Field preservation and DNA extraction methods for intestinal microbial diversity analysis in earthworms

Gut commensal bacteria influence colorectal cancer development by modulating immune response in AOM/DSS-treated mice

The gut microbiota has been closely associated with the pathogenesis of colorectal cancer (CRC). However, precise identification of particular microorganisms promoting CRC carcinogenesis, and more importantly those blocking tumor development, has been challenging based on human gut microbiota profiling studies. With a well-established azoxymethane/dextran sodium sulfate induction murine CRC model, we found a subset of mice consistently failed to develop CRC. This genetically homogeneous but cancer-refractory population gave us a unique opportunity to reveal that the microbial compositions between mice with and without CRC formation are indeed distinct, indicating key different gut microbiota between those groups are responsible for the differential susceptibility of the animals to CRC development. Our analysis revealed that Ruminococcus flavefaciens (R.f) and Fibrobacter succinogenes (F.s) were significantly enriched in CRC-free mice, while the presence of Eubacterium dolichum (E.d) was dramatically reduced. The correlative evidence was further substantiated as important causal factors, with subsequent bacteria intragastric administration experiments demonstrating independent, protective roles of R.f and F.s and a correspondingly detrimental role of E.d in inflammation-induced CRC initiation. Notably, E.d strongly activates NF-κB and promotes the local accumulation of myeloid-derived suppressor cells and macrophages. Significant disturbance of gut immune homeostasis, therefore, might be a critical trigger leading to subsequent CRC development. These findings indicate a clear direction for precise and rational gut microbiota-mediated CRC prevention.IMPORTANCEThere is a complex ecosystem of different microbes residing within the gut, which is highly relevant to health and diseases. The causal linkage between specific gut microbes and the development of colorectal cancer has been established with a mouse model, pinpointing specific bacteria species either promoting or preventing colorectal cancer development. A key aspect of these gut residual bacteria in colorectal cancer development is through exaggerating or easing gut inflammation. Therefore, by taking probiotics composed of corresponding cancer-preventing bacteria from human microbiota, it can be an effective and economic way to reduce human colorectal cancer risks.

Diversity and composition of rare bacterial community in gut and vermicompost of Eudrilus eugeniae fed with multiple substrates during vermicomposting

Vermicomposting has been recognized as a sustainable solution for the managing of organic waste, primarily because of the bacterial communities that drive microbial decomposition. However, while the roles of abundant bacteria in composting processes are well-documented, the contributions of rare bacteria remain underexplored. In this study, we investigated the diversity and composition of abundant and rare bacterial communities in gut of Eudrilus eugeniae and resulting vermicompost, comparing okara as a single substrate compared to a combination of more substrates, such as kitchen waste or okara and kitchen waste. Amplicon sequencing revealed a total of 3085 operational taxonomic units (OTUs), comprising 188 abundant OTUs and 2127 rare OTUs. Significant differences in bacterial community composition were observed between vermicompost and the earthworm gut, particularly in the rare bacterial communities, with distinct abundances of Gemmatimonadota, Desulfobacteria, Myxococcota, Acidobacteria, and Firmicutes. Interestingly, no significant differences were found between treatments in the abundant bacterial communities, suggesting that okara alone can sustain a bacterial community comparable to mixed substrates. However, rare bacterial communities were more sensitive to substrate variation, with okara fostering distinct rare microbial populations in the vermicompost and earthworm gut. Our results indicate okara can support both abundant and rare bacteria, producing compost with similar physico-chemical properties to those derived from mixed substrates. The study highlights the importance of rare bacterial communities in vermicomposting and demonstrates the potential of okara as a valuable resource for sustainable waste management and soil improvement.

