Gut Bacterial Microbiome Research Articles

Gut Bacterial Microbiome Profiles Associated with Colorectal Cancer Risk: A Narrative Review and Meta-Analysis

Objective: Recent studies have shown a potential link between the gut microbiome and colorectal cancer (CRC). A wide array of research into this topic was performed over the past decade, illustrating a keen interest in the potential causal relationship between the gut microbiome and CRC. However, the cancer research community is lacking a concise review of this kind, which aims to explore the evidence linking the human gut microbiome to the risk of developing CRC. Design: This narrative review was carried out by two independent reviewers who assessed the database outcomes from Medline and EMBASE during May 2020. A meta-analysis was undertaken to study the link between Helicobacter pylori and CRC. The meta-analysis was processed through Stata (StataCorp LLC, Lakeway Drive, College Station, Texas, USA). Results: Thirty one papers were included in this narrative review, of which 12 were included in the meta-analysis. From these papers, Fusobacterium and Bacteroides were reported most frequently as enriched in those with CRC versus the control populations. The meta-analysis showed an odds ratio of 1.49 (95% CI: 1.19–1.86), including a total of 20,001 events. This meta-analysis concluded that H. pylori infection significantly increases the risk of CRC, albeit with evidence of publication bias. Conclusion: Bacteria have been found to increase the risk of CRC; however, a definitive causal relationship cannot be concluded or excluded using case-control studies. To fully understand the potential link of the bacteria listed, alterations in research design and execution are required. The assessment found a need for a large-scale cohort study conducted over a significant period of time to thoroughly evaluate the potential relationship between gut microbiome and CRC risk.

Lethal disruption of the bacterial gut community in Eastern subterranean termite caused by boric acid.

The Eastern subterranean termite, Reticulitermes flavipes (Kollar) (Blattodea: Rhinotermitidae), is a significant pest, causing extensive damage to structures that amount to substantial economic losses. Boric acid is widely used for wood preservation due to its stability and broad-spectrum insecticidal properties, yet its impact on termite gut microbiomes and the implications of such effects remain understudied. Our study evaluates the dose-dependent mortality of R. flavipes upon being provided boric acid treated filter papers and investigates the resulting dysbiosis within the termite gut microbiome. Consistent with reports from other insects, mortality increased in a dose-dependent manner, with the highest boric acid concentration (203.7 µg/cm2 of filter paper) significantly reducing termite survival. 16S rRNA gene sequencing of the gut bacterial microbiome revealed notable shifts in composition, indicating boric acid-induced dysbiosis. Aside from an overall decrease in bacterial diversity, the relative abundance of some symbionts essential for termite nutrition decreased in response to higher boric acid concentrations, while several opportunistic pathogens increased. Our findings extend the understanding of boric acid's mode of action in termites, emphasizing its ability to significantly modulate the bacterial symbiont community, which can have dire effects on termite biology. Considering its ability to protect wood from further termite consumption, our study supports the continued use of boric acid and related compounds for termite-resistant treatments for wood.

Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia

BackgroundObesity, and in particular abdominal obesity, is associated with an increased risk of developing a variety of chronic diseases. Obesity, aging, and menopause are each associated with differential shifts in the gut microbiome. Obesity causes chronic low-grade inflammation due to increased lipopolysaccharide (LPS) levels which is termed “metabolic endotoxemia.” We examined the association of visceral adiposity tissue (VAT) area, circulating endotoxemia markers, and the gut bacterial microbiome in a cohort of aged postmenopausal women.MethodsFifty postmenopausal women (mean age 78.8 ± 5.3 years) who had existing adipose measurements via dual x-ray absorptiometry (DXA) were selected from the extremes of VAT: n = 25 with low VAT area (45.6 ± 12.5 cm2) and n = 25 with high VAT area (177.5 ± 31.3 cm2). Dietary intake used to estimate the Healthy Eating Index (HEI) score was assessed with a food frequency questionnaire. Plasma LPS, LPS-binding protein (LBP), anti-LPS antibodies, anti-flagellin antibodies, and anti-lipoteichoic acid (LTA) antibodies were measured by ELISA. Metagenomic sequencing was performed on fecal DNA. Female C57BL/6 mice consuming a high-fat or low-fat diet were treated with 0.4 mg/kg diet-derived fecal isolated LPS modeling metabolic endotoxemia, and metabolic outcomes were measured after 6 weeks.ResultsWomen in the high VAT group showed increased Proteobacteria abundance and a lower Firmicutes/Bacteroidetes ratio. Plasma LBP concentration was positively associated with VAT area. Plasma anti-LPS, anti-LTA, and anti-flagellin IgA antibodies were significantly correlated with adiposity measurements. Women with high VAT showed significantly elevated LPS-expressing bacteria compared to low VAT women. Gut bacterial species that showed significant associations with both adiposity and inflammation (anti-LPS IgA and LBP) were Proteobacteria (Escherichia coli, Shigella spp., and Klebsiella spp.) and Veillonella atypica. Healthy eating index (HEI) scores negatively correlated with % body fat and anti-LPS IgA antibodies levels. Preclinical murine model showed that high-fat diet-fed mice administered a low-fat diet fecal-derived LPS displayed reduced body weight, decreased % body fat, and improved glucose tolerance test parameters when compared with saline-injected or high-fat diet fecal-derived LPS-treated groups consuming a high-fat diet.ConclusionsIncreased VAT in postmenopausal women is associated with elevated gut Proteobacteria abundance and immunogenic metabolic endotoxemia markers. Low-fat diet-derived fecal-isolated LPS improved metabolic parameters in high-fat diet-fed mice giving mechanistic insights into potential pro-health signaling mediated by under-acylated LPS isoforms.7yVbQmTTfsF9b4Af3tznWNVideo

Gut Bacterial Communities in the Ground Beetle Carabus convexus.

Biological interactions, including symbiotic ones, have vital roles in ecological and evolutionary processes. Microbial symbionts in the intestinal tracts, known as the gut microbiome, are especially important because they can fundamentally influence the life history, fitness, and competitiveness of their hosts. Studies on the gut-resident microorganisms of wild animals focus mainly on vertebrates, and studies on species-rich invertebrate taxa, such as ground beetles, are sparse. In fact, even among the species-rich genus Carabus, only the gut microbiome of two Asian species was studied, while results on European species are completely missing. Here, we investigated the gut bacterial microbiome of a widespread European Carabus species, targeting the V3 and V4 regions of the 16S ribosomal RNA genes by next-generation high-throughput sequencing. We identified 1138 different operational taxonomic units assigned to 21 bacterial phyla, 90 families, and 197 genera. Members of the carbohydrate-degrading Prevotellaceae family, previously not detected in ground beetles, were the most abundant in the gut microbiome of the carnivorous C. convexus. Presumably, individuals from the studied wild populations also consume plant materials, especially fruits, and these carbohydrate-degrading bacterial symbionts can facilitate both the consumption and the digestion of these supplementary foods.

Fecal bacterial communities of the platypus (Ornithorhynchus anatinus) reflect captivity status-Implications for conservation and management.

The duck-billed platypus (Ornithorhynchus anatinus) is currently listed as near-threatened. A key part of the conservation strategy for this species is its captive maintenance; however, captive animals often have dysbiotic gut bacterial microbiomes. Here, for the first time, we characterize the gut microbiome of wild platypus via fecal samples using high-throughput sequencing of the bacterial 16S rRNA gene and identify microbial biomarkers of captivity in this species. At the phylum level, Firmicutes (50.4%) predominated among all platypuses, followed by Proteobacteria (28.7%), Fusobacteria (13.4%), and Bacteroidota (6.9%), with 21 "core" bacteria identified. Captive individuals did not differ in their microbial α-diversity compared to wild platypus but had significantly different community composition (β-diversity) and exhibited higher abundances of Enterococcus, which are potential pathogenic bacteria. Four taxa were identified as biomarkers of wild platypus, including Rickettsiella, Epulopiscium, Clostridium, and Cetobacterium. This contrast in gut microbiome composition between wild and captive platypus is an essential insight for guiding conservation management, as the rewilding of captive animal microbiomes is a new and emerging tool to improve captive animal health, maximize captive breeding efforts, and give reintroduced or translocated animals the best chance of survival.

