Indigenous Microbiome Research Articles

Microbial Metabolites, Postbiotics, and Intestinal EpithelialFunction.

Chronic inflammatory disorders are rising worldwide. The implication of the microbiota in persistent inflammation has been studied for years, but a direct causal relationship has not yet been stablished. Intestinal epithelial cells (IECs) form a protective barrier against detrimental luminal components. Indeed, a decrease in epithelial integrity may trigger a severe inflammatory reaction due to the infiltration of potentially harmful molecules and microorganisms. Bacterial imbalance, more commonly known as dysbiosis, occurs during inflammation and several strategies have been proposed to counteract this condition. Probiotics have been widely used to positively alter the inherited microbial composition and recover a eubiotic status. Nevertheless, probiotics are thought to impair the return of the indigenous microbiome, and to aggravate inflammation in compromised patients. In contrast, postbiotics-bacterial-free metabolites secreted by probiotic strains-have been proposed as a better and safer strategy. Recent scientific studies that have demonstrated the immunomodulatory properties and epithelial protection of postbiotics are summarized in this review, with an emphasis on the available methods that are currently in use to better understand the role of postbiotics in health and nutrition.

Insights into the mechanisms underlying efficient Rhizodegradation of PAHs in biochar-amended soil: From microbial communities to soil metabolomics

The combined effects of biochar amendment and the rhizosphere on the soil metabolic microbiome during the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil remain unknown. In this study, we attempted to characterize a PAH degradation network by coupling the direct PAH degradation with soil carbon cycling. From microbial community structure and functions to metabolic pathways, we revealed the modulation strategies by which biochar and the rhizosphere benefited PAH degradation in soil. Firstly, some PAH degraders were enriched by biochar and the rhizosphere, and their combination promoted the cooperation among these PAH degraders. Simultaneously, under the combined effects of biochar and the rhizosphere, the functional genes participating in upstream PAH degradation were greatly upregulated. Secondly, there were strong co-occurrences between soil microbial community members and metabolites, in particular, some PAH degraders and the metabolites, such as PAH degradation products or common carbon resources, were highlighted in the networks. It shows that the overall downstream carbon metabolism of PAH degradation was also greatly upregulated by the combined effects of biochar and plant roots, showing good survival of the soil microbiome and contributing to PAH biodegradation. Taken together, both soil carbon metabolism and direct contaminant biodegradation are likely to be modulated by the combined effects of biochar and plant roots, jointly benefitting to PAH degradation by soil microbiome. Our study is the first to link PAH degradation with native carbon metabolism by coupling sequencing and soil metabolomics technology, providing new insights into a systematic understanding of PAH degradation by indigenous soil microbiome and their networks.

The gut microbiome stability is altered by probiotic ingestion and improved by the continuous supplementation of galactooligosaccharide

ABSTRACT The stable gut microbiome plays a key role in sustaining host health, while the instability of gut microbiome also has been found to be a risk factor of various metabolic diseases. At the ecological and evolutionary scales, the inevitable competition between the ingested probiotic and indigenous gut microbiome can lead to an increase in the instability. It remains largely unclear if and how exogenous prebiotic can improve the overall gut microbiome stability in probiotic consumption. In this study, we used Lactobacillus plantarum HNU082 (Lp082) as a model probiotic to examine the impact of the continuous or pulsed supplementation of galactooligosaccharide (GOS) on the gut microbiome stability in mice using shotgun metagenomic sequencing. Only continuous GOS supplement promoted the growth of probiotic and decreased its single-nucleotide polymorphisms (SNPs) mutation under competitive conditions. Besides, persistent GOS supplementation increased the overall stability, reshaped the probiotic competitive interactions with Bacteroides species in the indigenous microbiome, which was also evident by over-abundance of carbohydrate-active enzymes (CAZymes) accordingly. Also, we identified a total of 793 SNPs arisen in probiotic administration in the indigenous microbiome. Over 90% of them derived from Bacteroides species, which involved genes encoding transposase, CAZymes, and membrane proteins. However, neither GOS supplementation here de-escalated the overall adaptive mutations within the indigenous microbes during probiotic intake. Collectively, our study demonstrated the beneficial effect of continuous prebiotic supplementation on the ecological and genetic stability of gut microbiomes.

