DADA2: High-resolution sample inference from Illumina amplicon data

Mucosal immune responses and intestinal microbiome associations in wild spotted hyenas (Crocuta crocuta)

Little is known about host-gut microbiome interactions within natural populations at the intestinal mucosa, the primary interface. We investigate associations between the intestinal microbiome and mucosal immune measures while controlling for host, social and ecological factors in 199 samples of 158 wild spotted hyenas (Crocuta crocuta) in the Serengeti National Park, Tanzania. We profile the microbiome composition using a multi-amplicon approach and measure faecal immunoglobulin A and mucin. Probabilistic models indicate that both immune measures predicted microbiome similarity among individuals in an age-dependent manner. These associations are the strongest within bacteria, intermediate within parasites, and weakest within fungi communities. Machine learning models accurately predicted both immune measures and identify the taxa driving these associations: symbiotic bacteria reported in humans and laboratory mice, unclassified bacteria, parasitic hookworms and fungi. These findings improve our understanding of the gut microbiome, its drivers, and interactions in wild populations under natural selection.

Two decades long-term field trial data on fertilization, tillage, and crop rotation focusing on soil microbes

Agricultural long-term field trials provide fundamental data on crop performance and soil characteristics under diverse management practices. This information represents essential knowledge for upcoming challenges in food and nutrition security. Data provided here have been compiled since 2004 from a nitrogen(N)-fertilization intensity, tillage, and crop rotation field trial in Central Germany including standardized metrics regarding soil management, physical soil properties, crop management, crop characteristics, yield, and harvest quality parameters. In 2015, the field trial became a member of the German Agricultural Soil Research Program BonaRes. Numerous measurement results were added including plant physiology and soil and rhizosphere microbiology. DNA of bacterial/archaeal and fungal microbiomes was sequenced in the rhizosphere and root-associated soil following a meta-barcoding approach. Taxonomic and relative abundance data were included in the dataset. The dataset is the first to include information on root characteristics, soil and rhizosphere microbiomes, and crop gene expression. We encourage reuse of these biological field trial data in terms of meta-analysis, modeling and AI approaches.

Selective recruitment of beneficial microbes in the rhizosphere of maize affected by microbial inoculants, farming practice, and seasonal variations

BACKGROUND

Plant beneficial microorganisms as inoculants can improve crop performance, but factors affecting their impact on plant performance under field conditions remain unclear, thereby limiting their use in farming. Here, we investigated how farming practices (e.g., tillage and N-fertilization intensity) and growing seasons influenced the impact of a beneficial microorganism consortium (BMc: Trichoderma, Bacillus, and Pseudomonas strains) in maize and affected the rhizosphere competence of each BMc strain. In addition, we tested whether the consortium affects the resident rhizosphere microbiome and crop performance. In two growing seasons (2020 and 2021), we assessed how BMc inoculation affects maize growth, nutritional status, gene expression, and rhizosphere microbiome under different farming practices at the flowering stage.

RESULTS

Inoculated strains successfully colonized the maize rhizosphere independently of farming practice. BMc inoculation improved plant growth and iron uptake in 2020, regardless of farming practice. These effects co-occurred with lower precipitation levels in 2020 compared to 2021. BMc inoculation reduced the expression of several stress-related genes in maize in 2020 under drought. An increased iron uptake by the BMc-inoculated plants was observed in 2020 and was associated with the upregulation of the gene ZmNAS3, which is linked to iron uptake. Therefore, BMc inoculation mitigated the drought impact on maize. The microbial rhizosphere communities were altered by BMc inoculation in both years, but patterns of responder taxa differed between seasons. Metagenome analysis revealed that more genes (e.g., genes encoding biosurfactants and siderophores) were enriched in the rhizosphere of BMc-inoculated plants in 2020 than in 2021. Moreover, we identified bacterial and fungal taxa positively associated with maize iron uptake. The relative abundance of these iron uptake-associated bacterial and fungal taxa significantly increased due to BMc inoculation in 2020, while they showed overall higher relative abundances in 2021, independently of BMc inoculation. We mapped the sequences of these iron-associated taxa to publicly available genomes and verified the occurrence of various plant beneficial traits in several mapped genomes.

CONCLUSIONS

Overall, we show that the growing season determined the effect of BMc inoculation on maize plants by shaping microbiome composition and function in the maize rhizosphere more than farming practice. These findings highlight the importance of the complex interplay between microbial inoculants and the resident rhizosphere microorganisms under abiotic stress conditions.

Antarctic Krill with parasites grow slower than uninfected peers

Antarctic krill, Euphausia superba (Dana i Am J Sci Arts Ser 2(9):129-133, 1850), are both central ecosystem components in the Southern Ocean, and the target of a growing commercial fishery. Understanding the trophic interactions which shape krill population dynamics is essential to sustainably managing human impacts on this key species. While the roles of krill as grazers of phytoplankton and as prey for vertebrate predators are relatively well understood, very little is known about interactions with their smallest predators- the parasites. We investigated the assemblage of parasites present in E. superba, and the impacts of parasites on krill somatic growth. We found 15 distinct parasite types across a sample of 100 krill, including seven types of Gregarine Apicomplexa, two types of internally infecting ciliates, three types of epibiotic ciliates, fungi, syndiniales, and a Parorchites zederi cestode worm. Apicomplexa and epibiotic ciliate infections were linked with lower growth rates, with these two parasites explaining 10% and 24% of the observed variation in krill growth, respectively. Although much uncertainty remains, scaling these results to the population level suggests parasites may be responsible for as much reduction in krill biomass annually as vertebrate predators, indicating the importance of considering these trophic links in food web modelling and ecosystem-based management.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00227-025-04673-w.

An integrated microbial genome-wide association studies-based characterization of nitric oxide homeostasis by probiotic Bacillus subtilis on aging and neurodegeneration using Caenorhabditis elegans and mouse models

Microbial nitric oxide (NO) metabolism plays a critical role in regulating host redox homeostasis, yet its probiotic relevance remains largely unexplored. In this study, we performed a genome-wide phenotypic screen of 3984 Bacillus subtilis 168 (B. subtilis 168) gene deletion strains in Caenorhabditis elegans (C. elegans), identifying 12 core genetic factors linked to aging modulation. Among these, nosA (nitric oxide synthase) and yojO (putative nitric oxide reductase) were prioritized for validation based on their consistent host phenotypic effects and defined roles in NO regulation. Treatment with wild-type B. subtilis 168 extended C. elegans lifespan by 20 %, enhanced locomotor activity and chemotaxis index by 30-40 %, and reduced amyloid-beta accumulation by over 35 %. In contrast, ΔnosA and ΔyojO strains abolished these benefits, resulting in lifespan and behavior indices comparable to Escherichia coli OP50. In a BSO-induced oxidative stress mouse model, B. subtilis 168 administration significantly improved performance in Y-maze, open field, and novel object recognition tasks, whereas ΔnosA and ΔyojO groups exhibited diminished behavioral recovery and no improvement in cognitive outcomes. These findings demonstrate that microbial NO synthesis and detoxification are critical for mediating the anti-aging and neuroprotective functions of B. subtilis. Our study highlights a genetically tractable framework for dissecting host-microbe interactions relevant to redox signaling and age-associated neurodegeneration.

Lvvibriocin-GK effectively reduced skin ulcer syndrome of Apostichopus japonicus by eliminating surface bacteria, modulating gut microbiota, and enhancing host immune responses

Skin ulceration syndrome (SUS) is a major threat to the aquaculture of Apostichopus japonicus, particularly in southern China, where it has shown high mortality rates and infectious potential. Traditional antibiotic treatments often lead to challenges such as antibiotic resistance. Antimicrobial peptides (AMPs), which are vital elements of innate immunity, represent a promising alternative for treating SUS. In the study, a novel AMP named Lvvibriocin-GK identified in Litopenaeus vannamei was found to have a strong antibacterial activity against multiple Vibrio species that possibly cause SUS. Through constructing a Vibrio harveyi-induced SUS model, we evaluated the efficacy of a 7-day Lvvibriocin-GK immersion treatment to SUS. Compared to doxycycline hydrochloride at the same concentration, Lvvibriocin-GK treatments could have ulcer area and numbers reduced, mortality decreased, the DAI index significantly lowered, as well as intestinal inflammatory cell infiltration decreased but no significant effect on body weight. The therapeutic effects of Lvvibriocin-GK were accompanied by significantly enhancing the activities of trypsin, lysozyme, T-NOS, and T-SOD and reducing Vibrio harveyi load in tissues. qPCR results indicated that Lvvibriocin-GK upregulated the expression of intestinal barrier proteins ZO-1 and Occludin, and downregulated pro-inflammatory factors such as IL17, p105, NLRP3, Rel, and Stat5. Furthermore, 16S rRNA sequencing revealed that the beneficial effects of Lvvibriocin-GK might be linked to favorable changes in A. japonicus 's gut microbiota, including increased microbial diversity, enhanced abundance of potential probiotics (Rhodobacteraceae, Bacillus, Serratia liquefaciens), and reduced the abundance of opportunistic pathogens (Acinetobacter and Bacteroides vulgatus). These changes resulted in a more complex microbial network and improved immune-associated functions, particularly through pathways such as NF-κB signaling. Mantel tests indicated stronger correlations between Lvvibriocin-GK-treated gut microbiota and disease phenotypes (gut pathology), enzymatic activities (lipase, lysozyme, T-NOS, T-SOD), intestinal barrier markers (Occludin), and immune-related genes (Stat5, Rel, FoxP, VEGF). Taken together, this study proposes a novel, environmentally friendly AMP immersion treatment for severe cases of SUS. The therapeutic effects are closely to effectively eliminate pathogens, modulate the gut microbiota and enhance host immunity. A comprehensive evaluation of the efficacy and mechanisms of AMP treatment in A. japonicus SUS will contribute to assessing its advantages and potential applications as an antibiotic alternative, promoting A. japonicus health and improving aquaculture practices.

Fecal microbiome analysis in patients with metabolic syndrome and type 2 diabetes

Background

Metabolic syndrome (MS) and type 2 diabetes (T2D) are metabolically related diseases with rising global prevalence and increasingly evident links to the intestinal microbiota. Research suggests that imbalances in microbiota composition may play a crucial role in their pathogenesis. Specific population cohorts, such as the one in Galicia, Spain, offer the opportunity to analyze microbiota patterns within a distinct geographical and genetic context. This study was performed to investigate the relationship between the intestinal microbiota and MS and T2D.