Characterization of double humanized BLT-mice with stable engraftment of a human gut bacterial microbiome

Characterization of double humanized BLT-mice with stable engraftment of a human gut bacterial microbiome

Synthesis of fucosyllactose using α-L-fucosidases GH29 from infant gut microbial metagenome

Fucosyl-oligosaccharides (FUS) provide many health benefits to breastfed infants, but they are almost completely absent from bovine milk, which is the basis of infant formula. Therefore, there is a growing interest in the development of enzymatic transfucosylation strategies for the production of FUS. In this work, the α-L-fucosidases Fuc2358 and Fuc5372, previously isolated from the intestinal bacterial metagenome of breastfed infants, were used to synthesize fucosyllactose (FL) by transfucosylation reactions using p-nitrophenyl-α-L-fucopyranoside (pNP-Fuc) as donor and lactose as acceptor. Fuc2358 efficiently synthesized the major fucosylated human milk oligosaccharide (HMO) 2′-fucosyllactose (2′FL) with a 35% yield. Fuc2358 also produced the non-HMO FL isomer 3′-fucosyllactose (3′FL) and traces of non-reducing 1-fucosyllactose (1FL). Fuc5372 showed a lower transfucosylation activity compared to Fuc2358, producing several FL isomers, including 2′FL, 3′FL, and 1FL, with a higher proportion of 3′FL. Site-directed mutagenesis using rational design was performed to increase FUS yields in both α-L-fucosidases, based on structural models and sequence identity analysis. Mutants Fuc2358-F184H, Fuc2358-K286R, and Fuc5372-R230K showed a significantly higher ratio between 2′FL yields and hydrolyzed pNP-Fuc than their respective wild-type enzymes after 4 h of transfucosylation. The results with the Fuc2358-F184W and Fuc5372-W151F mutants showed that the residues F184 of Fuc2358 and W151 of Fuc5372 could have an effect on transfucosylation regioselectivity. Interestingly, phenylalanine increases the selectivity for α-1,2 linkages and tryptophan for α-1,3 linkages. These results give insight into the functionality of the active site amino acids in the transfucosylation activity of the GH29 α-L-fucosidases Fuc2358 and Fuc5372.Key pointsTwo α-L-fucosidases from infant gut bacterial microbiomes can fucosylate glycansTransfucosylation efficacy improved by tailored point-mutations in the active siteF184 of Fuc2358 and W151 of Fuc5372 seem to steer transglycosylation regioselectivity

Effects of polymerization types on plastics ingestion and biodegradation by Zophobas atratus larvae, and successions of both gut bacterial and fungal microbiomes

