over 24 days following three pre-treatments: freezing with UV exposure (PS1), UV exposure (PS2), and freezing (PS3), compared to pristine PS (PSv) microplastic. The pretreatments deteriorated PS polymers, resulting in slightly higher specific PS consumption (602.8, 586.1, 566.7, and 563.9 mg PS·100 larvae−1·d−1, respectively) and mass reduction rates (49.6 %, 49.5 %, 49.2 %, and 48.7 %, respectively) in PS1, PS2, and PS3 compared to PSv. Improved biodegradation correlated with reduced molecular weights and the formation of oxidized functional groups. Larvae fed more aged PS exhibited greater gut microbial diversity, with microbial community and metabolic pathways shaped by PS aging, as supported by co-occurrence network analysis. These findings indicated that the aging treatments enhanced PS biodegradation by only limited extent but impacted greater on gut microbiome and bacterial metabolic genes, indicating that the T. molitor host have highly predominant capability to digest PS plastics and alters gut microbiome to adapt the PS polymers fed to them.

Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics

The widespread application of macrolide antibiotics has caused antibiotic resistance pollution, threatening the river ecological health. In this study, five macrolide antibiotics (azithromycin, clarithromycin, roxithromycin, erythromycin, and anhydro erythromycin A) were monitored in the Zao River across three hydrological periods (April, July, and December). Simultaneously, the changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and planktonic bacterial communities were determined using metagenomic sequencing. A clear pollution gradient was observed for azithromycin and roxithromycin, with the concentrations in the dry season surpassing those in other seasons. The highest concentration was observed for azithromycin (1.36 μg/L). The abundance of MLS resistance genes increased along the Zao River during the dry season, whereas the opposite trend was obtained during the wet season. A significant correlation between the levels of MLS resistance genes and macrolide antibiotics was identified during the dry season. Notably, compared with the reference site, the abundance of transposase in the effluent from wastewater treatment plants (WWTPs) was significantly elevated in both dry and wet seasons, whereas the abundance of insertion sequences (IS) and plasmids declined during the dry season. The exposure to wastewater containing macrolide antibiotics altered the diversity of planktonic bacterial communities. The bacterial host for ARGs appeared to be Pseudomonas, primarily associated with multidrug subtypes. Moreover, the ARG subtypes were highly correlated with MGEs (transposase and istA). The partial least-squares path model (PLS-PM) demonstrated a positive correlation between the abundance of MGEs and ARGs, indicating the significance of horizontal gene transfer (HGT) in the dissemination of ARGs within the Zao River. Environmental variables, such as TN and NO3−-N, were significantly correlated with the abundance of MGEs, ARGs, and bacteria. Collectively, our findings could provide insights into the shift patterns of the microbiome and ARGs across the contamination gradient of AZI and ROX in the river.

Organic management improved the multifunctionality in recolonization soil by increasing microbial diversity and function

Abstract Organic management enhances the formation of distinct and stable soil microbial communities, however, its influence on the temporal recovery of microbiome and multifunctionality of sterilized soil remains poorly understood. We used amplicon sequencing and metagenomic sequencing to investigate the effects of microbial communities in long‐term organic and conventional managed soils on restoring soil microbiome and functionality. We calculated multifunctionality of soils at days 30 and 90 of recolonization using the averaging approach. Results showed that organic management (O) significantly increased alpha diversity, niche width and network complexity of microbial community compared to conventional management (C). The alpha diversity, niche width and network complexity of microbial community in soils with organic soil suspension were significantly increased compared to conventional management at days 30 and 90 of recolonization. Soil multifunctionality of sterilized organic managed soil inoculated with organic soil suspension (OO) was 14.6% to 70.6% higher than that of the rest treatments. Macrogenomic analysis revealed that O significantly enriched functional pathways of ABC transporters, carbon metabolism, biosynthesis of amino acids, two‐component and nitrogen metabolism as well as most of the functional genes for carbon degradation, carbon fixation, nitrogen cycling and phosphorus cycles compared to C. These functional pathways and genes were also significantly enriched in soils with organic soil suspension at day 30 and 90 of recolonization. Furthermore, alpha diversity, niche width, network complexity, functional pathways and functional genes of microbiome correlated positively with soil multifunctionality. Synthesis and applications. Our results emphasize the importance of organic management induced changes in diversity, network complexity, and functionality of microbial communities for promoting recovery to soil microbial and functional losses, providing the theoretical basis for sustainable impact of organic management in agronomic production on soil microbiome and function. Read the free Plain Language Summary for this article on the Journal blog.