Methods

A cohort of 79 volunteers was analyzed over a 2-year study period. Recruitment posed significant challenges because of strict inclusion criteria (918PTE0540; PCI2018-093284), which required participants to be free from chronic medications and have a moderate to high risk of developing T2D. Volunteers were classified based on their serum glucose levels, body mass index, and the presence or absence of MS. To analyze the microbiota composition, amplicon sequencing of 16S rRNA genes was performed on stool samples. Alpha diversity was assessed using the Chao and Shannon indices, while beta diversity was evaluated using permutational analysis of variance with Bray-Curtis and Chao distances. Differential abundance analysis was conducted using the LinDA method.

Results

In patients with MS, we observed a higher Firmicutes/Bacteroidetes ratio and an increased prevalence of Blautia compared to healthy patients. than in healthy individuals. Other enriched taxa in patients with MS included Tyzerella, Streptococcus, and Ruminococcus callidus. In patients with T2D, we observed a higher Bacteroidetes/Firmicutes ratio and a decrease in the phylum Actinobacteria compared with healthy individuals. Taxa such as Dorea, Prevotella, Dialister invisus, Fusicatenibacter, and Coprococcus were associated with T2D, while beneficial taxa such as Eubacterium, Ligilactobacillus, and Acidaminococcus were more prevalent in healthy or prediabetic individuals.

Conclusions

This study reveals notable differences in the intestinal microbiota composition among patients with MS and T2D. Changes in microbial composition, particularly the Firmicutes/Bacteroidetes ratio, may serve as indicators of underlying pathology. At more specific taxonomic levels, several enriched taxa were identified in patients with MS, including Blautia, Tyzzerella, Dorea, Streptococcus, and Ruminococcus callidus. Additionally, species such as Dorea longicatena and Dialister invisus were enriched in prediabetic and diabetic patients, whereas beneficial genera (Eubacterium, Acidaminococcus, Bifidobacterium, and Ligilactobacillus) were more prevalent in healthy and prediabetic individuals than in those with T2D.

Effects of mulches on greenhouse gas emissions and soil microbial communities in cabbage production

Agricultural plastic mulches are widely used for their agronomic benefits, but their impact on greenhouse gas (GHG) emissions and soil microbes remains unclear. This study examines the effects of mulching on soil properties, microbial communities, and GHG emissions in cabbage cultivation using four treatments: NF (no mulching), FT (black traditional mulch, 0.015 mm), FBS (black biodegradable mulch, 0.010 mm), and FBB (black biodegradable mulch, 0.015 mm). The results showed no significant differences in cabbage biomass and yield across treatments. However, FT and FBB significantly reduced cumulative CO₂ emissions by 32.07 % and 26.70 %, respectively, compared to NF, while FT increased N₂O emissions and FBB reduced them (p < 0.05). Biodegradable mulch enhanced bacterial network complexity and stability, whereas traditional mulch strengthened fungal network stability. Soil properties, including porosity (19.82 %), NH₄⁺ (18.55 %∼20.19 %), and dissolved organic nitrogen (42.29 %∼85.61 %), improved under biodegradable mulch. Bacterial communities were positively correlated with soil nutrients, while fungal communities showed negative correlations. The reduction in GHG emissions could be attributed to the blocking effect of the mulch during the early stages of crop growth. Partial least squares path modeling analysis revealed that mulching-induced changes in soil hydrothermal conditions can influence soil nutrients and microbial communities, ultimately affecting GHG emissions. These findings offer insights into sustainable agricultural practices that promote soil health and reduce GHG emissions.

Plastic Biodegradation by Sediment Microbial Populations under Denitrifying Conditions

Biodegradation is critical for eliminating plastic contaminants from environments, and understanding its mechanisms under in situ conditions is crucial. The plastic biodegradation process in sediments, a major reservoir of plastic contamination with reduced redox conditions, remains elusive. This study compared the plastisphere communities and metabolic potentials of typical polyethylene (PE) contaminants collected from the Pearl River Estuary to their counterparts in the surrounding sediments. The results revealed a distinct plastisphere community composition, with the consistent enrichment of a group of core plastisphere populations compared to those of the sediments. Functional genes related to both potential aerobic and anaerobic PE biodegradation were encoded by the core plastisphere populations. Microcosm incubations were performed to assess the PE biodegradation potentials under denitrifying conditions. The results demonstrated that the polyethylene (PE) mineralization efficiencies were comparable under aerobic and denitrifying conditions through incubations with 13C-PE. Development of functional groups on PE surfaces and the reduction in molecular weights further supported PE biodegradation under denitrifying conditions. The elevated laccase and lignin peroxidase activities implied their potential contribution to PE depolymerization under denitrifying conditions. Together, the sediment plastisphere microbiome holds the potential for plastic degradation under denitrifying conditions, which should be considered when assessing the fate of plastic contaminants.

Microbial Dysbiosis in the Lung and Gut in Response to Inhalable Particulate Matters in Pneumoconiosis Patients and Animals

Pneumoconiosis is a progressive and life-threatening fibrotic lung disorder caused by the prolonged deposition of inhaled particulate matters (PMs); thus far, no cure is available. Emerging evidence has suggested that the resulting disordered respiratory microbiome is caused by disturbed lung architecture and homeostasis responding to inhalable PMs. Lung microbiome dysbiosis also contributes to injury to the lung and distant organs, such as the intestine, through the lung-gut axis. Current studies on the microbiome-disease interplay are still in their infancy, and sufficient understanding of microbial heterogeneity in pathological processes is lacking. Here we investigated the microbiome in the lung and gut of patients with pneumoconiosis in comparison to healthy individuals. Our findings indicated reciprocal causation between lung injuries and microbial dysbiosis under particle exposure; pulmonary Streptococcus and Stenotrophomonas, along with intestinal Ligilactobacillus and Blautia, may represent key microbial communities influencing pneumoconiosis progression. We defined close microbiota crosstalk between the lung and gut, as evidenced by their interaction networks, implying considerable effects on the gut microenvironment through either direct microbial translocation or other mechanisms such as inflammation-driven alterations. Animal experiments further corroborated the findings in humans. Collectively, our results highlight the potential involvement of the lung-gut axis microbial dysbiosis in pneumoconiosis pathogenesis and open a new avenue to develop microbiome-targeted diagnosis and treatment strategies.

Disentangling the gut microbiota of Aldabra giant tortoises of different ages and environments

Background

The gut microbiota plays a pivotal role in regulating the physiological functions of its host, including immunity, metabolism, and digestion. The impact of environment and age on microbiota can be assessed by observing long-lived animals across different age groups and environments. The Aldabra giant tortoise (Aldabrachelys gigantea) is an ideal species for this study due to its exceptionally long lifespan of over 100 years.

Methods

Using 16S rRNA gene amplicon analysis, we analyzed 52 fecal samples from giant tortoises in Seychelles (Curieuse and Mahé islands) and in a zoological park in Italy, from very young individuals to those of >100 years old. We performed Alpha and Beta diversity analysis, relative abundance analysis, and complex upset plot analysis, comparing the results of tortoises from different environments and age groups.

Results

The diversity and overall composition of the gut microbiota of tortoises were impacted mainly by geolocation rather than their age. The greater diversity of microbiota in wild tortoises was attributed to their food variance such as wild leaves and branches, compared to captive or domesticated conditions. Beta diversity analysis also revealed the contribution of both environment and age to the variation between samples, with environments accounting for a larger proportion of this contribution. Certain bacterial families, such as Spirochaetota and Fibrobacterota, were more prevalent in environments with higher fiber intake, reflecting dietary differences. Additionally, a range of host-independent environmental bacteria was found to be specific to individuals in Curieuse and not in other geolocations. On the other hand, there were no bacterial taxa specific to centenarians, whose microbial complexity was reduced compared to adult or elderly tortoises.

Conclusions

Our records showed that environment is the primary influence in the overall composition and diversity of the gut microbiota of Aldabra giant tortoises. As giant tortoises are amongst the longest-lived vertebrate animals, these findings can be utilized to monitor their health according to their ages, and enhance their conservation efforts.

Characterization of prokaryotic communities in Puerto Rican caves using 16S rDNA amplicon sequencing

The cave ecosystems host microbial communities adapted to extreme environments. This study utilized 16S rDNA to investigate the prokaryotic diversity across seven caves in Puerto Rico's northern limestone karst belt. Microbial profiling revealed distinct subterranean communities, enhancing our understanding of cave microbiology and potential applications in environmental conservation and microbial research.

Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies

Microbes play an important role in soil functioning, underpinning food production systems and delivering an array of essential ecosystem services. To elucidate how these microbes relate to ecosystem functions, accurate identification and classification of soil microorganisms are important. We evaluated the comparability of shotgun and amplicon sequencing approaches by profiling soil microbiota from 131 diverse temperate grassland soils across Ireland. We assessed method comparability in terms of (i) detection and classification of the most abundant phyla, (ii) their capacity to differentiate samples based on their microbial community, and (iii) their capacity to link microbial communities to measured nitrogen cycle functions. Our findings reveal that both methods offer moderately similar outcomes, providing consistent detection of major phyla, similar microbial community differentiation patterns, and largely identifying the same relationships between the phyla and nitrogen functions. The variations observed between the two methods were mostly associated with differences in the choice of reference taxonomy. Amplicon sequencing represents a cost-effective, less computationally demanding option, while shotgun sequencing provides deeper taxonomic resolution and access to the latest databases, making it suitable for detailed microbial profiling. Our study underscores the need for careful method selection based on project requirements, database availability, and financial resources.IMPORTANCEStudying the microorganisms in soil remains a challenge as soils are one of the most complex and diverse environments. Compounding these challenges is the lack of culturable representatives in soil, with over 99% of soil microorganisms yet to be cultivated in a laboratory setting. Leveraging next-generation sequencing technologies, which bypass traditional culture-dependent methods, scientists are now able to attain low-cost, high-throughput DNA sequencing that can detect even the rarest microorganisms within samples. The present study rigorously compares amplicon and shotgun sequencing techniques in profiling microbial communities across diverse temperate grassland soil samples, focusing on how different databases, classifiers, and sequencing methods influence the results. Our study underscores the crucial need for a harmonized taxonomic database that could greatly enhance comparability and accuracy in the understanding of soil microbiomes.