Recent studies demonstrated that plastic degradation in Zophobas atratus superworms is related to the gut microbiota. To determine whether the biodegradation and gut-microbiota were influenced by ingested plastic polymerization types, foams of polypropylene (PP), polyurethane (PU) and ethylene vinyl acetate (EVA) were selected as representatives of polyolefins, polyester and copolymers, and the sole feedstock for superworms for 45 d. Both growth and survival rates of superworms were influenced by the type of plastic diet. Although the total consumptions of EVA- and PP-fed groups were similar at 29.03 ± 0.93 and 28.89 ± 1.14 mg/g-larva, which were both significantly higher than that of PU-fed groups (21.63 ± 2.18 mg/g-larva), the final survival rates of the EVA-fed group of 36.67 ± 10.41% exhibited significantly lower than that of the PP- and PU-fed groups of 76.67 ± 2.89% and 75.00 ± 7.07%, respectively, and even the starvation group of 51.67 ± 10.93%. The Illumina MiSeq results revealed similarities in the dominant gut bacterial communities between PU- and EVA-fed groups, with an increase in relative abundance of Lactococcus, but significant differences from the PP-fed groups, which had two predominant genera of unclassified Enterobacteriaceae and Enterococcus. Compared to bran-fed groups, changes in gut fungal communities were similar across all plastics-fed groups, with an increase in the dominant abundance of Rhodotorula. The abundance of Rhodotorula increased in the order of polyolefin, polyester, and copolymer. In summary, plastic ingestion, larval growth, and changes in gut bacterial and fungal community of superworms were all influenced by foam diets of different polymerization types, and especially influences on the gut microbiomes were different from each other.

Differences in ingestion and biodegradation of the melamine formaldehyde plastic by yellow mealworms Tenebrio molitor and superworms Zophobas atratus, and the prediction of functional gut microbes

Plastics biodegradation by insect larvae is considered as a new strategy for plastic wastes treatment. To uncover the biodegradation of a more complex chemical polymer of melamine formaldehyde (MF) by insect larvae, two worm species of yellow mealworm Tenebrio molitor and superworm Zophobas atratus were fed on MF foam as sole diet for 45 days with sole bran diet as control. Although the MF foam consumption by yellow mealworms of 0.38 mg/d/g-larvae was almost 40% higher than that by superworms of 0.28 mg/d/g-larvae, a similar decrease of survival rates in both species were obtained at about 58%, indicating the adverse effects on their growth. Depolymerization and biodegradation of MF foam occurred in both larval guts, but was more extensive in yellow mealworms. MF foam sole diet influenced gut bacterial and fungal microbiomes of both larvae species, which were assessed by Illumina MiSeq on day 45. Compared to the bran-fed group, both gut bacterial and fungal communities significantly changed in MF-fed groups, but differed in the two larvae species. The results demonstrated a strong association between the distinctive gut microbiome and MF foam degradation, such as unclassified Enterobacteriaceae, Hyphopichia and Issatchenkia. However, sole MF foam diet negatively influenced worms, like lower survival rates and gut abnormalities. In summary, MF foam could be degraded by both yellow mealworms and superworms, albeit with adverse effects. Gut microbes were strongly associated to MF foam degradation, especially the gut fungi.

Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition

BackgroundThe gut microbiome undergoes primary ecological succession over the course of early life before achieving ecosystem stability around 3 years of age. These maturational patterns have been well-characterized for bacteria, but limited descriptions exist for other microbiota members, such as fungi. Further, our current understanding of the prevalence of different patterns of bacterial and fungal microbiome maturation and how inter-kingdom dynamics influence early-life microbiome establishment is limited.ResultsWe examined individual shifts in bacterial and fungal alpha diversity from 3 to 12 months of age in 100 infants from the CHILD Cohort Study. We identified divergent patterns of gut bacterial or fungal microbiome maturation in over 40% of infants, which were characterized by differences in community composition, inter-kingdom dynamics, and microbe-derived metabolites in urine, suggestive of alterations in the timing of ecosystem transitions. Known microbiome-modifying factors, such as formula feeding and delivery by C-section, were associated with atypical bacterial, but not fungal, microbiome maturation patterns. Instead, fungal microbiome maturation was influenced by prenatal exposure to artificially sweetened beverages and the bacterial microbiome, emphasizing the importance of inter-kingdom dynamics in early-life colonization patterns.ConclusionsThese findings highlight the ecological and environmental factors underlying atypical patterns of microbiome maturation in infants, and the need to incorporate multi-kingdom and individual-level perspectives in microbiome research to improve our understandings of gut microbiome maturation patterns in early life and how they relate to host health.5AtmDGbifCkZAT-p1B-BuFVideo

Urbanization reduces gut bacterial microbiome diversity in a specialist ground beetle, Carabus convexus.

