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Reductive soil disinfestation (RSD) is an effective bioremediation technique to restructure the soil microbial community and eliminate soilborne phytopathogens. Yet we still lack a comprehensive understanding of the keystone taxa involved and their roles in ecosystem functioning in degraded soils treated by RSD. In this study, the bacteriome network structure in RSD-treated soil and the subsequent cultivation process were explored. As a result, bacterial communities in RSD-treated soil developed more complex topologies and stable co-occurrence patterns. The richness and diversity of keystone taxa were higher in the RSD group (module hub: 0.57%; connector: 23.98%) than in the Control group (module hub: 0.16%; connector: 19.34%). The restoration of keystone taxa in RSD-treated soil was significantly (P < 0.01) correlated with soil pH, total organic carbon, and total nitrogen. Moreover, a strong negative correlation (r =  −0.712; P < 0.01) was found between keystone taxa richness and Fusarium abundance. Our results suggest that keystone taxa involved in the RSD network structure are capable of maintaining a flexible generalist mode of metabolism, namely with respect to nitrogen fixation, methylotrophy, and methanotrophy. Furthermore, distinct network modules composed by numerous anti-pathogen agents were formed in RSD-treated soil; i.e., the genera Hydrogenispora, Azotobacter, Sphingomonas, and Clostridium_8 under the soil treatment stage, and the genera Anaerolinea and Pseudarthrobacter under the plant cultivation stage. The study provides novel insights into the association between fungistasis and keystone or sensitive taxa in RSD-treated soil, with significant implications for comprehending the mechanisms of RSD.Key points• RSD enhanced bacteriome network stability and restored keystone taxa.• Keystone taxa richness was negatively correlated with Fusarium abundance.• Distinct sensitive OTUs and modules were formed in RSD soil.

Smokeless tobacco (SLT) is certainly one of the major risk factors associated with oral cancer. Disruption of oral microbiota-host homeostasis contributes to the progression of oral cancer. Here, we profiled SLT users’ oral bacterial composition and inferred their functions by sequencing 16S rDNA V3-V4 region and PICRUSt2, respectively. Oral bacteriome of SLT users (with or without oral premalignant lesions), SLT with alcohol co-users, and non-SLT consumers were compared. Oral bacteriome is shaped primarily by SLT use and the incidence of oral premalignant lesions (OPL). A significantly increased bacterial α-diversity was monitored in SLT users with OPL compared to in SLT users without OPL and non-users, whereas β-diversity was significantly explained by OPL status. Overrepresented genera were Prevotella, Fusobacterium, Veillonella, Haemophilus, Capnocytophaga, and Leptotrichia in SLT users having OPL. LEfSe analysis identified 16 genera as a biomarker that were differentially abundant in SLT users having OPL. The functional prediction of genes significantly increased for several metabolic pathways, more importantly, were nitrogen metabolism, nucleotide metabolism, energy metabolism, and biosynthesis/biodegradation of secondary metabolites in SLT users having OPL. Furthermore, HPV-16 and EBV, but not HPV-18, were considerably connected with the SLT users having OPL. Overall, this study provides evidence that SLT utilization and OPL development are associated with oral bacteriome dysbiosis indicating the enrichment of bacterial species known for their contribution to oral carcinogenesis. Therefore, delineating the cancer-inducing bacterial population in SLT users will facilitate the future development of microbiome-targeted therapies.Key points• SLT consumption significantly elevates oral bacterial diversity.• Prevalent significant genera are Prevotella, Veillonella, and Haemophilus in SLT users with OPL.• SLT promotes the occurrence of the cancer-inducing bacterial population.