Isolation and characterization of mollicute symbionts from a fungus-growing ant reveals high niche overlap leading to co-exclusion

Two mollicute species belonging to the Mesoplasma and Spiroplasma genera have been detected in several species of fungus-growing ants using molecular methods. However, their ecological roles remain largely inferred from metagenomic data. To better understand their diversity and specialization, we cultured both of these Mesoplasma and Spiroplasma symbionts from the fungus-growing ant Trachymyrmex septentrionalis, providing the first isolated mollicutes from any fungus-growing ant species. The genomes of our isolates and related metagenome-assembled genomes (MAGs) from T. septentrionalis fungus gardens comprise two unique phylogenetic lineages compared to previously described Mesoplasma and Spiroplasma species, and from related MAGs previously sequenced from the leaf-cutting ant Acromyrmex echinatior. This suggests that the T. septentrionalis symbionts comprise undescribed species that can exclude each other from a niche that is largely shared between them. Mesoplasma genomes and MAGs also demonstrate regional specificity with their T. septentrionalis ant hosts. Both Mesoplasma and Spiroplasma strains from T. septentrionalis can catabolize glucose and fructose; both sugars are common in the ant's diet. Similarly, both these Mesoplasma and Spiroplasma can catabolize arginine, but only Mesoplasma can catabolize N-acetylglucosamine; both could produce ammonia for the ants or fungus garden. Based on our genomic and phenotypic analyses, we describe these T. septentrionalis symbionts as Mesoplasma whartonense sp. nov. and Spiroplasma attinicola sp. nov., providing insight into their genomic and phenotypic diversity and cultures to facilitate future studies of how these common but poorly understood members of the fungus-growing ant symbiosis separately colonize different ant colonies despite having highly overlapping niches.

IMPORTANCE

Fungus-growing ants partner with multiple microbial symbionts to obtain food and remain free from disease. Of these symbionts, those inhabiting the ant gut remain the least understood and are known only from environmental surveys. Such surveys can infer potential functions of gut symbionts, but cultures are required to experimentally validate these hypotheses. Here, we describe the first cultures of the ant gut symbionts of the fungus-growing ant Trachymyrmex septentrionalis, using comparative genomics and phenotypic experiments to describe them as two novel species: Mesoplasma whartonense sp. nov. and Spiroplasma attinicola sp. nov. This genomic analysis suggests that these species are highly specialized to T. septentrionalis and are distinct from related environmental data generated from the related ant species Acromyrmex echinatior, implying substantial host specificity. Our phenotypic experiments and genomic reconstructions highlight the highly overlapping niches and likely costs and benefits of these symbionts to their ant host, setting the stage for further experimentation.

Chinese yam starch and non-starch polysaccharides alleviated antibiotic-associated diarrhea by ameliorating intestinal inflammation and regulating intestinal microbiotas

BACKGROUND

Yam is a typical food and can also be used as traditional medicine in treating diarrhea. Yam non-starch polysaccharides (SYP) and starch (SYS) are the most abundant ingredients in yam. The present study aimed to study the antidiarrheal effects and potential mechanisms of SYP and SYS on antibiotic-associated diarrhea (AAD) rats.

RESULTS

A rat model of antibiotic-associated diarrhea was prepared by orally administering a mixed antibiotic solution once a day for 10 consecutive days. Then, the rats were orally administered with SYS and SYP once a day for 7 consecutive days to treat antibiotic associated diarrhea. Fecal water content, colonic histopathology, inflammatory cytokines and intestinal microbiotas were used to evaluate the antidiarrheal effect and elucidate the potential mechanism. SYP and SYS reduced the fecal water content, improved the integrity of the colonic mucosa and alleviated the colonic inflammatory response of AAD rats. Moreover, SYP and SYS significantly increased the abundance and diversity of intestinal microbiotas in AAD rats. The relative abundance of Enterococcus, Lachnoclostridium, Bacteroides, Clostridioides, Clostridiales_unclassified, Serratia and Lachnospiraceae_NK4A136_group had significantly changed in the model (antibiotic control) group. The abundance of Enterococcus, Bacteroides, Clostridioides, Clostridiales_unclassified, Serratia and Lachnospiraceae_NK4A136_group was restored after treatment with SYS. The abundance of Enterococcus, Clostridioides and Serratia was recalled after SYP treatment.

CONCLUSION

SYS and SYP could improve antibiotic-associated diarrhea by ameliorating the colon inflammatory response and rebuilding intestinal microbiotas. © 2025 Society of Chemical Industry.

Dual-mycorrhizal colonization is determined by plant age and host identity in two species of Populus

Plants have evolved symbioses with mycorrhizal and endophytic fungi that are essential for their growth and survival. While most plants associate with a single guild of mycorrhizal fungi, a select group termed "dual-mycorrhizal plants" associate with both arbuscular mycorrhizal and ectomycorrhizal fungi. Although a shift from predominance of arbuscular mycorrhizal to ectomycorrhizal colonization with plant development has been demonstrated on other dual-mycorrhizal hosts, it is not known how mycorrhizal colonization shifts with plant age in Populus species. We performed a controlled growth experiment with natural field-sourced inocula to test for age-dependent shifts in fungal colonization rates and for host-specific patterns of colonization in two species of Populus (P. tremuloides and P. trichocarpa). We found that only P. trichocarpa displayed dual-mycorrhizal colonization, while P. tremuloides associated with ectomycorrhizal fungi, but not arbuscular mycorrhizal fungi. Both guilds of mycorrhizal fungi increased in abundance with plant age, while root endophytic fungal colonization decreased. Many of the early-colonizing endophytic fungi that we documented have strong saprotrophic capabilities, which may be an important trait for fast colonization. Dark septate endophytes were more abundant than either guild of mycorrhizal fungi, and are likely to be functionally important members of the Populus root fungal community. Our findings represent a novel pattern in the development of dual-mycorrhizal colonization and illustrate that Populus species vary in their association with arbuscular mycorrhizal fungi. Our results also highlight the importance of dark septate endophyte colonization dynamics on dual-mycorrhizal plants.

Co-Infection of Fungi and Bacteria in the Gills of Kuruma Shrimp (Penaeus japonicus) Afflicted by Fusarium Disease

Fusarium disease is an infectious condition that occurs in the cultivation of kuruma shrimp (Penaeus japonicus), primarily presenting as lesions in the gills. These lesions contain proteolytic enzymes of likely bacterial origin. This is the first study to demonstrate fungal-bacterial mixed infection in gill lesions of Fusarium-infected kuruma shrimp. Tenacibaculum spp. showing proteolytic activity were isolated from the lesions, whereas Fusarium spp. showed no such activity. Two Tenacibaculum strains were identified as Tenacibaculum mesophilum based on whole-genome sequencing (WGS) using MiSeq and GridION. Comparative analysis with the type strain DSM 13764 revealed > 95% nucleotide identity and 82.7% DNA-DNA hybridization similarity, with average genome coverage of 250×. Genomic analysis predicted that the genomes encode multiple protease and antibiotic resistance genes. Histopathology and SEM revealed that Fusarium hyphae had penetrated gill tissue, accompanied by infiltration of blood cells. Both fungal hyphae and T. mesophilum co-localised around gill cells. Bacterial diversity, assessed by 16S rRNA gene sequencing (V4 region), declined with tissue disintegration. Immune-related host genes such as anti-lipopolysaccharide factor (ALF) and lactate dehydrogenase (LDH) were upregulated, suggesting innate immune activation. These findings provide novel insights into the disease pathogenesis and contribute to the establishment of early detection systems and biosecurity-based control strategies.

Substitution of polysorbates by plant-based emulsifiers: impact on vitamin D bioavailability and gut health in mice

Although long considered safe, recent data have shown that emulsifiers such as polysorbates promoted intestinal inflammation and were associated with increased risks of developing chronic pathologies. We evaluated the potential of plant-based emulsifiers (pea protein isolate, PPI, and corn arabinoxylans, CAX) as alternatives to Polysorbate 80 (Tween 80, T80). Combining PPI and CAX led to a similar vitamin D3 bioavailability to T80 in vitro and in vivo in mice. We then exposed female and male mice to dietary doses of emulsifiers in oil-in-water emulsions (180 mg/kg/day for T80, 5 days/week) for 11 weeks. Conversely to previous studies conducted with higher doses of emulsifiers, T80, PPI, and PPI + CAX groups were similar to the control group (oil alone) in terms of physiological characteristics and inflammation biomarkers. However, LPS-specific serum IgG levels were reduced in the PPI (-31.05%, p = 0.0006) and PPI + CAX (-34.66%, p = 0.0001) groups compared to the T80 group at the end of the intervention. Exposure to T80, but not to PPI or PPI + CAX, reduced the distance between bacteria and the jejunal epithelium (-60.67%, p = 0.0779) and significantly increased Firmicutes_D phylla in male mice. Overall, we showed that a combination of pea protein and arabinoxylans appears as a sustainable alternative to polysorbates for vitamin D3 delivery.

Gut microbiota diversity and composition in children with autism spectrum disorder: associations with symptom severity

Background

Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder impairing social and communication skills. Gut microbiota has become key in understanding ASD pathophysiology. However, the relationship between the ASD symptoms and alternation of gut microbiota still remains unknow. We hypothesize that the composition of gut microbiota in children with ASD may be strongly associated with the severity of their symptoms.

Methods

Here, fecal samples from children (divided in to three groups: neurotypical, severe ASD and mild ASD) at a hospital were collected. The symptoms of ASD were assessed by an experienced pediatric neurologist, and the severity of the symptoms in children with ASD was determined based on the assessment scores. Then the diversity and composition of gut microbiota were detected by high-throughput sequencing.

