Core Gut Research Articles

Involvement of Gut Microbiota, Microbial Metabolites and Interaction with Polyphenol in Host Immunometabolism.

Immunological and metabolic processes are inextricably linked and important for maintaining tissue and organismal health. Manipulation of cellular metabolism could be beneficial to immunity and prevent metabolic and degenerative diseases including obesity, diabetes, and cancer. Maintenance of a normal metabolism depends on symbiotic consortium of gut microbes. Gut microbiota contributes to certain xenobiotic metabolisms and bioactive metabolites production. Gut microbiota-derived metabolites have been shown to be involved in inflammatory activation of macrophages and contribute to metabolic diseases. Recent studies have focused on how nutrients affect immunometabolism. Polyphenols, the secondary metabolites of plants, are presented in many foods and beverages. Several studies have demonstrated the antioxidant and anti-inflammatory properties of polyphenols. Many clinical trials and epidemiological studies have also shown that long-term consumption of polyphenol-rich diet protects against chronic metabolic diseases. It is known that polyphenols can modulate the composition of core gut microbiota and interact with the immunometabolism. In the present article, we review the mechanisms of gut microbiota and its metabolites on immunometabolism, summarize recent findings on how the interaction between microbiota and polyphenol modulates host immunometabolism, and discuss future research directions.

Effects of Antibiotics on the Dynamic Balance of Bacteria and Fungi in the Gut of the German Cockroach.

The German cockroach, Blattella germanica (L.) (Blattaria: Blattidae) harbored diverse microorganisms in the digestive tract, including bacteria, fungi, viruses, archaea, and protozoa. This diverse community maintains a relatively stable balance. Some bacteria have been confirmed to play crucial roles in the insect's physiology, biochemistry, and behavior. Antibiotics can effectively eliminate bacteria and disrupt the balance of gut microbiota, but the time-course of this process, the structure of the new microbial community, and the dynamics of re-assemblage of a bacterial community after antibiotic treatment have not been investigated. In the present study, antibiotic (levofloxacin and gentamicin) ingestion reduced bacterial diversity and abundance in the cockroach gut. Within 14 d of discontinuing antibiotic treatment, the number of culturable gut bacteria returned to its original level. However, the composition of the new bacterial community with greater abundance of antibiotic-resistant Enterococcus and Dysgonomonas was significantly different from the original community. Network analysis showed that antibiotic treatment made the interaction between bacteria and fungi closer and stronger in the cockroach gut during the recovery of gut microorganisms. The study on the composition change, recovery rules, and interaction dynamics between gut bacteria and fungi after antibiotic treatment are helpful to explore gut microbes' colonization and interaction with insects, which contributes to the selection of stable core gut bacteria as biological carriers of paratransgenesis for controlling Blattella germanica.

Propolis Envelope Promotes Beneficial Bacteria in the Honey Bee (Apis mellifera) Mouthpart Microbiome.

Honey bees collect and apply plant resins to the interior of their nest cavity, in order to form a layer around the nest cavity called a propolis envelope. Propolis displays antimicrobial activity against honey bee pathogens, but the effect of propolis on the honey bee microbiome is unknown. Honey bees do not intentionally consume propolis, but they do manipulate propolis with their mouthparts. Because honey bee mouthparts are used for collecting and storing nectar and pollen, grooming and trophallaxis between adults, feeding larvae, and cleaning the colony, they are an important interface between the bees’ external and internal environments and serve as a transmission route for core gut bacteria and pathogens alike. We hypothesized that the antimicrobial activity of an experimentally applied propolis envelope would influence the bacterial diversity and abundance of the worker mouthpart microbiome. The results revealed that the mouthparts of worker bees in colonies with a propolis envelope exhibited a significantly lower bacterial diversity and significantly higher bacterial abundance compared to the mouthparts of bees in colonies without a propolis envelope. Based on the taxonomic results, the propolis envelope appeared to reduce pathogenic or opportunistic microbes and promote the proliferation of putatively beneficial microbes on the honey bee mouthparts, thus reinforcing the core microbiome of the mouthpart niche.

Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter

BackgroundMetagenomic analysis of the gut microbiome and resistome is instrumental for understanding the dynamics of diarrheal pathogenesis and antimicrobial resistance transmission (AMR). Metagenomic sequencing of 20 diarrheal fecal samples from Kolkata was conducted to understand the core and variable gut microbiota. Five of these samples were used for resistome analysis. The pilot study was conducted to determine a microbiota signature and the source of antimicrobial resistance genes (ARGs) in the diarrheal gut.Results16S rRNA amplicon sequencing was performed using Illumina MiSeq platform and analysed using the MGnify pipeline. The Genome Taxonomy Database (GTDB-Tk) was used for bacterial taxonomic identification. Diarrheal etiology was determined by culture method. Phylum Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were consistently present in 20 samples. Firmicutes was the most abundant phylum in 11 samples. The Bacteroidetes/Firmicutes ratio was less than 1 in 18 samples. 584 genera were observed. 18 of these were present in all the 20 samples. Proteobacteria was the dominant phylum in 6 samples associated with Vibrio cholerae infection. Conservation of operational taxonomic units (OTUs) among all the samples indicated the existence of a core microbiome. Asymptomatic carriage of pathogens like Vibrio cholerae and Helicobacter pylori was found. Signature of Candidate phyla or “microbial dark matter” occurred. Significant correlation of relative abundance of bacterial families of commensals and pathogens were found. Whole-genome sequencing (WGS) on Illumina MiSeq system and assembly of raw reads using metaSPAdes v3.9.1 was performed to study the resistome of 5 samples. ABRicate was used to assign ARG function. 491 resistance determinants were identified. In 80% of the samples tetracycline resistance was the most abundant resistance determinant. High abundance of ARGs against β-lactams, aminoglycosides, quinolones and macrolides was found. Eschericia sp. was the major contributor of ARGs.ConclusionsThis is the first comparative study of the gut microbiome associated with different diarrheal pathogens. It presents the first catalogue of different bacterial taxa representing the core and variable microbiome in acute diarrheal patients. The study helped to define a trend in the gut microbiota signature associated with diarrhea and revealed which ARGs are abundantly present and the metagenome-assembled genomes (MAGs) contributing to AMR.

High-throughput sequencing of the 16S rRNA gene to analyze the gut microbiome in juvenile and adult tropical gar (Atractosteus tropicus)

Tropical gar (Atractosteus tropicus) is freshwater and estuarine fish, inhabiting the Earth since the Mesozoic era and undergoing limited physiological variation ever since. Besides its recognized cultural andscientific relevance, the species has seen remarkable growth in its economic impact due to pisciculture. In this study, we present the first report of the whole taxonomic composition of microbial communities in gut contents in juveniles and adults of A. tropicus, by sex and origin (wild and cultivated). For this study, 508 genera were identified, with the most and least abundant being Cetobacterium and Paludibacter, respectively. Fusobacteria, Proteobacteria, Firmicutes, and Bacteroidetes phyla are the core gut microbiome of A. tropicus juvenile and adult by sex and origin. Deinococcus-Thermus phylum sequence was only identified in wild-type males. In the phylogenetic trees reconstruction Lactococcus lactis strains CAU929 and CAU6600, Cp6 and CAU9951,Cetobacterium strain H69, Aeromonas hydrophila strain P5 and WR-5-3-2, Aeromonas sobria strain CP DC28 and Aeromonas hydrophila were identified, some of them with probiotic potential within the three dominant phyla in core gut microbiome in A. tropicus adults, especially in wild-type organisms. Myroides genus was recognized in microbiota gut of the cultivated juvenile A. tropicus. Nevertheless, Alpha diversity indicated that the highest gut microbiota abundance and richness is found in cultivated juvenile and wild-type adult A. tropicus female, rather than adult wild-type males and the least gut microbiota abundance and richness is found in a cultivated adult of A. tropicus for both sexes.

Prakriti phenotypes as a stratifier of gut microbiome: A new frontier in personalized medicine?

Ayurveda has a rich history and its significance woven deeply in the Indian culture. The concept of prakriti (a person’s “nature” or constitutional type determined by the proportion of three doshas, namely - vata, pitta and kapha) in Ayurveda is deeply rooted in personalized health management. While the attributes of prakriti has been established to have a genomic basis, there is dearth of elaborate evidences linking prakriti with manifestation of diseases. Next generation sequencing studies have provided a causal link between variation in the gut microbiome and its effect on an individual’s fitness. Separately, reports have identified gut microbial patterns associated with several host variables such as geography, age, diet and extreme prakriti phenotypes. Recently, few reports have identified a “core gut microbiome” consisting of Bacteroides, Faecalibacterium, Prevotella and Ruminococcus prevalent across the Indian population; however, a few bacterial genera were specifically enriched in certain prakritis. Hence, in this review we aim to analyse the role of prakriti variations on dysbiosis of the gut microbiome and concomitantly its effect on human health. We suggest that prakriti phenotyping can function as a potential stratifier of the gut microbiome in a given population and may provide evidence for the conceptual framework of personalized medicine in Ayurvedic system of medicine.