Urbanization is rapidly shaping and transforming natural environments, creating networks of modified land types. These urbanization-driven modifications lead to local extinctions of several species, but the surviving ones also face numerous novel selection pressures, including exposure to pollutants, habitat alteration, and shifts in food availability and diversity. Based on the assumption that the environmental pool of microorganisms is reduced in urban habitats due to habitat alteration, biodiversity loss, and pollution, we hypothesized that the diversity of bacterial microbiome in digestive tracts of arthropods would be lower in urban than rural habitats. Investigating the gut bacterial communities of a specialist ground beetle, Carabus convexus, in forested rural versus urban habitats by next generation high-throughput sequencing of the bacterial 16S rRNA gene, we identified 3839 bacterial amplicon sequence variants. The composition of gut bacterial samples did not significantly differ by habitat (rural vs. urban), sex (female vs. male), sampling date (early vs. late spring), or their interaction. The microbiome diversity (evaluated by the Rényi diversity function), however, was higher in rural than urban adults. Our findings demonstrate that urbanization significantly reduced the diversity of the gut bacterial microbiome in C. convexus.

Gut mycobiome dysbiosis after sepsis and trauma

BackgroundSepsis and trauma are known to disrupt gut bacterial microbiome communities, but the impacts and perturbations in the fungal (mycobiome) community after severe infection or injury, particularly in patients experiencing chronic critical illness (CCI), remain unstudied.MethodsWe assess persistence of the gut mycobiome perturbation (dysbiosis) in patients experiencing CCI following sepsis or trauma for up to two-to-three weeks after intensive care unit hospitalization.ResultsWe show that the dysbiotic mycobiome arrays shift toward a pathobiome state, which is more susceptible to infection, in CCI patients compared to age-matched healthy subjects. The fungal community in CCI patients is largely dominated by Candida spp; while, the commensal fungal species are depleted. Additionally, these myco-pathobiome arrays correlate with alterations in micro-ecological niche involving specific gut bacteria and gut-blood metabolites.ConclusionsThe findings reveal the persistence of mycobiome dysbiosis in both sepsis and trauma settings, even up to two weeks post-sepsis and trauma, highlighting the need to assess and address the increased risk of fungal infections in CCI patients.Graphical

Effect of microplastic pollution on the gut microbiome of anecic and endogeic earthworms.

Microplastic (MP) pollution constitutes an emerging type of pollution threatening both aquatic and terrestrial ecosystems. The impact on aquatic ecosystems has been extensively studied, but the effect on terrestrial ecosystems and their inhabitants is mostly underexplored. In this study, we explored the effect of MP pollution on gut bacterial microbiome of endogeic (Aporrectodea caliginosa) and anecic (Lumbricus terrestris) earthworms. The experiments were performed in sandy soil with 0.2% of low-density polyethylene MPs (LDPE MPs). We observed that the endogeic earthworms had 100% survival, while anecic earthworms survived 25 days in the control (i.e. in absence of MPs) and 21 days in the treatment with LDPE MPs. The main driver of shifts in the diversity and composition of the bacterial communities in the gut of tested earthworms was the lifestyle of the worms, followed by the presence of MPs. The bacterial microbiome diversity was significantly different among the two types of earthworms, and the highest bacterial diversity was found in the gut of the endogeic earthworms. The effect of MPs on gut bacterial microbiome was clearly observed in the changes in the relative abundance of several phyla and families of the bacterial communities in both types of earthworms, although it was most evident in the anecic earthworms. The Actinobacteriota, Proteobacteria, and Firmicutes were the main groups enhanced in the MP treatments, suggesting enrichment of the bacterial communities with potential plastic degraders.

Probiotic and Muscadine Grape Extract Interventions Shift the Gut Microbiome and Improve Metabolic Parameters in Female C57BL/6 Mice.