Alterations of the gut microbiome are involved in the pathogenesis of Crohn's disease (CD). The role of fungi in this context is unclear. This study aimed to determine postoperative changes in the bacterial and fungal gut communities of CD patients undergoing intestinal resection, and to evaluate interactions between the bacteriome and mycobiome and their impact on the patients' outcome. We report a subgroup analysis of a prospective cohort study, focusing on 10 CD patients whose fecal samples were collected for bacterial 16S rRNA and fungal ITS2 genes next-generation sequencing the day before surgery and on the 5th or 6th postoperative day. No significant differences in bacterial and fungal diversity were observed between preoperative and postoperative stool samples. By in-depth analysis, significant postoperative abundance changes of bacteria and fungi and 17 interkingdom correlations were detected. Network analysis identified 13 microbial clusters in the perioperative gut communities, revealing symbiotic and competitive interactions. Relevant factors were gender, age, BMI, lifestyle habits (smoking, alcohol consumption) and surgical technique. Postoperative abundance changes and identified clusters were associated with clinical outcomes (length of hospital stay, complications) and levels of inflammatory markers. Our findings highlight the importance of dissecting the interactions of gut bacterial and fungal communities in CD patients and their potential influence on postoperative and disease outcomes.

Dendroctonus bark beetles are a worldwide significant pest of conifers. This genus comprises 20 species found in North and Central America, and Eurasia. Several studies have documented the microbiota associated with these bark beetles, but little is known regarding how the gut bacterial communities change across host range distribution. We use pyrosequencing to characterize the gut bacterial communities associated with six populations of Dendroctonus valens and D. mexicanus each across Mexico, determine the core bacteriome of both insects and infer the metabolic pathways of these communities with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to evaluate whether these routes are conserved across geographical locations. Our results show that the β-diversity with UniFrac unweighted varies among locations of both bark beetles mainly due to absence/presence of some rare taxa. No association is found between the pairwise phylogenetic distance of bacterial communities and geographic distance. A strict intraspecific core bacteriome is determined for each bark beetle species, but these cores are different in composition and abundance. However, both bark beetles share the interspecific core bacteriome recorded previously for the Dendroctonus genus consisting of Enterobacter, Pantoea, Providencia, Pseudomonas, Rahnella, and Serratia. The predictions of metabolic pathways are the same in the different localities, suggesting that they are conserved through the geographical locations.

Background: Knowledge of microbiota in health is essential for clinical research on the role of microbiota in disease. We aimed to characterize the intestinal microbiota in healthy Saudi children. Methods: In this community-based study, stool samples were collected from a randomly selected sample of 20 healthy school children of Saudi origin. The samples were frozen at -80°C till analysis. Bacterial DNA was isolated and libraries were prepared using the Illumina Nextera XT library preparation kit. Unassembled sequencing reads were directly analyzed and quantified for each organism's relative abundance. The abundance for each organism was calculated and expressed as the average relative percentage from phyla to species. Results: The median age was 11.3 (range 6.8-15.4) years, and 35% of them were males. The three most abundant phyla were Firmicutes, Bacteroidetes, and Actinobacteria accounting for 49%, 26%, and 24%, respectively. The most abundant genera included Bifidobacterium, Bacteroides, and Blautia accounting for 18.9%, 12.8%, and 8.2%, respectively. Finally, the most abundant species included 14 species belonging to the genus Bacteroides and nine species belonging to Bifidobacterium. Conclusions: The abundance of intestinal microbiome in healthy Saudi children is different from that of other populations. Further studies are needed to understand the causes of variation between populations, which might lead to new preventive methods and treatment strategies of diseases caused by microbial dysbiosis.

In many animal hosts, microbial symbionts are housed within specialized structures known as symbiotic organs, but the evolutionary origins of these structures have rarely been investigated. Here, I adopt an evolutionary developmental (evo-devo) approach, specifically to apply knowledge of the development of symbiotic organs to gain insights into their evolutionary origins and diversification. In particular, host genetic changes associated with evolution of symbiotic organs can be inferred from studies to identify the host genes that orchestrate the development of symbiotic organs, recognizing that microbial products may also play a key role in triggering the developmental programme in some associations. These studies may also reveal whether higher animal taxonomic groups (order, class, phylum, etc.) possess a common genetic regulatory network for symbiosis that is latent in taxa lacking symbiotic organs, and activated at the origination of symbiosis in different host lineages. In this way, apparent instances of convergent evolution of symbiotic organs may be homologous in terms of a common genetic blueprint for symbiosis. Advances in genetic technologies, including reverse genetic tools and genome editing, will facilitate the application of evo-devo approaches to investigate the evolution of symbiotic organs in animals. This article is part of the theme issue ‘The role of the microbiome in host evolution’.