Antitumor potentials of onco-microbial in Chinese patients with pancreatic cancer

Recent studies have revealed that intratumoral microbiota is implicated in pancreatic cancer (PC), yet the spectra of intratumoral microbiota and their relationship with PC in Chinese patients remained to be clarified. In this study, tumor and paired paracancerous tissue from 53 patients were profiled by bacterial 16S rRNA gene sequencing. Both α- and β-diversity displayed significant differences between tumors and adjacent tissues, with higher diversity in tumors. Three bacteria phyla (Proteobacteria, Firmicutes, and Actinobacteria) were prevalent in both cancers and adjacent normal tissues. A high prevalence of Pseudomonas has been identified in the PC tumor microenvironment and was associated with prolonged overall survival. Furthermore, the results of in vitro experiments suggested that Pseudomonas fluorescens (P. fluorescens) could inhibit the proliferation and induce apoptosis of pancreatic cancer cells. These findings revealed distinctive microbial features of the PC tumors and normal tissues in Chinese populations and exhibited the antitumor potential of P. fluorescens in PC.

Effects of lactic acid bacteria on rearing water bacterial community in Eriocheir sinensis culture

The Chinese mitten crab (CMC, Eriocheir sinensi) culture in ponds is a unique aquaculture system. Probiotics are commonly used in the maintenance of the health of pond-cultured CMCs. However, the effects of probiotics on the bacterial community of CMC-culturing water remain unclear. This study utilized 16S rRNA gene amplicon sequencing to assess changes in the bacterial community composition, diversity, assembly, and co-occurrence patterns in CMC-culturing water following probiotic application. The results indicate that the α-diversity of the bacterial community in CMC-culturing water varied with time following probiotic application. The addition of probiotics to the water resulted in an increase in the occurrence of new operational taxonomic units (OTUs). The bacterial community assembly in the CMC-culturing water was shaped by a balance between deterministic and stochastic processes, while commercial probiotics enhanced the proportion of heterogeneous selection. In addition, including OTU2953 (Burkholderiaceae) and OTU3005 (Lactobacillaceae), from the commercial probiotics served as keystone species in the bacterial network of CMC-culturing water. Overall, probiotic application had a significant impact on the bacterial ecology of CMC-culturing water.

Effects of scale worm parasitism on interactions between the symbiotic gill microbiome and gene regulation in deep sea mussel hosts

Diverse adaptations to the challenging deep sea environment are expected to be found across all deep sea organisms. Scale worms Branchipolynoe pettiboneae are believed to adapt to the deep sea environment by parasitizing deep sea mussels; this biotic interaction is one of most known in the deep sea chemosynthetic ecosystem. However, the mechanisms underlying the effects of scale worm parasitism on hosts are unclear. Previous studies have revealed that the microbiota plays an important role in host adaptability. Here, we compared gill-microbiota, gene expression and host-microorganism interactions in a group of deep sea mussels (Gigantidas haimaensis) parasitized by scale worm (PA group) and a no parasitic control group (NPA group). The symbiotic microorganism diversity of the PA group significantly decreased than NPA group, while the relative abundance of chemoautotrophic symbiotic bacteria that provide the host with organic carbon compounds significantly increased in PA. Interestingly, RNA-seq revealed that G. haimaensis hosts responded to B. pettiboneaei parasitism through significant upregulation of protein and lipid anabolism related genes, and that this parasitism may enhance host mussel nutrient anabolism but inhibit the host’s ability to absorb nutrients, thus potentially helping the parasite obtain nutrients from the host. In an integrated analysis of the interactions between changes in the microbiota and host gene dysregulation, we found an agreement between the microbiota and transcriptomic responses to B. pettiboneaei parasitism. Together, our findings provide new insights into the effects of parasite scale worms on changes in symbiotic bacteria and gene expression in deep sea mussel hosts. We explored the potential role of host-microorganism interactions between scale worms and deep sea mussels, and revealed the mechanisms through which scale worm parasitism affects hosts in deep sea chemosynthetic ecosystem.