Obesity and Western-like diet consumption leads to gut microbiome dysbiosis, which is associated with the development of cardio-metabolic diseases and poor health outcomes. The objective of this study was to reduce Western diet-mediated gut microbial dysbiosis, metabolic dysfunction, and systemic inflammation through the administration of a novel combined intervention strategy (oral probiotic bacteria supplements and muscadine grape extract (MGE)). To do so, adult female C57BL/6 mice were fed a low-fat control or Western-style diet and sub-grouped into diet alone, probiotic intervention, antibiotic treatments, MGE supplementation, a combination of MGE and probiotics, or MGE and antibiotics for 13 weeks. Mouse body weight, visceral adipose tissue (VAT), liver, and mammary glands (MG) were weighed at the end of the study. Fecal 16S rRNA sequencing was performed to determine gut bacterial microbiome populations. Collagen, macrophage, and monocyte chemoattractant protein-1 (MCP-1) in the VAT and MG tissue were examined by immunohistochemistry. Adipocyte diameter was measured in VAT. Immunohistochemistry of intestinal segments was used to examine villi length, muscularis thickness, and goblet cell numbers. We show that dietary interventions in Western diet-fed mice modulated % body weight gain, visceral adiposity, MG weight, gut microbial populations, and inflammation. Intervention strategies in both diets effectively reduced VAT and MG fibrosis, VAT and MG macrophages, adipocyte diameter, and VAT and MG MCP-1. Interventions also improved intestinal health parameters. In conclusion, dietary intervention with MGE and probiotics modulates several microbial, inflammatory, and metabolic factors reducing poor health outcomes associated with Western diet intake.

The Influence of Oral Terbinafine on Gut Fungal Microbiome Composition and Microbial Translocation in People Living with HIV Treated for Onychomycosis.

People living with HIV (PLWH) display altered gut epithelium that allows for the translocation of microbial products, contributing to systemic immune activation. Although there are numerous studies which examine the gut bacterial microbiome in PLWH, few studies describing the fungal microbiome, or the mycobiome, have been reported. Like the gut bacterial microbiome, the fungal microbiome and its by-products play a role in maintaining the body's homeostasis and modulating immune function. We conducted a prospective study to assess the effects of oral terbinafine, an antifungal agent widely used against onychomycosis, on gut permeability and microbiome composition in ART-treated PLWH (trial registration: ChiCTR2100043617). Twenty participants completed all follow-up visits. During terbinafine treatment, the levels of the intestinal fatty acid binding protein (I-FABP) significantly increased, and the levels of interleukin-6 (IL-6) significantly decreased, from baseline to week 12. Both markers subsequently returned to pre-treatment levels after terbinafine discontinuation. After terbinafine treatment, the abundance of fungi decreased significantly, while the abundance of the bacteria did not change. After terbinafine discontinuation, the abundance of fungi returned to the levels observed pre-treatment. Moreover, terbinafine treatment induced only minor changes in the composition of the gut bacterial and fungal microbiome. In summary, oral terbinafine decreases fungal microbiome abundance while only slightly influencing gut permeability and microbial translocation in ART-treated PLWH. This study's findings should be validated in larger and more diverse studies of ART-treated PLWH; our estimates of effect size can be used to inform optimal sample sizes for future studies.

Ingestion and biodegradation of disposable surgical masks by yellow mealworms Tenebrio molitor larvae: Differences in mask layers and effects on the larval gut microbiome