Results

In total, 2,021 amplicon sequence variants (ASVs) were obtained from 46 fecal samples, with highest in the neurotypical group. Alpha diversity in bacteria differed between severe and mild ASD. Microbiota health and dysbiosis indices varied with ASD severity. Beta diversity indicated that severe ASD differed from others, and mild ASD was closer to neurotypical in community structure. At the phylum level, Firmicutes was the dominant bacteria but abundances differed in different groups, and Ascomycota increased in severe ASD fungi. At the genus level, groups had distinct dominants, and mild ASD microbiota resembled that of neurotypical children. Function prediction revealed differences in bacteria and fungi, with severe ASD having higher amino acid metabolism, lower cofactor/vitamin metabolism, and more undefined saprotrophs.

Conclusion

This study revealed gut microbiota differences between ASD children (varying symptoms) and neurotypical ones, showing milder ASD closer in microbiota aspects. It offers insights for exploring ASD pathogenesis and devising interventions.

Severe drought impacts tree traits and associated soil microbial communities of clonal oaks

BACKGROUND

Biotic and abiotic factors, including plant age, soil pH, soil organic matter concentration, and especially water availability, significantly influence soil microbial populations and plant characteristics. While many ecosystems are adapted to occasional droughts, climate change is increasing the frequency and severity of drought events, which negatively impacts plant productivity and survival. Long-lived, drought-sensitive tree species such as Quercus robur are particularly vulnerable to water shortages. Drought also alters soil microbial communities, reducing and reshaping microbial diversity, biomass, and activity, which can in turn disrupt key ecosystem functions. The objective of this study was to investigate the effects of natural drought conditions on soil physicochemical variables, plant traits and microbial communities of the oak clone DF159 in Central Germany. Our research focuses on two study sites, Bad Lauchstädt and Kreinitz, which differ in soil water retention capacity. Data collection spans two periods: before and after a severe drought in 2018. Oak traits and environmental data was collected from 2011 to 2023 covering two oak time series with trees planted annually between 2010 and 2019. Microbial communities were analyzed every second year between 2015 and 2021 around trees representing five different ages.

RESULTS

We found that plant traits, including apical growth, branch elongation and number of shoot flushes, were positively correlated with precipitation and relative humidity. Although the study sites differed in oak leaf number per shoot flush and number of shoot flushes, the 2018 drought negatively impacted all measured plant traits, regardless of sites. Soil bacterial richness and diversity declined at both study sites, independent of plant age, while fungal richness specifically increased in Bad Lauchstädt, which has a higher water-holding capacity, following the drought event. Bacterial community composition was more strongly affected by drought than fungal communities, whereas the latter was more responsive to plant age than bacterial communities.

CONCLUSIONS

Given their strong functional links during drought, interactions among vegetation, microbial communities, and soil functioning may ultimately influence major ecosystem services. Bacterial communities were particularly sensitive to drought, while fungal communities exhibited greater resistance, suggesting their potential role in supporting plant survival under drought stress. These findings highlight the risk that prolonged drought may cause irreversible shifts in microbial communities, with significant implications for soil functions and plant-microbe interactions.

Indigenous bacterial adaptation and survival: Exploring the shifts in highly compacted bentonite over a 5-year long-term study for nuclear repository purposes

Compacted bentonite is one of the most promising engineered barrier materials used in Deep Geological Repositories (DGR) of high-level radioactive waste encapsulated in metal canisters. Determining bentonite compaction density threshold for bacterial presence and activity has been a long-standing objective, due to their implications for canisters' durability and, therefore, in the safety performance of DGR. This study provided new insights into the effect of dry density (1.5 and 1.7 g cm⁻³), acetate amendment, and long-term incubation (5 years) on the bentonite mineralogy as well as their bacterial community distribution and survival. Through Illumina sequencing, we demonstrated that higher dry density reduces the bacterial diversity with spore-forming bacteria such as Nocardioides, and Promicromonospora being predominant. Interestingly, Paracoccus and Pseudomonas were enriched in acetate-treated samples, suggesting the utilization of this carbon source and, consequently, supporting their viability and survival. In addition, spore-forming (e.g., Bacillus) and desiccation-resistant (e.g., Arthrobacter) microorganisms were isolated. X-ray diffraction and scanning electron microscopy analyses showed the stability of bentonite while indicating the probable formation of iron sulfides. These findings confirm the influence of bentonite compaction degree and long-term incubation on microbial viability and activity, highlighting their potential impact on the integrity and safety of future DGR.

New insights into efficient iron sulfide oxidation for arsenic immobilization by microaerophilic and acidophilic Fe(II)-oxidizing bacteria under micro-oxygen and acidic conditions

Microbial-mediated FeS oxidation to Fe(Ⅲ) minerals via chemolithoautotrophic Fe(Ⅱ) oxidizers under pH/O₂ limitations engages As immobilization. However, this process is constrained under the dual stress of micro-oxygen and acidic conditions due to the critically diminished Fe(Ⅱ) oxidation capacity. Therefore, the interplay between Fe(Ⅱ) oxidation, carbon metabolism, and As immobilization in Fe(Ⅱ)-oxidizing bacteria under micro-oxygen and acidic conditions remains unclear. This study presents the first successful enrichment of microaerophilic and acidophilic Fe(II)-oxidizing bacteria (MAFeOB). These bacteria are capable of oxidizing FeS to Fe(III) minerals and immobilizing up to 27,835 mg/kg of As(Ⅴ) under micro-oxygen content (below 3.2 mg/L) and acidic pH (4.5-6.2). Through comprehensive metagenomic analysis, it was speculated that MAFeOB harbor a suite of genes potentially participating in critical processes, including carbon fixation, Fe(II) oxidation, and arsenic detoxification. Notably, a potential electron transfer pathway from Cyc2_repCluster2 to Cytochrome cbb3-type oxidases facilitates Fe(II) oxidation. Furthermore, As(Ⅲ) efflux pump (arsA, arsB, acr3) and As(Ⅲ) oxidase (aioA) genes indicate MAFeOB's potential for As immobilization. Our findings underscore the pivotal role of MAFeOB in overcoming limitations associated with Fe(III) mineral formation, thereby enhancing arsenic immobilization under micro-oxygen and acidic water.

Identification of polychlorinated biphenyls (PCBs) and PCB metabolites associated with changes in the gut microbiome of female mice exposed to an environmental PCB mixture

Polychlorinated biphenyls (PCBs) are neurotoxic hazardous materials that may cause toxicity via the gut-liver-brain axis. This study investigated PCB × microbiome interactions in adult female mice exposed orally to an environmental PCB mixture. Female mice (6-week-old) were exposed daily for 7 weeks to peanut butter containing 0, 0.1, 1, or 6 mg/kg/day of PCBs. Twenty hours after the final exposure, the cecal content was collected to characterize the microbiome composition and predicted function. PCB and its metabolites in feces were analyzed using gas chromatography-tandem mass spectrometry (GC-MS/MS), while cecal content was assessed with liquid chromatography-high resolution mass spectrometry (LC-HRMS). PCB exposure influenced the abundance of microbial taxa and predicted functions within the cecal content. Complex PCB and metabolite mixtures were detected in the gastrointestinal tract. Network analysis revealed associations between specific parent PCBs and metabolites with changes in the abundance of bacteria in the gastrointestinal tract. These findings demonstrate that individual PCBs and their metabolites significantly influence the abundance of specific bacteria in the gastrointestinal tract following oral PCB exposure. These findings inform further research targeting the microbiome to attenuate the adverse health outcomes of PCB exposure.

Experimental evidence for viral impact on microbial community, nitrification, and denitrification in an agriculture soil

Viruses are ubiquitous, and their potential impacts on biogeochemical cycles in soil have largely been inferred from correlation evidence and virome studies. Manure has been demonstrated to affect nitrogen cycle by altering soil nutrients and microbial communities. However, the direct impacts of viruses derived from manure on microbial community, nitrification, and denitrification remained exclusive. In this study, concentrated viral extracts obtained from manure were added into an agricultural soil in varying dosages: a one-time addition of 10-fold viruses or a weekly addition of 1-fold viruses for ten weeks. The results showed that both viral extracts and manure significantly changed the microbial community compositions and structures. The effect of manure on microbial diversity was concentration-dependent, differing from the viral impact on microbial diversity in soil. Deterministic processes predominated in the assembly of microbial communities in both viral and manure treatments, with an increased contribution of deterministic processes observed after these treatments. Additionally, a high concentration (10-fold) of viruses enhanced N2O production and reduction in soil. In the control treatment, N2O production was driven by bacterial denitrification, fungal denitrification, and chemo-denitrification. However, bacteria became the dominant driver of N2O production in both virus and manure treatments. Overall, experimental evidence for viral impacts on the composition and assembly of microbial community, as well as on nitrification and denitrification processes, was provided through a 70-day microcosm experiment. These findings highlight the importance of viruses in regulating the distribution and functioning of microbes in terrestrial ecosystems.

Function of Yogurt Fermented with the Lactococcus lactis 11/19-B1 Strain in Improving the Lipid Profile and Intestinal Microbiome in Hemodialysis Patients

BACKGROUND/OBJECTIVES

The number of chronic kidney disease (CKD) patients is increasing in Japan, and this population is at high risk of death from cardiovascular and cerebrovascular diseases. Therefore, prevention of arteriosclerosis as a common underlying cause of these diseases is required. In this study, we examined whether 11/19-B1 yogurt, which has been proven to reduce serum low-density lipoprotein (LDL) levels, can decrease the serum levels of indoxylsulfate and trimethylamine-N-oxide (TMAO), which are produced by intestinal microbiota and known to cause arteriosclerosis, through improving dysbiosis in hemodialysis patients.

METHODS

Nineteen dialysis patients consumed 50 g of 11/19-B1 yogurt daily for 8 weeks, and changes in serum lipid profile and uremic toxin levels, intestinal microbiome, as well as the frequency of bowel movement and stool characteristics were observed.

RESULTS

The results demonstrated that an intake of yogurt decreased serum LDL 99.3 to 88.5 (p = 0.049) and indoxylsulfate in seven of nine subjects with previously high concentrations, and improved stool characteristics as estimated by the Bristle stool score, although decreased HDL and no beneficial effect on serum TMAO was observed.

CONCLUSIONS

These results may suggest that the ingestion of 11/19-B1 yogurt provides a preventative effect against the progression of atherosclerosis and renal dysfunction.