Verticillium Wilt in Oilseed Rape-the Microbiome is Crucial for Disease Outbreaks as Well as for Efficient Suppression.

Microbiome management is a promising way to suppress verticillium wilt, a severe disease in Brassica caused by Verticillium longisporum. In order to improve current biocontrol strategies, we compared bacterial Verticillium antagonists in different assays using a hierarchical selection and evaluation scheme, and we integrated outcomes of our previous studies. The result was strongly dependent on the assessment method chosen (in vitro, in vivo, in situ), on the growth conditions of the plants and their genotype. The most promising biocontrol candidate identified was a Brassica endophyte Serratia plymuthica F20. Positive results were confirmed in field trials and by microscopically visualizing the three-way interaction. Applying antagonists in seed treatment contributes to an exceptionally low ecological footprint, supporting efficient economic and ecological solutions to controlling verticillium wilt. Indigenous microbiome, especially soil and seed microbiome, has been identified as key to understanding disease outbreaks and suppression. We suggest that verticillium wilt is a microbiome-driven disease caused by a reduction in microbial diversity within seeds and in the soil surrounding them. We strongly recommend integrating microbiome data in the development of new biocontrol and breeding strategies and combining both strategies with the aim of designing healthy microbiomes, thus making plants more resilient toward soil-borne pathogens.

Differential pattern of indigenous microbiome responses to probiotic Bifidobacterium lactis V9 consumption across subjects

Various factors, including those associated with the host and environment, should be considered to further explore the health-promoting effects of probiotics. However, it is important to consider persistence as a basic but crucial factor in the function of probiotics in the gut. To date, few studies have investigated the factors that influence probiotic persistence. To address these challenges, we designed a cohort experiment that included 49 subjects and used the probiotic Bifidobacterium lactis V9 to identify intestinal microbiota related to probiotic persistence based on high-throughput amplicon sequencing. All of the subjects were divided into three groups (Persisters, Temporary and Non-Persisters) according to the detected amount of viable Bifidobacterium lactis V9 in their faeces. Accordingly, the intestinal microbiota fluctuations in the Persisters group were significant and persistent, whereas those observed in the Non-Persisters group were limited. At the genus level, up to seven genera changed significantly in Persisters group, whereas only the genus Anaerobacterium changed significantly in Non-Persisters group throughout the experiment. At baseline, we observed highly distinct microbial alpha diversity and taxonomic features between the Persisters and Non-Persisters groups. A total of 12 genera were associated with probiotic persistence, with Bifidobacterium and eight other genera negatively associated with probiotic persistence and Anaerobacterium, Paraprevotella and Erysipelatoclostridium positively associated with probiotic persistence. Based on these potential biomarkers, an “Anti-Engraftment Index” (AEI) was derived to classify and predict probiotic persistence in test and validation cohorts with high accuracy. However, we also observed that the AEI did not work in other probiotic consumption experiments, indicating that the AEI was strain-specific.

Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables.

Microbes play an important role in plants and interact closely with their host starting from sprouting seeds, continuing during growth and after harvest. The discovery of their importance for plant and postharvest health initiated a biotechnological development of various antagonistic bacteria and fungi for disease control. Nevertheless, their application often showed inconsistent effects. Recently, high-throughput sequencing-based techniques including advanced microscopy reveal fruits and vegetables as holobionts. At harvest, all fruits and vegetables harbor a highly abundant and specific microbiota including beneficial, pathogenic and spoilage microorganisms. Especially, a high microbial diversity and resilient microbial networks were shown to be linked to fruit and vegetable health, while diseased products showed severe dysbiosis. Field and postharvest handling of fruits and vegetables was shown to affect the indigenous microbiome and therefore has a substantial impact on the storability of fruits and vegetables. Microbiome tracking can be implemented as a new tool to evaluate and assess all postharvest processes and contribute to fruit and vegetable health. Here, we summarize current research advancements in the emerging field of postharvest microbiomes and elaborate its importance. The generated knowledge provides profound insights into postharvest microbiome dynamics and sets a new basis for targeted, microbiome-driven and sustainable control strategies.