Gut microbiome and antibiotic resistance genes in plateau model animal (Ochotona curzoniae) exhibit a relative stability under cold stress

Antibiotic resistance genes (ARGs) carried by gut pathogens may pose a threat to the host and ecological environment. However, few studies focus on the effects of cold stress on intestinal bacteria and ARGs in plateau animals. Here, we used 16S rRNA gene sequencing and gene chip technique to explore the difference of gut microbes and ARGs in plateau pika under 4 °C and 25 °C. The results showed that tetracycline and aminoglycoside resistance genes were the dominant ARGs in pika intestine. Seven kinds of high-risk ARGs (aadA-01, aadA-02, ermB, floR, mphA-01, mphA-02, tetM-02) existed in pika’s intestine, and cold had no significant effect on the composition and structure of pika’s intestinal ARGs. The dominant phyla in pika intestine were Bacteroidetes and Firmicutes. Cold influenced 0.47 % of pika intestinal bacteria in OTU level, while most other bacteria had no significant change. The diversity and community assembly of intestinal bacteria in pika remained relatively stable under cold conditions, while low temperature decreased gut microbial network complexity. In addition, low temperature led to the enrichment of glycine biosynthesis and metabolism-related pathways. Moreover, the correlation analysis showed that eight opportunistic pathogens (such as Clostridium, Staphylococcus, Streptococcus, etc.) detected in pika intestine might be potential hosts of ARGs.

High concentrate diets altered the structure and function of rumen microbiome in goats.

This study used metatranscriptomics to investigate the effects of concentrate diet level on rumen microbiome composition and function in goats. A total of 12 healthy 120-day-old Da'er goats were randomly allotted into two treatments: L group (low dietary concentrate level group, concentrate: forage ratio was 25: 75) and H group (high dietary concentrate level group, concentrate: forage ratio was 80: 20). The study included a 10-day pre-feeding period and a 60-day growth experiment. The results showed that compared with the L group, the average daily gain and the slaughter rate in the H group were increased, while the F/G was decreased; the concentration of lactate and ammonia nitrogen, and the proportion of butyrate and valerate in the rumen of the H group were increased, while the proportion of acetate, and the ratio of acetate to propionate were decreased (p < 0.05). Among rumen bacteria, compared with the L group, the H group significantly decreased the relative abundance of Firmicutes and Fibrobacteria at the phylum level, decreased the relative abundance of Bacteroidetes, Fibrobacter, and Sarcina and increased the relative abundance of Clostridium at the genus level, and decreased the relative abundance of Fibrobacter succinogenes, Sarcina sp. DSM 11001, Oscillibacter sp. KLE 1728, and Ruminococcus flavefaciens and increased the relative abundance of Clostridium sp. ND2 and Firmicutes bacteria CAG: 103 at the species level (p < 0.05). Among rumen fungi, the relative abundance of Basidiomycota, Neocallimastigomycota, Mortierella, Mortierella elongata, and Gonapodyna prolifera was lower in the H group than that in the L group (p < 0.05). Functional annotation results showed that the abundance of Glycoside hydrolases genes in rumen microbiome was significantly decreased in the H group compared to the L group (p < 0.05). The result of KEGG DEGs enrichment analysis showed that the gene expression of cellulose 1,4-β-cellobiosidase, acetyl-CoA hydrolase, lactate dehydrogenase, succinate-semialdehyde dehydrogenase, D-malate dehydrogenase and related genes in methane production pathways of rumen microbiome was decreased in the H group. In summary, feeding high concentrate diets improved the production performance of goats, altered the structure and composition of rumen microbiome and changed the function of rumen microbiome.