Background It has become increasingly accepted that establishing and maintaining a complex and diverse gut microbiota is fundamental to human health. There are growing efforts to identify means of modulating and influencing the microbiota, especially in individuals who have experienced a disruption in their native microbiota. Faecal microbiota transplantation (FMT) is one method that restores diversity to the microbiota of an individual by introducing microbes from a healthy donor. FMT introduces the total microbial load into the recipient, including the bacteria, archaea, yeasts, protists and viruses. In this study, we investigated whether an autochthonous faecal viral transfer (FVT), in the form of a sterile faecal filtrate, could impact the recovery of a bacteriome disrupted by antibiotic treatment. Results Following antibiotic disruption of the bacteriome, test mice received an FVT harvested prior to antibiotic treatment, while control mice received a heat- and nuclease-treated FVT. In both groups of mice, the perturbed microbiome reverted over time to one more similar to the pre-treatment one. However, the bacteriomes of mice that received an FVT, in which bacteriophages predominate, separated from those of the control mice as determined by principal co-ordinate analysis (PCoA). Moreover, analysis of the differentially abundant taxa indicated a closer resemblance to the pre-treatment bacteriome in the test mice that had received an FVT. Similarly, metagenomic sequencing of the virome confirmed that faecal bacteriophages of FVT and control mice differed over time in both abundance and diversity, with the phages constituting the FVT persisting in mice that received them. Conclusions An autochthonous virome transfer reshaped the bacteriomes of mice post-antibiotic treatment such that they more closely resembled the pre-antibiotic microbiota profile compared to mice that received non-viable phages. Thus, FVT may have a role in addressing antibiotic-associated microbiota alterations and potentially prevent the establishment of post-antibiotic infection. Given that bacteriophages are biologically inert in the absence of their host bacteria, they could form a safe and effective alternative to whole microbiota transplants that could be delivered during/following perturbation of the gut flora.

Background Insect gut microbiomes play a fundamental role in various aspects of insect physiology, including digestion, nutrient metabolism, detoxification, immunity, growth and development. The wild Muga silkworm,  Antheraea assamensis  Helfer holds significant economic importance, as it produces golden silk. Methods and results In the current investigation, we deciphered its intricate gut bacteriome through high-throughput 16S rRNA amplicon sequencing. Further, to understand bacterial community dynamics among silkworms raised under outdoor environmental conditions, we compared its gut bacteriomes with those of the domesticated mulberry silkworm,  Bombyx mori  L. Most abundant bacterial phyla identified in the gut of  A. assamensis  were Proteobacteria (78.1%), Bacteroidetes (8.0%) and Firmicutes (6.6%), whereas the most-abundant phyla in  B. mori  were Firmicutes (49–86%) and Actinobacteria (10–36%). Further, Gammaproteobacteria (57.1%), Alphaproteobacteria (10.47%) and Betaproteobacteria (8.28%) were the dominant bacterial classes found in the gut of  A. assamensis . The predominant bacterial families in  A. assamensis  gut were Enterobacteriaceae (27.7%), Comamonadaceae (9.13%), Pseudomonadaceae (9.08%) Flavobacteriaceae (7.59%) Moraxellaceae (7.38%) Alteromonadaceae (6.8%) and Enterococcaceae (4.46%). In  B. mori , the most-abundant bacterial families were Peptostreptococcaceae, Enterococcaceae, Lactobacillaceae and Bifidobacteriaceae, though all showed great variability among the samples. The core gut bacteriome of  A. assamensis  consisted of Pseudomonas, Acinetobacter, Variovorax, Myroides, Alteromonas, Enterobacter, Enterococcus, Sphingomonas, Brevundimonas, Oleispira, Comamonas, Oleibacter Vagococcus, Aminobacter, Marinobacter, Cupriavidus, Aeromonas, and Bacillus. Comparative gut bacteriome analysis revealed a more complex gut bacterial diversity in wild  A. assamensis  silkworms than in domesticated  B. mori  silkworms, which contained a relatively simple gut bacteriome as estimated by OTU richness. Predictive functional profiling of the gut bacteriome suggested that gut bacteria in  A. assamensis  were associated with a wide range of physiological, nutritional, and metabolic functions, including biodegradation of xenobiotics, lipid, amino acid, carbohydrate metabolism, and biosynthesis of secondary metabolites and amino acids. Conclusions These results showed great differences in the composition and diversity of gut bacteria between the two silkworm species. Both insect species harbored core bacterial taxa commonly found in insects, but the relative abundance and composition of these taxa varied markedly.