Effect of Indigenous Microbial Consortium on Bioleaching of Arsenic from Contaminated Soil by Shewanella putrefaciens

The effects of indigenous microbial consortium on removal of As from As-contaminated soil using an Fe(III)-reducing bacterium Shewanella putrefaciens were investigated under circumneutral pH condition. Sequential extraction of As revealed that more than 30% of As was associated with Fe(III)-(oxy)hydroxides in the soil. Bioleaching experiments were conducted anaerobically with a supply of lactate as a carbon source. The highest As removal efficiency (57.5%) was obtained when S. putrefaciens and indigenous bacterial consortium coexisted in the soil. S. putrefaciens and indigenous bacteria solely removed 30.1% and 16.4% of As from the soil, respectively. The combination of S. putrefaciens and indigenous bacteria led to a higher amount of labile As after microbial dissolution of Fe(III)-(oxy)hydroxides. After microbial treatment, soil quality represented by pH and organic content appeared to be preserved. The results indicated that the ecological and physiological understanding of the indigenous microbiome might be important for the efficient application of bioleaching technology to remove As from contaminated soils.

Carbon Amendments Influence Composition and Functional Capacities of Indigenous Soil Microbiomes.

Soil nutrient amendments are recognized for their potential to improve microbial activity and biomass in the soil. However, the specific selective impacts of carbon amendments on indigenous microbiomes and their metabolic functions in agricultural soils remain poorly understood. We investigated the changes in soil chemical characteristics and phenotypes of Streptomyces communities following carbon amendments to soil. Mesocosms were established with soil from two field sites varying in soil organic matter content (low organic matter, LOM; high organic matter, HOM), that were amended at intervals over nine months with low or high dose solutions of glucose, fructose, malic acid, a mixture of these compounds, or water only (non-amended control). Significant shifts in soil chemical characteristics and antibiotic inhibitory capacities of indigenous Streptomyces were observed in response to carbon additions. All high dose carbon amendments consistently increased soil total carbon, while amendments with malic acid decreased soil pH. In LOM soils, higher frequencies of Streptomyces inhibitory phenotypes of the two plant pathogens, Streptomyces scabies and Fusarium oxysporum, were observed in response to soil carbon additions. Additionally, to determine if shifts in Streptomyces functional characteristics correlated with microbiome composition, we investigated whether shifts in functional characteristics of soil Streptomyces correlated with composition of soil bacterial communities, analyzed using 16S rRNA gene sequencing. Regardless of dose, community composition differed significantly among carbon-amended and non-amended soils from both sites. Carbon type and dose had significant effects on bacterial community composition in both LOM and HOM soils. Relationships among microbial community richness (observed species number), diversity, and soil characteristics varied among soils from different sites. These results suggest that manipulation of soil resource availability has the potential to selectively modify the functional capacities of soil microbiomes, and specifically to enhance pathogen inhibitory populations of high value to agricultural systems.

Bioaugmentation of triclocarban and its dechlorinated congeners contaminated soil with functional degraders and the bacterial community response

Partial removal of haloaromatic antimicrobial triclocarban (TCC) during wastewater treatment caused the final introduction of residual TCC into soils. Bioaugmentation has been proposed for the biodegradation of TCC and its dechlorinated congeners 4,4′-dichlorocarbanilide (DCC) and carbanilide (NCC) in soil. The isolated TCC-degrading strain Ochrobactrum sp. TCC-2 and chloroanilines-degrading strain Diaphorobacter sp. LD72 were used to study the removal efficiency of TCC, DCC and NCC mixture and their chloroanilines intermediates, respectively. The potential degradation competition between TCC and its dechlorinated congeners, and the response of bacterial community during the bioremediation were also investigated. The biodegradation of DCC and TCC was significantly enhanced for soil with inoculums compared with sterilized and natural soils. Chloroanilines products could also be effectively removed. For the degradation of combined substrates in the aqueous medium, NCC had negative effect on the degradation of TCC and DCC, while TCC and DCC negatively influenced each other. The bioaugmentation with two degraders obviously changed the phylogenetic composition and function of indigenous soil microbiome. Importantly, the inoculated degraders could be maintained, suggesting their adaptability and potential application in bioaugmentation for such recalcitrant contaminants. This study offers new insights into the enhanced bioremediation of TCC and its dechlorinated congeners contaminated soils by the bioaugmentation of functional degraders and the structure and function response of the indigenous soil microbiome to the bioremediation process.