16S rRNA amplicon sequencing and antimicrobial resistance profile of intensive care units environment in 41 Brazilian hospitals.

Infections acquired during healthcare setting stay pose significant public health threats. These infections are known as Healthcare-Associated Infections (HAI), mostly caused by pathogenic bacteria, which exhibit a wide range of antimicrobial resistance. Currently, there is no knowledge about the global cleaning process of hospitals and the bacterial diversity found in ICUs of Brazilian hospitals contributing to HAI. Characterize the microbiome and common antimicrobial resistance genes present in high-touch Intensive Care Unit (ICU) surfaces, and to identify the potential contamination of the sanitizers/processes used to clean hospital surfaces. In this national, multicenter, observational, and prospective cohort, bacterial profiles and several antimicrobial resistance genes from 41 hospitals across 16 Brazilian states were evaluated. Using high-throughput 16S rRNA amplicon sequencing and real-time PCR, the bacterial abundance and resistance genes presence were analyzed in both ICU environments and cleaning products. We identified a wide diversity of microbial populations with a recurring presence of HAI-related bacteria among most of the hospitals. The median bacterial positivity rate in surface samples was high (88.24%), varying from 21.62 to 100% in different hospitals. Hospitals with the highest bacterial load in samples were also the ones with highest HAI-related abundances. Streptococcus spp., Corynebacterium spp., Staphylococcus spp., Bacillus spp., Acinetobacter spp., and bacteria from the Flavobacteriaceae family were the microorganisms most found across all hospitals. Despite each hospital particularities in bacterial composition, clustering profiles were found for surfaces and locations in the ICU. Antimicrobial resistance genes mecA, bla KPC-like, bla NDM-like, and bla OXA-23-like were the most frequently detected in surface samples. A wide variety of sanitizers were collected, with 19 different active principles in-use, and 21% of the solutions collected showed viable bacterial growth with antimicrobial resistance genes detected. This study demonstrated a diverse and spread pattern of bacteria and antimicrobial resistance genes covering a large part of the national territory in ICU surface samples and in sanitizers solutions. This data should contribute to the adoption of surveillance programs to improve HAI control strategies and demonstrate that large-scale epidemiology studies must be performed to further understand the implications of bacterial contamination in hospital surfaces and sanitizer solutions.

Interplay among manures, vegetable types, and tetracycline resistance genes in rhizosphere microbiome.

The rapid global emergence of antibiotic resistance genes (ARGs) is a substantial public health concern. Livestock manure serves as a key reservoir for tetracycline resistance genes (TRGs), serving as a means of their transmission to soil and vegetables upon utilization as a fertilizer, consequently posing a risk to human health. The dynamics and transfer of TRGs among microorganisms in vegetables and fauna are being investigated. However, the impact of different vegetable species on acquisition of TRGs from various manure sources remains unclear. This study investigated the rhizospheres of three vegetables (carrots, tomatoes, and cucumbers) grown with chicken, sheep, and pig manure to assess TRGs and bacterial community compositions via qPCR and high-throughput sequencing techniques. Our findings revealed that tomatoes exhibited the highest accumulation of TRGs, followed by cucumbers and carrots. Pig manure resulted in the highest TRG levels, compared to chicken and sheep manure, in that order. Bacterial community analyses revealed distinct effects of manure sources and the selective behavior of individual vegetable species in shaping bacterial communities, explaining 12.2% of TRG variation. Firmicutes had a positive correlation with most TRGs and the intl1 gene among the dominant phyla. Notably, both the types of vegetables and manures significantly influenced the abundance of the intl1 gene and soil properties, exhibiting strong correlations with TRGs and elucidating 30% and 17.7% of TRG variance, respectively. Our study delineated vegetables accumulating TRGs from manure-amended soils, resulting in significant risk to human health. Moreover, we elucidated the pivotal roles of bacterial communities, soil characteristics, and the intl1 gene in TRG fate and dissemination. These insights emphasize the need for integrated strategies to reduce selection pressure and disrupt TRG transmission routes, ultimately curbing the transmission of tetracycline resistance genes to vegetables.