Effect of rifaximin on gut-lung axis in mice infected with influenza A virus

Gut-lung axis injury is a common finding in patients with respiratory diseases as well as in animal model of influenza virus infection. Influenza virus damages the intestinal microecology while affecting the lungs. Rifaximin, a non-absorbable derivative of rifamycin, is an effective antibiotic that acts by inhibiting bacterial RNA synthesis. This study aimed to determine whether rifaximin-perturbation of the intestinal microbiome leads to protective effects against influenza infection, via the gut-lung axis. Our results showed that influenza virus infection caused inflammation of and damage to the lungs. The expression of tight junction proteins in the lung and colon of H1N1 infected mice decreased significantly, attesting that the barrier structure of the lung and colon was damaged. Due to this perturbation in the gut-lung axis, the intestinal microbiota became imbalanced as Escherichia coli bacteria replicated opportunistically, causing intestinal injury. When influenza infection was treated with rifamixin, qPCR results from the gut showed significant increases in Lactobacillus and Bifidobacterium populations, while Escherichia coli populations markedly decreased. Furthermore, pathology sections and western blotting results illustrated that rifaximin treatment strengthened the physical barriers of the lung-gut axis through increased expression of tight junction protein in the colon and lungs. These results indicated that rifaximin ameliorated lung and intestine injury induced by influenza virus infection. The mechanisms identified were the regulation of gut flora balance and intestinal and lung permeability, which might be related to the regulation of the gut-lung axis. Rifaximin might be useful as a co-treatment drug for the prevention of influenza virus infection.

Study on the characteristics and mechanisms of nicosulfuron biodegradation by Bacillus velezensis CF57

Nicosulfuron is one of the main sulfonylurea herbicides that have been widely used to protect maize crops. A total of 10 nicosulfuron-degrading strains were isolated from the intestine tract of earthworm Eisenia foetida. Among them, Bacillus velezensis CF57 with the highest degradation efficiency was selected and studied in detail. The degradation characteristics of CF57 showed that it was able to effectively degrade nicosulfuron in a wide range of temperature, pH, and a low inoculation amount, and the response surface analysis revealed that the optimum degradation conditions were 30.8 °C, pH 6.31, and inoculation amount 3.04%. Meanwhile, CF57 could degrade high-concentration nicosulfuron efficiently and posed a broad degradation spectrum of other sulfonylurea herbicides. Furthermore, the localization of degradation enzyme indicated that the nicosulfuron-degrading enzyme was an extracellular fraction. By analyzing the metabolites of nicosulfuron, it could be further determined that the degradation of nicosulfuron by strain CF57 was mainly through the extracellular enzyme, and its possible degradation pathway was mainly derived from the cleavage of the C-N bond of the sulfonylurea bridge. These results may provide new insights into bioremediation of nicosulfuron-contaminated environments and enrich the resources of degrading bacteria of sulfonylurea herbicides.

Biodiversity and richness shifts of mucosa-associated gut microbiota with progression of colorectal cancer

The host-associated gut microbiota is considered critical for the occurrence and progression of colorectal cancer (CRC); however, systematic evaluations of the changes in the biodiversity and richness of mucosa-associated gut microbiota with the development of CRC have been limited. Twenty-three paired samples from colorectal tumor sites and the surrounding non-tumor tissues were collected from stage I to IV CRC patients. The microbial compositions of the samples were analyzed by Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene. Gut bacterial alterations at the tumor sites and surrounding healthy tissue sites collected from the different stages of CRC patients were analyzed. No significant differences were observed in the overall microbial richness and biodiversity between the CRC tissue and surrounding non-CRC tissue samples, however, composition and community segregation of the gut microbiota with the progression of CRC were observed. A general increasing trend of Bacteroidetes, Firmicutes, and Fusobacteria and decreasing trend of Proteobacteria were observed at the phylum level with the development of CRC. Further analysis revealed that thirty-four taxa differed significantly with the progression of CRC. Conclusively, our findings provide a comprehensive view of the human mucosa-associated gut microbiota, in association with the different stages of CRC.