Antifungal activity of titanium dioxide nanoparticles against Candida albicans

The unregulated release of titanium dioxide nanoparticles into the environment has raised concern, in particular due to the impact of the nanoparticles on indigenous micro-biome in our ecosystem. This paper reports a study on antifungal activity of titanium dioxide nanoparticles on a healthy growing fungi species, Candida albicans, a known opportunistic pathogen. A quantification of the total cell death was performed using a direct staining method, Trypan blue exclusion assay. Exposure to nanoparticles not only altered the growth rate, but also affected the onset and length of Candida albicans growth phases. The log and the onset of the death phase were shortened and accelerated, respectively. Up to 65% of the Candida albicans were killed after exposure to 100 μg/mL of the anatase titanium dioxide nanoparticles, while only 33% were killed with rutile. A higher dosage and incubation time of the nanoparticles increased their toxicity. Cells suffered from morphological changes upon the nanoparticle exposure, which correlates well with the results showing an altered growth phase culture.

Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly

BackgroundPlants have evolved intimate interactions with soil microbes for a range of beneficial functions including nutrient acquisition, pathogen resistance and stress tolerance. Further understanding of this system is a promising way to advance sustainable agriculture by exploiting the versatile benefits offered by the plant microbiome. The rhizosphere is the interface between plant and soil, and functions as the first step of plant defense and root microbiome recruitment. It features a specialized microbial community, intensive microbe-plant and microbe-microbe interactions, and complex signal communication. To decipher the rhizosphere microbiome assembly of soybean (Glycine max), we comprehensively characterized the soybean rhizosphere microbial community using 16S rRNA gene sequencing and evaluated the structuring influence from both host genotype and soil source.ResultsComparison of the soybean rhizosphere to bulk soil revealed significantly different microbiome composition, microbe-microbe interactions and metabolic capacity. Soil type and soybean genotype cooperatively modulated microbiome assembly with soil type predominantly shaping rhizosphere microbiome assembly while host genotype slightly tuned this recruitment process. The undomesticated progenitor species, Glycine soja, had higher rhizosphere diversity in both soil types tested in comparison to the domesticated soybean genotypes. Rhizobium, Novosphingobium, Phenylobacterium, Streptomyces, Nocardioides, etc. were robustly enriched in soybean rhizosphere irrespective of the soil tested. Co-occurrence network analysis revealed dominant soil type effects and genotype specific preferences for key microbe-microbe interactions. Functional prediction results demonstrated converged metabolic capacity in the soybean rhizosphere between soil types and among genotypes, with pathways related to xenobiotic degradation, plant-microbe interactions and nutrient transport being greatly enriched in the rhizosphere.ConclusionThis comprehensive comparison of the soybean microbiome between soil types and genotypes expands our understanding of rhizosphere microbe assembly in general and provides foundational information for soybean as a legume crop for this assembly process. The cooperative modulating role of the soil type and host genotype emphasizes the importance of integrated consideration of soil condition and plant genetic variability for future development and application of synthetic microbiomes. Additionally, the detection of the tuning role by soybean genotype in rhizosphere microbiome assembly provides a promising way for future breeding programs to integrate host traits participating in beneficial microbiota assembly.

The pros, cons, and many unknowns of probiotics.

Consumption of over-the-counter probiotics for promotion of health and well-being has increased worldwide in recent years. However, although probiotic use has been greatly popularized among the general public, there are conflicting clinical results for many probiotic strains and formulations. Emerging insights from microbiome research enable an assessment of gut colonization by probiotics, strain-level activity, interactions with the indigenous microbiome, safety and impacts on the host, and allow the association of probiotics with physiological effects and potentially useful medical indications. In this Perspective, we highlight key advances, challenges and limitations in striving toward an unbiased interpretation of the large amount of data regarding over-the-counter probiotics, and propose avenues to improve the quality of evidence, transparency, public awareness and regulation of their use.