During the COVID-19 pandemic, the usage and production of face masks considerably increased, resulting in large quantities of mask waste accumulating in the natural environment. To investigate whether masks of polypropylene (PP) material could be ingested and degraded by insect worms like PP foam plastic, yellow mealworms were provided with different layers of disposable surgical masks as sole diets for 30 d. Although mask layers, especially the middle layer of melt-blown filter, could be ingested by yellow mealworms, sole mask layer diets had adverse effects on the larval survival and growth. Analyses of Fourier transform infrared spectroscopy, differential scanning calorimeter and thermogravimetric, and gel permeation chromatography demonstrated the changes of functional groups, thermostability and molecular weights in frass compared to original masks, indicating the partial oxidation and degradation of masks. And the depolymerization of the middle layer of masks by yellow mealworms was different from that of other layers. The larval gut bacterial and fungal microbiomes were assessed by Illumina MiSeq, indicating that both of them shifted upon sole layer mask diets. Changes in relative abundances of dominant bacterial and fungal genera demonstrated the strong association between gut microbiome and mask degradation. For instance, unclassified Enterobacteriaceae was closely associated with outer layers degradation. Lactococcus and unclassified Ascomycota were responsible for middle layers degradation, while Lactococcus and Morganella for inner layers degradation. In conclusion, disposable surgical masks of PP material could be ingested and biodegraded by yellow mealworms. The diversities of gut bacterial and fungal microbiomes were associated with the differences in rigid crystalline structures of the layer masks.

Ingestion preference and efficiencies of different polymerization types foam plastics by Tenebrio molitor larvae, associated with changes of both core gut bacterial and fungal microbiomes

The discovery that insect larvae can feed on kinds of foam plastics opened new avenues and provided a potential solution for plastic wastes biodegradation. This study aimed to investigate whether plastic polymerization types had regular impacts on larvae growth, gut microbial communities and functional microbes, foam plastics of polypropylene (PP), polyurethane (PU) and ethylene vinyl acetate (EVA) were selected as the representatives of different polymerized plastic and sole diets for yellow mealworms of Tenebrio molitor larvae for 45 days, with sole bran diet as control. Our findings showed that although slightly weight gains were obtained in plastic-fed groups, the larval survival rates decreased to 61.33 %, 59.67 % and 24.00 % in PP-, PU- and EVA-fed groups, respectively. The EVA-fed group was even lower than the starvation group, indicating that the more complex polymers diet had worse adverse effects on larval survival. The gut bacterial- and fungal-microbiomes assessed by Illumina MiSeq indicated that both gut bacterial and fungal communities shifted upon diets of different polymerization types compared to the control. The gut dominant abundances of Spiroplasma, Acinetobacter and Pseudomonas in PP-fed group were significantly different from that of unclassified Enterobacteriaceae in both PU- and EVA-fed groups. In contrast, all gut fungal communities in plastics-fed groups were similar with the dominants of Rhodotorula and Cryptococcus, but more abundances that had been reported with plastics degradation ability were obtained, such as Aspergillus and Cladosporium. In summary, T. molitor could efficiently degrade complex polymers, albeit with adverse effects. Core gut microbiomes were strongly associated with polymerization types of plastic diet, especially gut fungi.

Altered gut microbiota community structure and correlated immune system changes in dibutyl phthalate exposed mice

Di-n-butyl phthalate (DBP) is a ubiquitous environmental contaminant linked with various adverse health effects, including immune system dysfunction. Gut microbial dysbiosis can contribute to a wide range of pathogenesis, particularly immune disease. Here, we investigated the impact of DBP on the gut microbiome and examined correlations with immune system changes after five weeks oral exposure (10 or 100 mg/kg/day) in adult male mice. The fecal microbiome composition was characterized using 16S rRNA sequencing. DBP-treated mice displayed a significantly distinct microbial community composition, indicated by Bray-Curtis distance. Numerous amplicon sequence variants (ASVs) at the genus level were altered. Compared to the vehicle control group, the 10 mg/kg/day DBP group had 63 more abundant and 65 less abundant ASVs, while 60 ASVs were increased and 76 ASVs were decreased in the 100 mg/kg/day DBP group. Both DBP treatment groups showed higher abundances of ASVs assigned to Desulfovibrio (Proteobacteria phylum) and Enterorhabdus genera, while ASVs belonging to Parabacteroides, Lachnospiraceae UCG-006 and Lachnoclostridium were less common compared to the control group. Interestingly, an ASV belonging to Rumniniclostridium 6, which was less abundant in DBP-treated mice, demonstrated a negative correlation with the increased number of non-classical monocytes observed in the blood of DBP-treated animals. In addition, an ASV from Lachnospiraceae UCG-001, which was more abundant in the DBP-treated animals, showed a positive correlation with the non-classical monocyte increase. This study shows that DBP exposure greatly modifies the gut bacterial microbiome and indicates a potential contribution of microbial dysbiosis to DBP-induced immune system impairment, illustrating the importance of investigating how interactions between exposome components can affect health.