Toxic responses of metabolites, organelles and gut microorganisms of Eisenia fetida in a soil with chromium contamination

The toxic sensitivity in different physiological levels of chromium (Cr) contaminated soils with environmentally equivalent concentrations (EEC) was fully unknown. The earthworm Eisenia fetida was exposed to a Cr-contaminated soil at the EEC level (referred to as Cr-CS) to characterize the induced toxicity at the whole body, organ, tissue, subcellular structure and metabolic levels. The results showed that the survival rate, weight and biodiversity of the gut microorganisms (organ) had no significant difference (p > 0.05) between control and Cr-CS groups. Qualitative histopathological and subcellular evaluations from morphology showed earthworms obvious injuries. The organelle injuries combined with the metabolic changes provided additional evidence that the Cr-CS damaged the nucleus and probably disturbed the nucleic acid metabolism of earthworms. 2-hexyl-5-ethyl-3-furansulfonate, dimethylglycine, betaine and scyllo-inositol were sensitive and relatively quantitative metabolites that were recommended as potential biomarkers for Cr-CS based on their significant weights in the multivariate analysis model. In addition, the relative abundance of Burkholderiaceae, Enterobacteriaceae and Microscillaceae of the earthworm guts in the Cr-CS group significantly increased, particularly for Burkholderiaceae (increased by 13.1%), while that of Aeromonadaceae significantly decreased by 5.6% in contrast with the control group. These results provided new insights into our understanding of the toxic effects of the EEC level of Cr contaminated soil from different physiological levels of earthworms and extend our knowledge on the composition and sensitivity of the earthworm gut microbiota in Cr contaminated soil ecosystems. Furthermore, these toxic responses from gut microorganisms to metabolites of earthworms provided important data to improve the adverse outcome pathway and toxic mechanism of the Cr-CS if the earthworm genomics and proteomics would be also gained in the future.

Land cover and forest connectivity alter the interactions among host, pathogen and skin microbiome

Deforestation has detrimental consequences on biodiversity, affecting species interactions at multiple scales. The associations among vertebrates, pathogens and their commensal/symbiotic microbial communities (i.e. microbiomes) have important downstream effects for biodiversity conservation, yet we know little about how deforestation contributes to changes in host microbial diversity and pathogen abundance. Here, we tested the effects of landcover, forest connectivity and infection by the chytrid fungus Batrachochytrium dendrobatidis (Bd) on amphibian skin bacterial diversity along deforestation gradients in Brazilian landscapes. If disturbance to natural habitat alters skin microbiomes as it does in vertebrate host communities, then we would expect higher host bacterial diversity in natural forest habitats. Bd infection loads are also often higher in these closed-canopy forests, which may in turn impact skin-associated bacterial communities. We found that forest corridors shaped composition of host skin microbiomes; high forest connectivity predicted greater similarity of skin bacterial communities among host populations. In addition, we found that host skin bacterial diversity and Bd loads increased towards natural vegetation. Because symbiotic bacteria can potentially buffer hosts from Bd infection, we also evaluated the bi-directional microbiome-Bd link but failed to find a significant effect of skin bacterial diversity reducing Bd infections. Although weak, we found support for Bd increasing bacterial diversity and/or for core bacteria dominance reducing Bd loads. Our research incorporates a critical element in the study of host microbiomes by linking environmental heterogeneity of landscapes to the host-pathogen-microbiome triangle.

Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon

The analysis of environmental microbial communities has largely relied on a PCR-dependent amplification of genes entailing species identity as 16S rRNA. This approach is susceptible to biases depending on the level of primer matching in different species. Moreover, possible yet-to-discover taxa whose rRNA could differ enough from known ones would not be revealed. DNA-based methods moreover do not provide information on the actual physiological relevance of each taxon within an environment and are affected by the variable number of rRNA operons in different genomes. To overcome these drawbacks we propose an approach of direct sequencing of 16S ribosomal RNA without any primer- or PCR-dependent step. The method was tested on a microbial community developing in an anammox bioreactor sampled at different time-points. A conventional PCR-based amplicon pyrosequencing was run in parallel. The community resulting from direct rRNA sequencing was highly consistent with the known biochemical processes operative in the reactor. As direct rRNA-seq is based not only on taxon abundance but also on physiological activity, no comparison between its results and those from PCR-based approaches can be applied. The novel principle is in this respect proposed not as an alternative but rather as a complementary methodology in microbial community studies.