Sputum quality affects assessment of airway microbiology in childhood asthma

BACKGROUND

The analysis of sputum is the principal basis for characterising lower airway microbiology in those with chronic respiratory conditions. For such analysis to be informative, samples that poorly reflect the lower airways must be identified and removed. Our cross-sectional study explored the relationship between the quality of sputum samples and their microbiological content. We further investigated the impact of excluding low quality samples on observed microbiota-disease relationships in childhood asthma.

METHODS

Induced sputum was collected from children with or without asthma. Sputum quality was assessed according to squamous cell%, cell viability%, detection of sputum plugs, and salivary α-amylase levels. Sputum microbiota was characterised by 16S rRNA amplicon sequencing and qPCR.

RESULTS

Of 170 participants, 130 had asthma. Between 19% (32/170) and 29% (53/170) of samples were deemed to be of insufficient quality, depending on the quality criterion applied. Stratification of samples based on any of the sputum quality cut-offs resulted in significant differences in microbiota characteristics (all p < 0.05), with salivary α-amylase the least discriminant between microbiota of acceptable and unacceptable samples. The removal of 53 poor-quality samples based on ≥ 30% squamous cells identified a difference in the sputum microbiota by asthma status (p = 0.017) that was not evident otherwise, including significantly higher levels of Haemophilus and Gemella in asthma samples.

CONCLUSIONS

Upper airway contamination of induced sputum samples from children is common. Exclusion of samples based on ≥ 30% squamous cells enables identification of asthma-airway microbiology relationships that are otherwise not apparent.

Use of Multi-Locus Metabarcoding to Inform an Australian Government Biosecurity Response on the Origins of Suspected Illegal Plant Products

Biosecurity is vital to Australia's efforts to prevent and respond to pests and diseases. Here, we report on testing suspected illegal goods (SIGs) as part of an active Australian biosecurity response in Sydney. The Australian Government, Department of Agriculture, Fisheries and Forestry detected and secured consignments containing tuber products of unknown biosecurity risk and origin. Swab samples were collected from vacuum-sealed yam products, organic packing material (background negative controls), and field negative controls to assess possible cross-contamination from the storage facility. DNA from all samples was analysed using high-throughput metabarcoding targeting the Internal Transcribed Spacer 2 (ITS2) and the chloroplast trnL (UAA) P6 Loop gene regions by two independent teams in Australia. A plant community profile comprising Australian native species and other non-native established species would support the notion of produce being harvested and/or packaged domestically, while their absence would suggest foreign production. Of the 5,764,942 total reads produced, the bioinformatic analysis generated 5,181,530 amplicon sequencing variants employed for species identification. Twenty plant taxa were identified via ITS2 and 15 via trnL, corresponding to worldwide distributed plants, non-native species established in Australia, or species not recorded in Australia. No Australian endemic species were detected. The absence of common Australian native plants, combined with the presence of species not known to occur in Australia, provided strong evidence that the suspect tuber products were illegally imported.

Role of the upper airway microbiota in respiratory virus and bacterial pathobiont dynamics in the first year of life

The mechanisms by which respiratory viruses predispose to secondary bacterial infections remain poorly characterized. Using 2,409 nasopharyngeal swabs from 300 infants enrolled in a prospective cohort study in Botswana, we perform a detailed analysis of factors that influence the dynamics of bacterial pathobiont colonization during infancy. We quantify the extent to which viruses increase the acquisition of Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae. We provide evidence of cooperative interactions between these pathobionts while identifying host characteristics and environmental exposures that influence the odds of pathobiont colonization during early life. Using 16S rRNA gene sequencing, we demonstrate that respiratory viruses result in losses of putatively beneficial Corynebacterium and Streptococcus species that are associated with a lower odds of pathobiont acquisition. These findings provide important insights into viral-bacterial relationships in the upper respiratory tract of direct relevance to respiratory infections and suggest that the bacterial microbiota is a potentially modifiable mechanism by which viruses promote bacterial respiratory infections.

Gut microbiota composition differences are associated with geographic location and age in malaria-endemic regions of Rwanda

Evidence suggests that a significant interplay exists between the host gut microbiota and both the transmission and severity of malaria. Therefore, we explored the association between malaria and the gut microbiota across various geographic regions, considering host's nutritional habits, helminth coinfections and age. This observational study was conducted in 3 malaria-endemic provinces of Rwanda: West, South and East. Demographic data, blood and fecal samples were collected from 169 participants (85 females and 84 males) aged between 2-78 years. We used questionnaire-derived qualitative data based on geographic regions, age, and nutrition. Malaria and soil-transmitted helminth diagnosis was assessed by microscopy. The gut microbial composition was analyzed based on bacterial 16S rRNA gene amplicon sequencing. We observed that preschool children had a significantly lower microbiota diversity compared to both school children (q = 0.027, K-Wallis) and adults (q = 0.011, K-Wallis). Unlike age, infection status (uninfected, malaria alone, soil-transmitted helminth alone or coinfection) was not significantly associated with the gut microbiota. However, using Bray-Curtis distances, we found a significantly differential gut microbial beta-diversity with a convergent distribution in the Western province compared to the other provinces (q = 0.0045, pairwise PERMANOVA). This geographic difference was not explained by any change in energy intake, protein, lipids, or carbohydrates consumption but was likely due to lower dietary fibre intake in the West compared to the South (q < 0.0001, ANOVA) and the East (q = 0.07, ANOVA). In conclusion, we have not found significant links between infection and gut microbiota. However, we showed a significant difference in the gut microbiota composition of people living in different geographic locations in Rwanda, possibly due to their nutritional habits.

Two Species of Long-Day Breeding Hamsters Exhibit Distinct Gut Microbial Responses to Photoperiodic Variations

The relationship between the gut microbiota and photoperiod has received widespread attention, and it is necessary to explore the probable common mechanisms involved. We tested whether the gut microbiota of animals with similar light-regulated life history traits would also exhibit consistent responses to the photoperiod. Here, two species of long-day breeders, striped hamsters (Cricetulus barabensis) and Djungarian hamsters (Phodopus sungorus), were raised under different photoperiods (long daylight, LD; short daylight, SD), and their cecal contents were collected to assess the gut microbiota. There was no difference in the gut microbial diversity between the groups of striped hamsters; however, in the Djungarian hamsters, lower Chao and Shannon indices were observed in the LD group than in the SD group. The bacterial community variation in the striped hamsters was reflected mainly in the enrichment of the genera Enterorhabdus and Jeotgalicoccus in the LD group; meanwhile, more taxa with significant changes in relative abundance under different photoperiods were found in the Djungarian hamsters, such as the enrichment of the genera Lactobacillus and Faecalibaculum in the LD group and the enrichment of the genera Ruminococcus and Colidextribacter in the SD group. The LD conditions substantially reduced the complexity of the gut microbial network in the Djungarian hamsters and increased the R2 value of the striped hamster gut microbiota under fitting with a neutral community model. Moreover, the potential gut microbial functions in the striped hamsters were relatively stable, but variations were observed in multiple pathways between the groups of Djungarian hamsters. These results contribute to the understanding of host species specificity in the response of the gut microbiota to external changes.

Microbial dynamics in seagrass restoration: Unveiling hidden indicators of ecological success

Seagrass transplantation significantly alters sediment microbial communities, shaping their composition and metabolic functions. One year after Zostera marina transplantation, the microbial community structure and functions at the recipient site began shifting toward those of the donor site. Key microbial taxa associated with seagrass meadow sediment, such as Firmicutes (Hungateiclostridiaceae, Defluviitaleaceae) and Campylobacterota (Sulfurovum), increased in abundance, correlating with sediment organic matter content and carbon availability. Four functional groups were identified, each with distinct metabolic roles: (1) Opportunistic Anaerobic Degraders, (2) Seagrass-Driven Carbon Recyclers, (3) Anaerobic Fermenters and Hydrocarbon Recyclers and (4) Oxygen-Linked Carbon and Sulfur Cyclers. The sediments of transplanted Z. marina meadows exhibited increased cellulolysis and aerobic chemoheterotrophy, along with a reduction in nitrogen metabolism one year post transplant. Despite these microbial shifts, sediment isotopic signatures remained indicative of algal biomass, suggesting an incomplete transition toward a mature seagrass environment. Multivariate analysis further confirmed that the microbial community at the recipient site had not yet fully converged with that of the donor meadow, indicating that complete sediment maturation may require longer timescales. These findings demonstrate that microbial community composition and functional annotations serve as early indicators of seagrass restoration success. Long-term monitoring is essential to track ecosystem recovery and assess the stabilization of sediment conditions.

Microbiota associated with caries and apical periodontitis: A next-generation sequencing study

AIM

This study investigated the correlation between microbiota of caries-free enamel and caries-affected dentine biofilms and that of root canals with primary apical periodontitis, by using an Illumina MiSeq platform.

METHODOLOGY

Biofilm from caries-free enamel surface (Biofilm-C) or caries-affected dentine (Biofilm-E) and root canal paper point samples (Canal) were collected from 31 teeth with primary apical periodontitis. Microbial composition was analysed by amplicon sequencing that targeted the V3-V4 region of 16S rRNA gene. Alpha and beta diversities of bacterial communities between sampling sites were compared using the Kruskal-Wallis test and pairwise permutational multivariate analysis of variance, respectively. Differentially abundant taxa identified using MaAsLin2 were adjusted for multiple comparisons using the Benjamini-Hochberg method.

RESULTS

Totals of 16 phyla, 130 genera and 314 species were identified. Distinct and shared bacterial communities were observed between biofilm and canal samples. No significant differences in alpha diversity were observed across all sampling sites. A total of 32 genera including Acinetobacter, [Eubacterium], Dialister, Erysipelotrichaceae UCG-006, Lawsonella, W5053, Phocaeicola, Mogibacterium, Pyramidobacter and Parvimonas were more abundant in Canal samples compared to both Biofilm-C and Biofilm-E. The genera Hallella, Lactobacillus, Shuttleworthella, Olsenella, Cryptobacterium, Alloprevotella, Phocaeicola, Limosilactobacillus, Selenomonadaceae and Anaeroglobus were increased significantly in Biofilm-E compared to Biofilm-C. Hallela multisaccharivorax, Olsenella uli, Lactobacilllus gasseri, Selenomonadaceae species and Scardovia inopinata exhibited higher abundance in both Biofilm-E and Canal, than Biofilm-C. These differences in bacterial composition among sampling sites, including the increased presence of specific taxa in caries-affected dentine and root canals, suggest that these microorganisms may contribute to the development of primary apical periodontitis.