Investigation of the fall armyworm (Spodoptera frugiperda) gut microbiome and entomopathogenic fungus-induced pathobiome

The gut microflora plays an important role in insect development and physiology. The gut bacterial microbiome of the fall armyworm (FAW), Spodoptera frugiperda, in both cornfield and laboratory-reared populations was investigated using a 16S metagenomic approach. The alpha- and beta-diversity of the cornfield FAW populations varied among sampling sites and were higher than those of the laboratory-reared FAW population, indicating that different diets and environments influence the gut bacterial composition. To better understand the interaction between the microbiome and entomopathogenic fungi (EPF), FAWs from organic and conventionally managed corn fields and from the laboratory-reared colony were inoculated with Beauveria bassiana NCHU-153 (Bb-NCHU-153). A longer median lethal time (LT50) was observed in the Bb-NCHU-153-infected cornfield FAW population than in the laboratory-reared FAWs. In terms of the microbiome, three Bb-NCHU-153-infected FAW groups showed different gut bacterial compositions compared to noninfected FAW. Further investigation of the cooccurrence network and linear discriminant analysis (LDA) of effect size (LEfSe) revealed that the enriched bacterial genera, such as Enterococcus, Serratia, Achromobacter, and Tsukamurella, in the gut might play the role of opportunistic pathogens after fungal infection; in contrast, some gut bacteria of Methylobacterium, Marinomonas, Paenochrobactrum, Pseudomonas, Acinetobacter, Delftia, Dietzia, Gordonia, Leucobacter, Paracoccus, and Stenotrophomonas might be probiotics against EPF infection. These results indicated that EPF infection can change the gut bacterial composition and lead to a pathobiome in the FAW and that some bacterial species might protect the FAW from EPF infection. These findings could be applied to the design of pathobiome-inducing biocontrol strategies.

Microniches harbor distinct bacterial communities at the soil-plant-earthworm interface

Earthworms modify soil physicochemical properties and microbial communities, although their effect on different soil microniches is unclear. Here, we aimed to elucidate the effect of the geophagous earthworm Pontoscolex corethrurus on bacterial communities in the bulk soil, rhizosphere and rhizoplane of two cultivated Coffea species. In addition, we assessed the similarity of the earthworm bacterial microbiome (anterior and posterior intestine and casts) with the soil bacterial communities. We implemented a mesocosm experiment with four treatments: 1) Coffea arabica with earthworms; 2) C. arabica without earthworms; 3) Coffea canephora with earthworms; 4) C. canephora without earthworms. We used 16S rDNA amplicon sequencing to study bacterial communities associated with soil microniches and P. corethrurus intestine content and casts. Our findings show that rhizoplane bacterial communities were markedly distinct from those of the bulk and rhizosphere soils, regardless of the coffee species or the presence of earthworms. Nonetheless, P. corethrurus influenced bacterial community composition and structure in the different soil microniches, at the phylum and genus levels. Strong differences were observed in bacterial community structure and diversity between soil and earthworm gut and cast samples, which suggests that the P. corethrurus gut bacterial microbiome is not predominantly derived from the surrounding soil. Bacterial communities from the anterior and posterior gut sections were dominated by different bacterial taxa than those in the casts. Our study is the first one to demonstrate earthworm-induced shifts in rhizoplane-associated bacterial communities and emphasizes the need to consider the earthworm gut as a complex environment with a specific bacterial community.