Seasonal and ontogenetic variation of skin microbial communities and relationships to natural disease dynamics in declining amphibians

Recently, microbiologists have focused on characterizing the probiotic role of skin bacteria for amphibians threatened by the fungal disease chytridiomycosis. However, the specific characteristics of microbial diversity required to maintain health or trigger disease are still not well understood in natural populations. We hypothesized that seasonal and developmental transitions affecting susceptibility to chytridiomycosis could also alter the stability of microbial assemblages. To test our hypothesis, we examined patterns of skin bacterial diversity in two species of declining amphibians (Lithobates yavapaiensis and Eleutherodactylus coqui) affected by the pathogenic fungus Batrachochytrium dendrobatidis (Bd). We focused on two important transitions that affect Bd susceptibility: ontogenetic (from juvenile to adult) shifts in E. coqui and seasonal (from summer to winter) shifts in L. yavapaiensis. We used a combination of community-fingerprinting analyses and 16S rRNA amplicon sequencing to quantify changes in bacterial diversity and assemblage composition between seasons and developmental stages, and to investigate the relationship between bacterial diversity and pathogen load. We found that winter-sampled frogs and juveniles, two states associated with increased Bd susceptibility, exhibited higher diversity compared with summer-sampled frogs and adult individuals. Our findings also revealed that hosts harbouring higher bacterial diversity carried lower Bd infections, providing support for the protective role of bacterial communities. Ongoing work to understand skin microbiome resilience after pathogen disturbance has the potential to identify key taxa involved in disease resistance.

Effect of dietary prebiotic (mannan oligosaccharide) supplementation on the caecal bacterial community structure of turkeys

The identification of specific bacterial species influenced by mannan oligosaccharide (MOS) supplementation may assist in the formulation of new and improved diets that promote intestinal health and improve bird performance, offering suitable alternatives to antimicrobials in feed for sustainable poultry production. This study has been conducted to evaluate the use of a MOS compound derived from the yeast cell wall of Saccharomyces cerevisiae on turkey performance, bacterial community structure and their phylogenetic associations. A 42-day turkey trial was carried out on birds fed control and MOS-supplemented diets. Bird performance data (weight gains, feed consumption and feed efficiency ratios) were collected, and caecal contents were extracted from randomly caught poults on days 28, 35 and 42 posthatch. Bird performance data showed no improvements as a result of dietary supplementation. Automated ribosomal intergenic spacer analysis (ARISA) revealed the bacterial community structure to be significantly altered on days 28 and 35 posthatch but not day 42 as a result of dietary supplementation. This technique was coupled with 16S rRNA gene sequence analysis to elucidate phylogenetic identities of bacteria. The dominant bacteria of the caecum on all days in both treatment groups were members of phylum Firmicutes, followed by the Bacteroidetes and Proteobacteria phyla, respectively. Statistical analysis of the 16S rRNA gene libraries showed that the composition of the MOS clone library differed significantly to the control on day 35 posthatch. It can be concluded that MOS alters the bacterial community structure in the turkey caecum.