Ruminal ciliates are linked to methane production and nitrogen utilization efficiency in ruminants due to their association with other ruminal microorganisms. However, research on the specific interplay between ruminal bacteria and ciliates is still limited, particularly in different dietary conditions. This study examines the effect of the forage-to-concentrate (F:C) ratio on the ruminal bacteriome in vitro, focusing on bacteria associated with Isotricha spp. and small entodinia. The rumen fluid used as the inoculum for this experiment was collected from two cannulated Hanwoo cows. Dietary treatments included high-forage (HF, F:C of 7:3), high-concentrate (HC, F:C of 3:7), and control (CON, F:C of 5:5). After 24-hour incubation, fractions for entodinia-associated bacteria (EAB), Isotricha-associated bacteria (IAB), and total bacteria (TB) were collected for bacteriome analysis using QIIME2 with full-length 16S rRNA gene sequences on the PacBio system. All fermentation parameters, except for NH -N, showed linear changes with increasing F:C ratios (p ≤ 0.05). F:C ratio affected Isotricha spp. and Dasytricha spp. counts. Ciliate-associated bacterial fractions were significantly less diverse than the total bacterial group, as indicated by richness, phylogenetic diversity, and evenness indices. This suggests potential specific associations within ciliate-provided microhabitats. Both diet and ciliate fractions significantly influenced the overall bacteriome (p ≤ 0.05). More bacteriome features were differentially abundant due to the ciliate fraction effect rather than diet (q ≤ 0.05). Our newly proposed washing procedure, using higher ciliate cell counts and minimal bacterial contamination, effectively removed free-living or loosely associated bacteria. This allows focus on ciliate-associated bacterial populations, which may include potential symbionts or engulfed bacteria of host ruminal ciliates. Verifying these associations could provide insights into rumen microbiome dynamics, nitrogen utilization, hydrogen balance, and microbiome variation under different F:C ratios.

Bacterial intracellular symbiosis (endosymbiosis) is widespread in nature and impacts many biological processes. In holometabolous symbiotic insects, metamorphosis entails a complete and abrupt internal reorganization that creates a constraint for endosymbiont transmission from larvae to adults. To assess how endosymbiosis copes—and potentially evolves—throughout this major host-tissue reorganization, we used the association between the cereal weevil Sitophilus oryzae and the bacterium Sodalis pierantonius as a model system. S. pierantonius are contained inside specialized host cells, the bacteriocytes, that group into an organ, the bacteriome. Cereal weevils require metabolic inputs from their endosymbiont, particularly during adult cuticle synthesis, when endosymbiont load increases dramatically. By combining dual RNA-sequencing analyses and cell imaging, we show that the larval bacteriome dissociates at the onset of metamorphosis and releases bacteriocytes that undergo endosymbiosis-dependent transcriptomic changes affecting cell motility, cell adhesion, and cytoskeleton organization. Remarkably, bacteriocytes turn into spindle cells and migrate along the midgut epithelium, thereby conveying endosymbionts to midgut sites where future mesenteric caeca will develop. Concomitantly, endosymbiont genes encoding a type III secretion system and a flagellum apparatus are transiently up-regulated while endosymbionts infect putative stem cells and enter their nuclei. Infected cells then turn into new differentiated bacteriocytes and form multiple new bacteriomes in adults. These findings show that endosymbiosis reorganization in a holometabolous insect relies on a synchronized host–symbiont molecular and cellular “choreography” and illustrates an adaptive feature that promotes bacteriome multiplication to match increased metabolic requirements in emerging adults.