Biochar immobilized hydrolase degrades PET microplastics and alleviates the disturbance of soil microbial function via modulating nitrogen and phosphorus cycles

Microplastics (MPs) pose an emerging threat to soil ecological function, yet effective solutions remain limited. This study introduces a novel approach using magnetic biochar immobilized PET hydrolase (MB-LCC-FDS) to degrade soil polyethylene terephthalate microplastics (PET-MPs). MB-LCC-FDS exhibited a 1.68-fold increase in relative activity in aquatic solutions and maintained 58.5 % residual activity after five consecutive cycles. Soil microcosm experiment amended with MB-LCC-FDS observed a 29.6 % weight loss of PET-MPs, converting PET into mono(2-hydroxyethyl) terephthalate (MHET). The generated MHET can subsequently be metabolized by soil microbiota to release terephthalic acid. The introduction of MB-LCC-FDS shifted the functional composition of soil microbiota, increasing the relative abundances of Microbacteriaceae and Skermanella while reducing Arthobacter and Vicinamibacteraceae. Metagenomic analysis revealed that MB-LCC-FDS enhanced nitrogen fixation, P-uptake and transport, and organic-P mineralization in PET-MPs contaminated soil, while weakening the denitrification and nitrification. Structural equation model indicated that changes in soil total carbon and Simpson index, induced by MB-LCC-FDS, were the driving factors for soil carbon and nitrogen transformation. Overall, this study highlights the synergistic role of magnetic biochar-immobilized PET hydrolase and soil microbiota in degrading soil PET-MPs, and enhances our understanding of the microbiome and functional gene responses to PET-MPs and MB-LCC-FDS in soil systems.

From pollen to putrid: Comparative metagenomics reveals how microbiomes support dietary specialization in vulture bees.

For most animals, the microbiome is key for nutrition and pathogen defence, and is often shaped by diet. Corbiculate bees, including honey bees, bumble bees, and stingless bees, share a core microbiome that has been shaped, at least in part, by the challenges associated with pollen digestion. However, three species of stingless bees deviate from the general rule of bees obtaining their protein exclusively from pollen (obligate pollinivores) and instead consume carrion as their sole protein source (obligate necrophages) or consume both pollen and carrion (facultative necrophages). These three life histories can provide missing insights into microbiome evolution associated with extreme dietary transitions. Here, we investigate, via shotgun metagenomics, the functionality of the microbiome across three bee diet types: obligate pollinivory, obligate necrophagy, and facultative necrophagy. We find distinct differences in microbiome composition and gene functional profiles between the diet types. Obligate necrophages and pollinivores have more specialized microbes, whereas facultative necrophages have a diversity of environmental microbes associated with several dietary niches. Our study suggests that necrophagous bee microbiomes may have evolved to overcome cellular stress and microbial competition associated with carrion. We hypothesize that the microbiome evolved social phenotypes, such as biofilms, that protect the bees from opportunistic pathogens present on carcasses, allowing them to overcome novel nutritional challenges. Whether specific microbes enabled diet shifts or diet shifts occurred first and microbial evolution followed requires further research to disentangle. Nonetheless, we find that necrophagous microbiomes, vertebrate and invertebrate alike, have functional commonalities regardless of their taxonomy.