Effect of dietary supplementation with a Saccharomyces cerevisiae mannan oligosaccharide on the bacterial community structure of broiler cecal contents

This study investigated the effects of dietary supplementation with a prebiotic mannan oligosaccharide (MOS) on broiler performance, bacterial community structure, and phylogenetic populations of cecal contents. Bird performance data were collected, and cecal samples were extracted from randomly caught poults from each treatment group every 7 days from hatching to the age of 42 days. Weight gain, feed consumption, and feed efficiency ratios did not differ significantly between groups. Automated ribosomal intergenic spacer analysis (ARISA) of the bacterial communities in birds receiving MOS-supplemented diets indicated that dietary supplementation with MOS at either of 2 levels significantly altered the bacterial community structure from that of the control group on all sample days. The phylogenetic identities of bacteria contained within the cecum were determined by constructing a 16S rRNA gene clone library. A total of 594 partial 16S rRNA gene sequences from the cecal contents were analyzed and compared for the three dietary treatments. The dominant bacteria of the cecum belonged to three phyla, Firmicutes, Bacteroidetes, and Proteobacteria; of these, Firmicutes were the most dominant in all treatment groups. Statistical analysis of the bacterial 16S rRNA gene clone libraries showed that the compositions of the clone libraries from broilers receiving MOS-supplemented diets were, in most cases, significantly different from that of the control group. It can be concluded that in this trial MOS supplementation significantly altered the cecal bacterial community structure.

Maintenance of phenol hydroxylase genotypes at high diversity in bioreactors exposed to step increases in phenol loading

To better understand how the composition of bacterial communities changes in response to different environmental conditions, we examined the influence of increasing phenol load on the distribution of the protein-coding functional gene of the largest subunit of phenol hydroxylase (LmPH) and of the 16S rRNA gene in lab-scale activated sludge reactors. LmPH diversity was assessed initially from a total of 124 clone sequences retrieved from two reactors exposed to a low (0.25 g L(-1)) and a high (2.5 g L(-1)) phenol concentration. The quantitative changes in the concentration of the eight detected genotypes accompanied changes in the phenol degradation rates, indicating a community structure-function relationship. Nonmetric dimensional analysis showed that LmPH genotypes and the denaturing gradient gel electrophoresis banding patterns clustered together by phenol concentration, rather than by reactor identity. Seven isolates, representing cultivated strains of each of the observed LmPH genotypes, exhibited a rather narrow range of physiological diversity, in terms of the growth rate and the kinetic parameters of the phenol-degrading activity. We suggest that lab-scale reactors support many ecological niches, which allow the maintenance of a high diversity of ecotypes through varying concentrations of phenol, but the ability of particular strains to become dominant members of the community under the different environmental conditions cannot be predicted easily solely from their phenol-degrading properties.

Gut wall bacteria of earthworms: a natural selection process

Earthworms and microorganisms are interdependent and their interactions regulate the biogeochemistry of terrestrial soils. Investigating earthworm-microorganism interactions, we tested the hypothesis that differences in burrowing and feeding habits of anecic and endogeic earthworms are reflected by the existence of ecological group-specific gut wall bacterial communities. Bacterial community was detected using automated ribosomal intergenic spacer analysis of 16S and 23S genes and ribotype data was used to assess diversity and community composition. Using soil and earthworm samples collected from adjacent wheat-barley and grass-clover fields, we found that the anecic Lumbricus terrestris and L. friendi, the endogeic Aporrectodea caliginosa and A. longa (classically defined as anecic, but now known to possess endogeic characteristics) contain ecological group-specific gut wall-associated bacterial communities. The abundance of specific gut wall-associated bacteria (identified by sequence analysis of ribotype bands), including Proteobacteria, Firmicutes and an actinobacterium, was ecological group dependent. A microcosm study, conducted using A. caliginosa and L. terrestris and five different feeding regimes, indicated that food resource can cause shifts in gut wall-associated bacterial community, but the magnitude of these shifts did not obscure the delineation between ecological group specificity. Using A. caliginosa and A. longa samples collected in six different arable fields, we deduced that, within an ecological group, habitat was a more important determinant of gut wall-associated bacterial community composition than was host species. Hence, we conclude that the selection of bacteria associated with the gut wall of earthworms is a natural selection process and the strongest determinant of this process is in the order ecological group>habitat>species.