Probiotics in the next-generation sequencing era

ABSTRACTTechnological developments, including massively parallel DNA sequencing, gnotobiotics, metabolomics, RNA sequencing and culturomics, have markedly propelled the field of microbiome research in recent years. These methodologies can be harnessed to improve our in-depth mechanistic understanding of basic concepts related to consumption of probiotics, including their rules of engagement with the indigenous microbiome and impacts on the human host. We have recently demonstrated that even during probiotic supplementation, resident gut bacteria in a subset of individuals resist the mucosal presence of probiotic strains, limiting their modulatory effect on the microbiome and on the host gut transcriptional landscape. Resistance is partly alleviated by antibiotics treatment, which enables probiotics to interact with the host at the gut mucosal interface, although rather than promoting reconstitution of the indigenous microbiome and of the host transcriptional profile, they inhibit these components from returning to their naïve pre-antibiotic configurations. In this commentary, we discuss our findings in the context of previous and recent works, and suggest that incorporating the state-of-the-art methods currently utilized in microbiome research into the field of probiotics may lead to improved understanding of their mechanisms of activity, as well as their efficacy and long-term safety.

Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes.

Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics and agricultural practices: more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes or those uninfected by nematodes. Based on a network analysis of potential microbe–microbe associations, we further found that several fungal taxa potentially preying on nematodes (Dactylellina (Orbiliales), Rhizophydium (Rhizophydiales), Clonostachys (Hypocreales), Pochonia (Hypocreales) and Purpureocillium (Hypocreales)) co-occurred in the soybean rhizosphere at a small spatial scale. This study suggests how ‘consortia’ of anti-nematode microbes can derive from indigenous (resident) microbiomes, providing basic information for managing anti-nematode microbial communities in agroecosystems.

The tea leaf microbiome shows specific responses to chemical pesticides and biocontrol applications

The plant microbiome is known to be influenced by certain biotic as well as abiotic factors. Nevertheless, the drivers for specific changes in microbial community composition and structure are largely unknown. In the present study, the effects of chemical and biological treatments for plant protection on the indigenous microbiome of Camellia sinensis (L.) Kuntze were contrasted. Assessment of bacteria-specific ribosomal RNA gene fragment amplicons from a representative set of samples showed an increased microbial diversity in treated plants when compared to untreated samples. Moreover, distinct microbial fingerprints were found for plants subjected to a conventional pesticide treatment with lime sulfur as well as for plants that were biologically treated with a Piriformospora indica spore solution. The bacterial community of pesticide-treated plants was augmented by 11 taxa assigned to Proteobacteria and Actinobacteria. In contrast, plants from biological control treatments were augmented by 10 taxa representing a more diversified community enrichment and included members of Actionobacteria, Proteobacteria, Bacteroidetes, Planctomycetes, and Verrucomicrobia. Complementary, molecular quantification of fungi in the samples showed a significantly lower number of internal transcribed spacer copies in plants subjected to biological control treatments, indicating the highest efficiency against fungal pathogens. The overall results show that leaves that are used for tea production show distinct microbiome shifts that are elicited by common pest and pathogen management practices. These shifts in the microbial population indicate non-target effects of the applied treatments.

Enterobacteriaceae dominate the core microbiome and contribute to the resistome of arugula (Eruca sativa Mill.)

BackgroundArugula is a traditional medicinal plant and popular leafy green today. It is mainly consumed raw in the Western cuisine and known to contain various bioactive secondary metabolites. However, arugula has been also associated with high-profile outbreaks causing severe food-borne human diseases. A multiphasic approach integrating data from metagenomics, amplicon sequencing, and arugula-derived bacterial cultures was employed to understand the specificity of the indigenous microbiome and resistome of the edible plant parts.ResultsOur results indicate that arugula is colonized by a diverse, plant habitat-specific microbiota. The indigenous phyllosphere bacterial community was shown to be dominated by Enterobacteriaceae, which are well-equipped with various antibiotic resistances. Unexpectedly, the prevalence of specific resistance mechanisms targeting therapeutic antibiotics (fluoroquinolone, chloramphenicol, phenicol, macrolide, aminocoumarin) was only surpassed by efflux pump assignments.ConclusionsEnterobacteria, being core microbiome members of arugula, have a substantial implication in the overall resistome. Detailed insights into the natural occurrence of antibiotic resistances in arugula-associated microorganisms showed that the plant is a hotspot for distinctive defense mechanisms. The specific functioning of microorganisms in this unusual ecosystem provides a unique model to study antibiotic resistances in an ecological context.