CONCLUSION

Bacterial community structure differed significantly between biofilm and root canal samples, but showed no significant differences among biofilm samples based on dental caries status. However, some taxa were shared among caries-affected lesions, including dentine and root canals. H. multisaccharivorax, O. uli, L. gasseri, Selenomonadaceae species and S. inopinata exhibited higher abundance in caries-affected dentine and root canals with primary apical periodontitis, suggesting that specific bacteria in caries-affected dentine play a crucial role in the development of root canal infections and the pathogenesis of primary apical periodontitis.

Ginsenoside Rh4 inhibits colorectal cancer via the modulation of gut microbiota-mediated bile acid metabolism

INTRODUCTION

Dysbiosis of the gut microbiota is emerging as a pivotal factor in the pathogenesis of colorectal cancer (CRC). Ginsenoside Rh4 (Rh4) is an active compound isolated from ginseng with beneficial effects in modulating intestinal inflammation and gut microbiota dysbiosis, but how Rh4 regulates the gut microbiota to alleviate CRC remains underexplored.

OBJECTIVES

We investigated the impact of Rh4 on CRC and the mechanism of its action in inhibiting CRC via modulation of gut microbiota.

METHODS

We used the AOM/DSS model and employed transcriptomics, genomics and metabolomics techniques to explore the inhibitory impact of Rh4 on CRC. Furthermore, we employed experiments involving antibiotic treatment and fecal microbiota transplantation (FMT) to investigate the role of the gut microbiota. Finally, we elucidated the pivotal role of key functional bacteria and metabolites regulated by Rh4 in CRC.

RESULTS

Our research findings indicated that Rh4 repaired intestinal barrier damage caused by CRC, alleviated intestinal inflammation, and inhibited the development of CRC. Additionally, Rh4 inhibited CRC in a gut microbiota-dependent manner. Rh4 increased the diversity of gut microbiota, enriched the probiotic Akkermansia muciniphila (A. muciniphila), and alleviated gut microbiota dysbiosis caused by CRC. Subsequently, Rh4 regulated A. muciniphila-mediated bile acid metabolism. A. muciniphila promoted the production of UDCA by enhancing the activity of 7α-hydroxysteroid dehydrogenase (7α-HSDH). UDCA further activated FXR, modulated the TLR4-NF-κB signaling pathway, thus inhibiting the development of CRC.

CONCLUSION

Our results confirm that Rh4 inhibits CRC in a gut microbiota-dependent manner by modulating gut microbiota-mediated bile acid metabolism and promoting the production of UDCA, which further activates the FXR receptor and regulates the TLR4-NF-κB signaling pathway. Our results confirm that Rh4 has the potential to be used as a modulator of gut microbiota for preventing and treatment of CRC.

A polyphasic method for the characterization of epiphytic diatoms growing on Gelidium corneum

Epiphytic diatoms associated with marine macroalgae play vital ecological roles in nutrient cycling and primary production, yet their study remains limited due to the lack of standardized methodologies. This study focuses on diatom communities growing on Gelidium corneum, a key red alga in the Cantabrian coast (Spain). Samples were collected from two depths along the northern coast of Spain and processed using both morphological and molecular approaches. Morphological analysis involved diatom frustule preparation using hydrogen peroxide digestion, acid treatments, and permanent slide mounting, enabling identification through light microscopy. Molecular analysis employed DNA extraction and rbcL marker-based metabarcoding, allowing detailed taxonomic characterization. Results highlight the efficacy of combining morphological and molecular techniques to overcome the limitations of either approach individually. By standardizing procedures, we enhance the reproducibility and comparability of studies focused on diatom epiphytes. Our results highlight the ecological significance of diatom-macroalgal interactions and provide a framework for future investigations into these essential but underexplored communities.•A polyphasic method was developed for studying epiphytic diatoms on Gelidium corneum, combining morphological and molecular tools.•The approach overcomes challenges in diatom characterization, including intricate host morphology and cryptic species identification.•Standardized protocols enhance reproducibility and offer insights into diatom-macroalgal ecological interactions.

Diel Bacterioplankton Community Dynamics Under Contrasting Light Regimes

In the Boreal region, extreme seasonal variations in day-night length expose communities to dynamic light and temperature fluctuations. Freshwater bacterioplankton, representing key ecosystem components, faces climate-driven shifts; yet the fixed day-length patterns determined by latitude underscore the importance of studying light's role in predicting ecosystem responses. We investigated bacterial community composition in a brown peat bog and a clear oligotrophic lake across seasons with contrasting light regimes: the summer solstice (> 20 h of daylight) and the autumn equinox (equal day-night length). Using amplicon sequencing of 16S rRNA transcripts, alongside measurements of physicochemical parameters, organic matter characterisation and dissolved carbon dioxide and methane gas measurements, we found no diel cycling in the lake during either period or in the peat bog near the summer solstice. However, the structure of bacterial peat bog communities exhibited cyclic changes over diel cycles at the autumn equinox. Twelve amplicon sequence variants, including both phototrophic and heterotrophic taxa, increased in abundance at all measured morning sampling times. These findings provide valuable insights into the diel patterns of boreal lentic habitats and their bacterioplankton communities, highlighting the absence of diel fluctuations in some systems and seasons, while revealing cyclic dynamics in others, driven by conditionally rare taxa.

Alterations to the vaginal microbiota and their correlation with serum pro-inflammatory cytokines in post-weaning sows with endometritis

Endometritis is a prevalent disease in sows that strongly reduces reproductive performance. Its causes are complex and multifaceted, making disease management challenging without targeted measures. To provide a scientific basis for developing targeted disease management strategies, we examined vaginal microbiota diversity and its correlation with serum pro-inflammatory cytokine levels in sows with endometritis and the main pathogenic bacterial species contributing to endometritis. Fourteen post-weaning sows selected at a pig farm in Beijing, China, were randomly divided into healthy (C) and endometritis (E) groups. Levels of cytokines including interleukin-1α (IL-1α), IL-1β, IL-6, IL-8, and tumor necrosis factor-α (TNF-α) were quantified by enzyme-linked immunosorbent assays. Vaginal microbiota species were identified using 16S rDNA sequencing. Concentrations of IL-1α and IL-6 in serum and vaginal microbial diversity were significantly increased in group E versus group C. The relative abundance of Firmicutes exhibited a marked increase in group E, whereas that of Fusobacteriota was significantly decreased. The composition and relative abundance of dominant bacterial genera differed between the two groups, and the dominant genera in group E were Clostridium_sensu_stricto_1, UCG-005, UCG-002, Terrisporobacter, and Christensenellaceae_R-7_group. IL-6 was significantly positively correlated with Clostridium_sensu_stricto_1 and Terrisporobacter in group E. These results suggest that vaginal microbiota abundance and diversity and serum pro-inflammatory cytokine levels are increased in sows with endometritis, and the latter are closely associated with vaginal microbiota abundance and composition. This study provides a foundation for investigating the pathogenesis of endometritis in sows and a theoretical basis for disease prevention and treatment.

Shotgun sequencing of airborne eDNA achieves rapid assessment of whole biomes, population genetics and genomic variation

Biodiversity and its associated genetic diversity are being lost at an unprecedented rate. Simultaneously, the distributions of flora, fauna, fungi, microbes and pathogens are rapidly changing. Novel technology can help to capture and record genetic diversity before it is lost and to measure population shifts and pathogen distributions. Here we report the rapid application of shotgun long-read environmental DNA (eDNA) analysis for non-invasive biodiversity, genetic diversity and pathogen assessments from air. We also compared air eDNA with water and soil eDNA. Coupling long-read sequencing with established cloud-based biodiversity pipelines enabled a 2-day turnaround from airborne sample collection to completed analysis by a single investigator. To determine the full utility of airborne eDNA, we also conducted a local bioinformatic analysis and deep short-read shotgun sequencing. From outdoor air eDNA alone, comprehensive genetic analysis was performed, including population genetics (phylogenetic placement) of a charismatic mammal (bobcat, Lynx rufus) and a venomous spider (golden silk orb weaver, Trichonephila clavipes), and haplotyping humans (Homo sapiens) from natural complex community settings, such as subtropical forests and temperate locations. The rich datasets also enabled deeper analysis of specific species and genomic regions of interest, including viral variant calling, human variant analysis and antimicrobial resistance gene surveillance from airborne DNA. Our results highlight the speed, versatility and specificity of pan-biodiversity monitoring via non-invasive eDNA sampling using current benchtop/portable and cloud-based approaches. Furthermore, they reveal the future feasibility of scaling down (equipment and temporally) these approaches for near real-time analysis. Together these approaches can enable rapid simultaneous detection of all life and its genetic diversity from air, water and sediment samples for unbiased non-targeted information-rich genomics-empowered (1) biodiversity monitoring, (2) population genetics, (3) pathogen and disease-vector genomic surveillance, (4) allergen and narcotic surveillance, (5) antimicrobial resistance surveillance and (6) bioprospecting.