Association of tissue microbiota with cancer stages in lung adenocarcinoma.

e20061 Background: There has been a lack of comprehensive investigation into changes in the tissue microbial environment at various stages of lung adenocarcinoma (LUAD). This study aims to identify and analyze microbial markers that show significant differences at different stages of LUAD and to assess their impact on the tumor microenvironment. Methods: Microbiome data, gene expression, and clinical information from LUAD patient tissues were retrieved by reanalyzing the sample sequencing data from the Cancer Genome Atlas (TCGA) database, as conducted by Rob Knight’s group. The samples, categorized into early (pathological stage I) and late (stages II-IV) following the initial diagnosis, were subjected to comparative analyses. Firstly, microbial alpha diversity metrics, such as the Shannon index, were computed for each sample. Subsequently, Principal Coordinate Analysis (PCoA) and the Wilcoxon rank sum test were employed to assess differences in microbial communities between the two groups. Furthermore, the study delved into the associations between microbes and host gene expressions using Spearman rank correlation to construct a heterogeneous network encompassing microbial interaction networks at the genus level, microbe-gene interaction network, and gene co-expression network. Various network features, including the clustering coefficient, were examined. Finally, diverse machine learning algorithms were employed to develop a diagnostic model for cancer stage based on microbial and gene expression data. Results: A total of 491 samples, including 267 in the early group and 224 in the late group, were matched with microbial data, mRNA expression, and clinical information. Our findings revealed distinct differences in the microbiome of patients with LUAD at various stages, particularly in the tissues of advanced patients, where in the co-abundance network exhibited a significantly higher level of complexity. Furthermore, we identified five bacterial biomarkers (Pseudoalteromonas, Luteibacter, Caldicellulosiruptor, Loktanella, and Serratia) that were associated with the LUAD stage. Notably, Pseudoalteromonas, Luteibacter, Caldicellulosiruptor, and Serratia were significantly overexpressed in advanced patients. Utilizing the random forest model, we determined that microbial markers possess predictive capabilities for the stage of lung adenocarcinoma and can compensate for deficiencies in other omics data for determining tumor stage. Integration of the mRNA and intratumor microbe biomarkers yielded a prediction area under the Receiver Operating Characteristic curve of 0.70. Conclusions: Our study unveiled the microbial profile of LUAD patients, elucidating the intrinsic pathogenic mechanisms linking the microbiome and the disease. Additionally, we developed a multi-omics model for determining the tumor stage of LUAD.

Genetic architecture and correlations between the gut microbiome and gut gene transcription in Chinook salmon (Oncorhynchus tshawytscha).

Population divergence through selection can drive local adaptation in natural populations which has implications for the effective restoration of declining and extirpated populations. However, adaptation to local environmental conditions is complicated when both the host and its associated microbiomes must respond via co-evolutionary change. Nevertheless, for adaptation to occur through selection, variation in both host and microbiome traits should include additive genetic effects. Here we focus on host immune function and quantify factors affecting variation in gut immune gene transcription and gut bacterial community composition in early life-stage Chinook salmon (Oncorhynchus tshawytscha). Specifically, we utilized a replicated factorial breeding design to determine the genetic architecture (sire, dam and sire-by-dam interaction) of gut immune gene transcription and microbiome composition. Furthermore, we explored correlations between host gut gene transcription and microbiota composition. Gene transcription was quantified using nanofluidic qPCR arrays (22 target genes) and microbiota composition using 16 S rRNA gene (V5-V6) amplicon sequencing. We discovered limited but significant genetic architecture in gut microbiota composition and transcriptional profiles. We also identified significant correlations between gut gene transcription and microbiota composition, highlighting potential mechanisms for functional interactions between the two. Overall, this study provides support for the co-evolution of host immune function and their gut microbiota in Chinook salmon, a species recognized as locally adapted. Thus, the inclusion of immune gene transcription profile and gut microbiome composition as factors in the development of conservation and commercial rearing practices may provide new and more effective approaches to captive rearing.