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

BackgroundThe accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants—DNA sequences not truly present in the sample. Contaminants come from various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do not eliminate it. Here we introduce decontam (https://github.com/benjjneb/decontam), an open-source R package that implements a statistical classification procedure that identifies contaminants in MGS data based on two widely reproduced patterns: contaminants appear at higher frequencies in low-concentration samples and are often found in negative controls.ResultsDecontam classified amplicon sequence variants (ASVs) in a human oral dataset consistently with prior microscopic observations of the microbial taxa inhabiting that environment and previous reports of contaminant taxa. In metagenomics and marker-gene measurements of a dilution series, decontam substantially reduced technical variation arising from different sequencing protocols. The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome and that some low-frequency taxa seemingly associated with preterm birth were contaminants.ConclusionsDecontam improves the quality of metagenomic and marker-gene sequencing by identifying and removing contaminant DNA sequences. Decontam integrates easily with existing MGS workflows and allows researchers to generate more accurate profiles of microbial communities at little to no additional cost.

Long-term phosphorus limitation changes the bacterial community structure and functioning in paddy soils

The effects of phosphorus (P) availability on soil microbial community and its functional responses have not been widely explored till date. The present study involved high throughput sequencing of 16S rRNA to investigate the bacterial community structure, size and function in long-term fertilized paddy soils that received P fertilizers (+ P) and compared with soils without P fertilizer (− P) application. Data analysis revealed that changes in P availability in the soil significantly influenced the phylogenetic composition of bacterial communities and their functional profiles. The populations of bacterial phyla Verrucomicrobia, Bacteroidetes, Acidobacteria, Chloroflexi, and Cyanobacteria were significantly induced in (− P) treatment when compared with (+ P). The bacterial genus Geobacter reported to use high-affinity P transporter during P limitation and Massilia known as a prominent P solubilizer were significantly more abundant in (− P) soils. The functional profile analysis demonstrated (− P) soils were characterized by more abundant enzymes related to P cycling. The present study enabled us to characterize the dominant indigenous microbiome of (− P) soils and also provided a better insight into the ecological and evolutionary responses of microbes in P limited soils.

Consequences of colonialism: A microbial perspective to contemporary Indigenous health.

Nearly all Indigenous populations today suffer from worse health than their non-Indigenous counterparts, and despite interventions against known factors, this health "gap" has not improved. The human microbiome-the beneficial, diverse microbial communities that live on and within the human body-is a crucial component in developing and maintaining normal physiological health. Disrupting this ecosystem has repercussions for microbial functionality, and thus, human health. In this article, we propose that modern-day Indigenous population health may suffer from disrupted microbial ecosystems as a consequence of historical colonialism. Colonialism may have interrupted the established relationships between the environment, traditional lifeways, and microbiomes, altering the Indigenous microbiome with detrimental health consequences.

Shifts of the indigenous microbial communities from reservoir production water in crude oil- and asphaltene-degrading microcosms

Microbial metabolism of crude oil is an important process in both microbial enhanced oil recovery and bioremediation. Recently, diverse microorganisms have been detected and isolated from oil reservoirs. In this work, crude oil- and asphaltene-degrading microcosms were constructed using two different reservoir production water samples, which had distinct bacterial communities. After two three-week enrichments culture, GC-MS and FT-IR analysis showed that crude oil and asphaltene were biodegraded. Microbial communities in microcosms using the same carbon source showed high similarity, which suggested similar processes of microbial succession in both crude oil- and asphaltene-degrading consortia. Parvibaculum, Pseudomonas, Alcanivorax, Devosia, Hydrogenophaga and Dietzia were found in all crude oil degrading microcosms and Parvibaculum, Alcanivorax, Hyphomonas, Flavobacterium and Reyranella were found in all asphaltene degrading microcosms, which might play important roles in crude oil or asphaltene degradation. The results indicated that reservoir production water might serve as a microbial species pool which contained the indigenous core microbiomes for crude oil degradation. This work provided new insights into the understanding of microbial diversity in reservoir production water and the potential role of reservoir production water as a microbial species pool for oil degrading microorganisms.