Supplementation with ursodeoxycholic acid and bile salt benefits lactation performance, health, and rumen and fecal microbiota of transition dairy cows

This study investigated the effects of ursodeoxycholic acid (UDCA) and bile salt (BAS) supplementation on lactation performance, health, and gut microbiota in periparturient dairy cows. Fifty-one Holstein dairy cows were selected at d -28 before parturition and blocked into 3 dietary treatments, including the control (CON; n = 17) received a basal diet, whereas the UDCA (n = 17) and BAS groups (n = 17) were supplemented with 10 g/d UDCA and 20 g/d BAS from d -21 to +21, with an observation phase until d +35. Milk yield and composition were recorded weekly, whereas the DMI were measured biweekly. Blood samples were collected at d +7 and +21, whereas rumen fluid and fecal samples were collected at d +21. Milk yield was significantly higher in the UDCA group at d +21 compared with the CON group, whereas on d +28, milk yield was significantly higher in both the UDCA and BAS groups compared with the CON group, and the DMI of the UDCA group showed an increased tendency at prepartum. Plasma nonesterified fatty acids were significantly higher in the BAS group, whereas Ala aminotransferase content were significantly lower in the UDCA group compared with the control. Furthermore, the cholesterol, malondialdehyde, oxidative stress index, serum amyloid A, and haptoglobin content were significantly lower in the UDCA and BAS groups. In total, 35, 43, and 45 plasma bile acids (BA) were detected in the control, UDCA, and BAS groups, respectively. Compared with the control, 8 key BA, including UDCA, tauroursodeoxycholic acid, glycoursodeoxycholic acid, and 5 key BA, including tauro-β-muricholic acid and hyocholic acid, were identified in the UDCA and BAS groups, respectively. The concentrations of total VFA and acetate in the UDCA and BAS groups were higher than that in the CON group, and the concentration of propionate tended to be higher. The β-diversity of both rumen and gut microbiota was significantly higher in the CON, UDCA, and BAS groups, whereas no significant changes were observed in α-diversity. Key rumen VFA-production bacteria, including Prevotella_7, Succinivibrionaceae_UCG-001, and Selenomonas, were enriched in the UDCA and BAS groups, along with an increase in beneficial gut microbiota, such as Butyrivibrio, Ruminococcus, and Caproiciproducen, and a reduction in harmful bacteria, such as Stenotrophomonas and Chryseobacterium. These findings suggest that the observed improvements in production performance and health may be mediated by alterations in peripheral BA and rumen and gut microbiota, offering insights for optimizing the nutrition and health of transitional dairy cows.

Do the microbiota of larval breeding site and the blood meal influence the composition and diversity of bacterial communities in the midgut of Mansonia humeralis (Diptera: Culicidae) from the western Amazon?

Mansonia humeralis is a neotropical mosquito common in floodplain ecosystems and a potential host of Mayaro virus in the Amazon region. Studies show that bacterial communities associated with the midgut of mosquito vectors can mediate insecticide detoxification and modulate vector competence. Understanding the characteristics of the intestinal microbiota, and the factors that shape them, is essential for effective mosquito control. This study investigated the influence of bacterial communities in water from the larval environment on the composition and bacterial diversity in Ma. humeralis larval intestines and characterized the midgut microbiota of adult females with and without apparent blood. Samples were obtained from the Jirau Hydroelectric Plant, Madeira River, AM, Brazil, and their bacteria characterized using the 16S rRNA molecular marker. A total of 402 bacterial Amplicon Sequencing Variants (ASVs) were identified to genus level. The sample groups (water, larvae, blood + and blood-) had distinct bacterial communities, especially the larvae, probably due to the intense feeding activity which occurs at this stage. The phylum Proteobacteria was dominant in water, blood + and blood- (52.5; 99 and 98%), respectively, while Firmicutes dominated in larvae (45%). The most abundant taxa in water were: ASV Comamonadaceae (11.7%) and hgcI_clade (9.6%), in larvae: ASV Synergistaceae (11.1%) and ASV Rhodocyclaceae (7.8%), in blood-: Serratia (46.9%) and Asaia (12.6%) and, in blood+: ASV Enterobacteriaceae (54.5%) and Serratia (21.1%). Some 19% of the taxonomic groups from water were also recorded in larvae, while 46.7% of blood- microbiota were present in blood+. Wolbachia, Acinetobacter and Enterobacter bacteria were recorded at low frequency in all samples. This result provides a powerful tool for understanding the ecology of the intestinal microbiota of Ma. humeralis and the relationships with the ambient microbiota derived from larval filter, and adult blood, feeding. The results will also be useful for future studies which focusing the development of potential tools for the biological control of this vector.

Metabarcoding analysis of the microbiota in flocks naturally infected by Coxiella burnetii: First description of the global microbiota in domestic small ruminants

This study investigates Q fever in sheep and goats, key reservoirs for human infection, by metabarcoding and comparing it with q-PCR and serology. Samples from 26 small ruminants (aborted and normal-delivery) and six males across three Q fever-affected herds were analyzed. In sheep herds, seropositivity was 50 and 80 % respectively, with Coxiella (C.) burnetii shedding detected vaginally in the second herd. In goats, 100 % seropositivity and 90 % C. burnetii detection were observed, with nasal and vaginal samples showing the highest detection rates. Metabarcoding revealed significant differences in alpha diversity, with greater richness in blood and evenness in milk from normal-delivery sheep and higher evenness in faeces from aborted sheep. Beta diversity showed distinct vaginal microbiota in normal-delivery females compared to aborted ones. Firmicutes was the most abundant phylum observed. Dominant genera included: Moraxella (nasal), Mycoplasma (blood), Streptococcus (milk), Ureaplasma (vaginal and preputial), Rikenellaceae RC9 gut group (faeces). Significant differences in bacterial composition, including infertility-linked vaginal pathogens, were found across female groups in all herds in the anatomical locations studied, revealing new species and tropisms. Moreover, taxonomic analysis identified C. burnetii in vaginal, milk and environmental samples. This first report of C. burnetii in the caprine nasal cavity suggests an underestimated tropism that may improve Q fever diagnosis. These findings underscore the need for herd-wide Q fever control measures, including males and normal-delivery females. Our findings contribute to new insights into the pathogen's impact on small ruminant microbiota and a novel approach to studying infectious diseases in this sector.

Spatial patterns of soil bacterial communities in grazing areas of Southwest Spain

The spatial distribution of soil bacterial communities in agrosilvopastoral systems remains understudied, despite its fundamental role in ecosystem functioning. This study investigates the spatial dynamics of dominant copiotrophic and oligotrophic bacterial phyla in grazing areas of Southwest Spain, focusing on their interactions with land management, soil properties, and environmental covariates. Five management systems; occasional grazing (OG), holistic management (HM), organic farming (OF), conventional rangeland (CR), and conventional grassland (CG) were analyzed across three topographic positions (hilltop, mid-slope, valley bottom), representing a gradient of grazing intensity. A total of 71 soil samples were collected and analyzed using 16S rRNA metabarcoding. Alpha and beta diversity metrics revealed significant shifts in community composition driven by both management and topography, with HM showing higher richness compared to CR and CG. Among dominant phyla, copiotrophic groups such as Proteobacteria and Actinobacteriota were more abundant in upper slope areas and under higher grazing intensity, whereas oligotrophic Verrucomicrobiota was enriched in valley bottoms and under lower grazing pressure. Spatial prediction models based on Random Forest and recursive feature elimination (RFE) identified key environmental drivers, with vegetation indices being more relevant for Proteobacteria and Verrucomicrobiota, and topographic features for Actinobacteriota. RDA and SEM confirmed that animal stocking rate and soil organic matter were major predictors of β-diversity. This study provides novel insights into microbial spatial heterogeneity in Mediterranean grazing systems, highlighting the interplay of management practices, soil characteristics, and topography. The findings underscore the ecological benefits of holistic management in enhancing bacterial diversity and inform strategies for sustainable land use in agrosilvopastoral ecosystems.

Development of reference-based model for improved analysis of bacterial community

Probiotic bacteria play a vital role in maintaining gut microbial homeostasis and are widely used in various commercial products. Although 16S rRNA amplicon-based next-generation sequencing (NGS) is commonly used to analyze probiotic products, biases can arise from various 16S rRNA amplification regions, sequencing platforms, and library kits. In this study, a reference-based bias correction model was developed to correct sequencing biases. The model was validated using eight mock communities and 12 commercial products, which were analyzed across multiple NGS platforms and various 16S rRNA regions. Specific primer-probe assays were developed for accurate bacterial quantification, and their specificity was validated and used in conjunction with droplet digital PCR (ddPCR) to establish initial bacterial ratios within communities. Analysis of the mock communities revealed platform- and region-specific biases, with specific species consistently over- or under-represented. Similarly, commercial product analyses have shown biased outcomes owing to varying sequencing protocols. The correction model, based on PCR efficiencies from the reference communities, successfully corrected biased ratios across different amplification regions and platforms to achieve results that closely matched the proportions predicted by ddPCR. The model effectively corrected the biases arising from the different polymerases. Notably, partial references containing approximately 40 % of the species achieved correction results that were comparable to those of the complete references. This approach demonstrates the potential for improving microbiome analysis accuracy within predictable ranges, and could serve as a model for addressing sequencing bias in metagenomic research.

Divergences of granules and flocs microbial communities and contributions to nitrogen removal under varied carbon to nitrogen ratios

Aerobic granular sludge (AGS) reactors are promising for treating high ammonia wastewaters, yet the roles of granules and flocs in nitrogen removal under varying carbon to nitrogen (COD/N) ratios remain unclear. This study investigated microbial communities and their contributions to N removal as the COD/N ratio shifted from 6 to 4, and to 2. Results showed granules contributed 53-64 % nitrification capacity at higher COD/N ratios (6 and 4), but flocs contributed more (50-63 %) at a ratio of 2. Granules consistently exhibited higher denitrification capacity (>50 %). Heterotrophic bacteria dominated in both granules and flocs across all ratios. As the COD/N ratio reduced, the relative abundance of anaerobic ammonia oxidation microorganisms (Candidatus Anammoximicrobium) and filamentous bacteria increased in granules, while ammonia oxidizing bacteria (Nitrosomonas) and complex organic degraders increased in flocs. These findings highlight the importance of selectively retaining granules or flocs under varying COD/N ratios to optimize nitrogen removal efficiency.

A gut-focused perinatal dietary intervention is associated with lower alpha diversity of the infant gut microbiota: results from a randomised controlled trial

OBJECTIVES

In experimental models, the prenatal diet influences gut microbiota composition in mothers and offspring; however, it is unclear whether this occurs in humans. We investigated the effects of a gut-focused perinatal dietary intervention on maternal and infant gut microbiota composition four weeks after birth.

METHODS

This randomised controlled trial randomised pregnant women to receive dietary advice as part of standard care, or additionally receive a dietary intervention focused on the Australian Dietary Guidelines and increasing prebiotic and probiotic/fermented food intakes (ACTRN12616000936426). Study assessments occurred from gestation week 26 (baseline) to four weeks postpartum (follow-up). Faecal samples, collected at baseline for mothers, and follow-up for mothers and infants, underwent 16SrRNA sequencing. The primary outcome was a between-group mean difference in infant faecal Shannon index. Secondary outcomes included between-group differences in other microbiota measures, including maternal change from baseline CLR-transformed Prevotella abundance.

RESULTS

Forty-four women and 45 infants completed the study. The mean Shannon index of infants in the intervention group was -0.35 (95% CI: -0.64, -0.06, SD: 0.52) units lower than control group infants, corresponding to a medium effect size (Cohen's D: -0.74, 95% CI: -1.34, -0.13). The findings were similar using other metrics of α-diversity. There were no between-group differences in β-diversity, nor any differentially abundant taxa in infants. The intervention increased abundances of the genus Prevotella in mothers compared to controls.

DISCUSSION

This gut-focused perinatal dietary intervention was associated with differences in the maternal and infant gut microbiota composition. Larger studies are required to replicate and extend these findings.

Diverse effects of Bacillus sp. NYG5-emitted volatile organic compounds on plant growth, rhizosphere microbiome, and soil chemistry

Bacterial strains in the rhizosphere secrete volatile organic compounds (VOCs) that play critical roles in inter- and intra-kingdom signaling, influencing both microbe-microbe and microbe-plant interactions. In this study we evaluated the plant growth-promoting effects of VOCs emitted by Bacillus sp. NYG5 on Arabidopsis thaliana, Nicotiana tabacum, and Cucumis sativus, focusing on VOC-induced alterations in plant metabolic pathways, rhizosphere microbial communities, and soil chemical properties. NYG5 VOCs enhanced plant biomass across all tested species and induced significant shifts in rhizosphere microbial community composition, specifically increasing relative abundance of Gammaproteobacteria and reducing Deltaproteobacteria (Linear discriminant analysis Effect Size, p < 0.05). Soil analysis revealed a considerable reduction in humic substance concentrations following VOCs exposure, as detected by fluorescent spectral analysis. Using SPME-GC-MS, several novel VOCs were identified, some of which directly promoted plant growth. Transcriptomic analysis of N. tabacum exposed to NYG5 VOCs demonstrated activation of pathways related to phenylpropanoid biosynthesis, sugar metabolism, and hormone signal transduction. Within the phenylpropanoid biosynthesis pathway, a significant upregulation (p adj = 1.16e-14) of caffeic acid 3-O-methyltransferase was observed, a key enzyme leading to lignin and suberin monomer biosynthesis. These results highlight the complex mechanisms through which bacterial VOCs influence plant growth, including metabolic modulation, rhizosphere microbiome restructuring, and soil chemical changes. Collectively, this study highlights the pivotal role of bacterial VOCs in shaping plant-microbe-soil interactions.

CABO-16S-a Combined Archaea, Bacteria, Organelle 16S rRNA database framework for amplicon analysis of prokaryotes and eukaryotes in environmental samples

Identification of both prokaryotic and eukaryotic microorganisms in environmental samples is currently challenged by the need for additional sequencing to obtain separate 16S and 18S ribosomal RNA (rRNA) amplicons or the constraints imposed by "universal" primers. Organellar 16S rRNA sequences are amplified and sequenced along with prokaryote 16S rRNA and provide an alternative method to identify eukaryotic microorganisms. CABO-16S combines bacterial and archaeal sequences from the SILVA database with 16S rRNA sequences of plastids and other organelles from the PR2 database to enable identification of all 16S rRNA sequences. Comparison of CABO-16S with SILVA 138.2 results in equivalent taxonomic classification of mock communities and increased classification of diverse environmental samples. In particular, identification of phototrophic eukaryotes in shallow seagrass environments, marine waters, and lake waters was increased. The CABO-16S framework allows users to add custom sequences for further classification of underrepresented clades and can be easily updated with future releases of reference databases. Addition of sequences obtained from Sanger sequencing of methane seep sediments and curated sequences of the polyphyletic SEEP-SRB1 clade resulted in differentiation of syntrophic and non-syntrophic SEEP-SRB1 in hydrothermal vent sediments. CABO-16S highlights the benefit of combining and amending existing training sets when studying microorganisms in diverse environments.

Preliminary Insights Into the Relationship Between the Gut Microbiome and Host Genome in Posttraumatic Stress Disorder

Posttraumatic stress disorder (PTSD) may develop following trauma exposure; however, not all trauma-exposed individuals develop PTSD, suggesting the presence of susceptibility and resilience factors. The gut microbiome and host genome, which are interconnected, have been implicated in the aetiology of PTSD. However, their interaction has yet to be investigated in a South African population. Using genome-wide genotype data and 16S rRNA (V4) gene amplicon sequencing data from 53 trauma-exposed controls and 74 PTSD cases, we observed no significant association between the host genome and summed abundance of Mitsuokella, Odoribacter, Catenibacterium and Olsenella, previously reported as associated with PTSD status in this cohort. However, PROM2 rs2278067 T-allele was significantly positively associated with the summed relative abundance of these genera, but only in individuals with PTSD and not trauma-exposed controls (p < 0.014). Polygenic risk scores generated using genome-wide association study summary statistics from the PGC-PTSD Overall Freeze 2 were not predictive of gut microbial composition in this cohort. These preliminary results suggest a potential role for the interaction between genetic variation and gut microbial composition in the context of PTSD, underscoring the need for further investigation.

Differences in gut microbiota composition, diversity, and predicted functional activity between wild and captive zoo Carollia perspicillata in a One Health perspective

Bats play an important role in global microbial ecology, as they are the host of various microbes. Carollia perspicillata is one of the most popular bat species in zoos. The influence of the captive environment on the gut microbiota of this species is underinvestigated. In this study, we compared gut microbiota composition, diversity, and the potential functional activity of wild and captive C. perspicillata from Panama and Russia (Moscow Zoo), respectively, based on high-throughput 16S rRNA sequencing data. The abundance of 13 bacterial phyla and 35 bacterial genera significantly differed. Environment- and farm animal health-related bacteria (Mannheimia, unclassified Pasteurellaceae, Staphylococcus, and Mycoplasma) dominated wild bats, while bacteria important for public health (Bacteroides, Clostridium sensu stricto 1, and Acinetobacter) were higher in zoo bats. We also observed significantly greater alpha diversity in zoo bats, while there were no significant differences in beta diversity. These findings were accompanied by significant differences in the abundance of 32 functional pathways of gut bacteria, which are probably associated with the different diets of wild and zoo bats. This study shows that the rearing environment significantly affects the gut microbiota of C. perspicillata and highlights that the outcomes of microbiome research of captive bats need to be interpreted with care. Such differences in gut bacterial communities should be the basis for the development of new handling and veterinary care protocols, and also be the justification for further studies of the impact of microbiota of wild and zoo bats on One Health.

Alterations in Gut Microbiome Composition and Increased Inflammatory Markers in Post-COVID-19 Individuals

Dysfunctions in the immune system and alterations in the microbiome composition following SARS-CoV-2 infection contribute to persistent neurological issues observed in long COVID-19 survivors. We hypothesize that alterations in the gut microbiome composition and peripheral inflammatory profile following COVID-19 may play pivotal roles in behavior changes among individuals experiencing long-term illness. This cross-sectional study included a sample of post-COVID-19 and non-COVID-19 subjects. We assessed the presence of psychiatric conditions utilizing standardized diagnostic criteria, Hamilton Rating Scale for Anxiety (HAM-A), Hamilton Rating Scale for Depression (HAM-D), Biological Rhythms in Neuropsychiatry Assessment Interview (BRIAN), and Functional Assessment Short Test (FAST). Plasma samples were analyzed to examine lipid and inflammatory profiles. Fecal samples were evaluated by 16S rRNA sequencing to identify the gut microbiome composition. Noteworthy findings include a significant increase in the myeloid progenitor inhibitory factor 1 (MPIF-1), interleukin (IL)-17, and triglyceride among post-COVID-19 individuals. While α-diversity in the gut microbiome composition showed no significant differences, β-diversity demonstrated a notable distinction between the healthy control and post-COVID-19 groups. Post-COVID-19 individuals exhibited a decreased abundance of phylum, class, and order of Verrucomicrobia, family, and genus of Akkermansia, a short-chain fatty acid producer and microbial group significantly associated with intestinal barrier homeostasis and the amelioration of metabolic diseases. No difference was found between the behavioral and clinical data. In post-COVID-19 individuals, there were elevated IL-17 and MPIF-1 levels, compared to non-COVID-19 individuals. Additionally, there were notable alterations in gut microbiome composition, as evidenced by changes in β-diversity and a decrease of Verrucomicrobia, family, and Akkermansia genus abundance.

Integrated gut microbiota and multi-omics analysis revealed the growth differences of female giant freshwater prawn (Macrobrachium rosenbergii)

Macrobrachium rosenbergii (giant freshwater prawn; GFP) holds considerable importance in aquaculture due to its high market demand and economic significance. Female GFP growth varies significantly, however, the processes responsible for these growth disparities remain unknown. In this study, intestinal and hemolymph samples of large (FL), medium (FM), and small (FS) female GFPs were collected to investigate the molecular mechanism of female GFP growth. Through the utilization of 16S rRNA sequencing and liquid chromatography-mass spectrometry metabolomics, significant intestinal flora and metabolites linked to the growth performance of female GFPs were identified. The dominant phyla of the three groups were the same, namely Firmicutes and Proteobacteria. Among groups, small females exhibited the lowest abundance of Proteobacteria (27.26 %) and the highest abundance of Firmicutes (70.10 %). The most abundant genus in each group was Lactococcus. Liquid chromatography-mass spectrometry identified 115 annotated differential metabolites, and essential metabolites related to female GFP growth performance were screened. The concentration of serum metabolites in the larger females exhibited a statistically significant variance compared to that of the smaller females. Through association analysis, we identified key genes, metabolites, and gut microbiota that influence the growth of female GFPs. Likewise, we used multi-omics techniques to establish two relationship models ("gut microbiota-GFP phenotype-metabolite", "gut microbiota-GFP phenotype-transcript"), and three important network association models ("DN5520_c0_g1-CW1-Bacteroides", "DN537746_c0_g1-BW-Roseburia" and "Picolinic acid-phenotype-Roseburia") were further developed. The present study provides novel insights into the mechanisms underlying the variability in individual growth among female GFPs. Our findings offer valuable information for future investigations exploring the correlation between gut flora and host organisms in aquatic environments.