Age-related changes in the gut microbiota and the core gut microbiome of healthy Thai humans.

The gut microbial diversity of Thai people was investigated between two large cohorts, adult and elderly subjects, from the middle region of Thailand; the cohorts were divided into different age groups of healthy adult (73) and elderly subjects (47). The diversities of the groups were characterized using a pyrosequencing technique with primers targeting the V6-V8 region of the 16S rRNA gene, and a significant decrease in the Firmicutes and Bacteroidetes ratio from 7.3 to 4.5 was observed with increased age. The microbiota of the adult and elderly groups had a significantly higher abundance of the phylum Actinobacteria, including the three species Bifidobacterium adolescentis, Bifidobacterium longum and Bifidobacterium pseudocatenulatum, and the phylum Bacteroidetes containing the four species Bacteroides uniformis, Bacteroides ovatus, Bacteroides caccae and Bacteroides thetaiotaomicron. Firmicutes showed no significant differences between the two groups. Eleven species belonging to Firmicutes, Bacteroidetes and Proteobacteria were shared by at least 90% of all subjects and defined as core gut microbiota of healthy Thai, among which a high abundance of Escherichia coli was particularly characterized in Thai elderly individuals. Multiple linear regression analysis of age, gender, BMI and diet consumption frequency showed the correlation of age with Bacteroides and Bifidobacterium. Rice consumption frequency showed a significant positive correlation with Bacteroides, while no correlation was found for other factors. Taken together, in the gut of Thai adults, Bifidobacterium decreased and Bacteroides increased with age, while rice consumption increased the abundance of Bacteroides. These link of age and food, especially rice carbohydrate, to gut microbiota and health could be ultimately proposed as the Thai feature.

Core Fucosylation of Intestinal Epithelial Cells Protects Against Salmonella Typhi Infection via Up-Regulating the Biological Antagonism of Intestinal Microbiota.

The fucosylated carbohydrate moieties on intestinal epithelial cells (IECs) are involved in the creation of an environmental niche for commensal and pathogenic bacteria. Core fucosylation catalyzed by fucosyltransferase 8 (Fut8) is the major fucosylation pattern on the N-glycans of the surface glycoproteins on IECs, however, the role of IECs core fucosylation during infection remains unclear. This study was conducted to investigate the interaction between IECs core fucosylation and gut microbiota, and the effects of this interaction on protecting Salmonella enterica subsp. enterica serovar Typhi (S. Typhi) infection. Firstly, the Fut8+/+ and Fut8+/– mice were infected with S. Typhi. The level of IECs core fucosylation and protein expression of intestinal mucosa were then detected by LCA blot and Western blot, respectively. The gut microbiota of Fut8+/+ and Fut8+/– mice before and after S. Typhi infection was assessed by 16S rRNA sequencing. Our results showed that core fucosylation was ubiquitous expressed on the intestinal mucosa of mice and had significant effects on their gut microbiota. Fut8+/– mice was more susceptive to S. Typhi infection than Fut8+/+ mice. Interestingly, infection of S. Typhi upregulated the core fucosylation level of IECs and increased the abundances of beneficial microorganisms such as Lactobacillus and Akkermansia spp. Further in vitro and in vivo studies demonstrated that Wnt/β-catenin signaling pathway mediated the elevation of IECs core fucosylation level upon infection of S. Typhi. Taken together, our data in this study revealed that the IECs core fucosylation plays an important role in protecting against S. Typhi infection via up-regulating the biological antagonism of intestinal microbiota.

Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (Herpestes ichneumon) Gut Microbiome.

Recently, we unveiled taxonomical and functional differences in Egyptian mongoose (Herpestes ichneumon) gut microbiota across sex and age classes by microbial profiling. In this study, we generate, through culturomics, extended baseline information on the culturable bacterial and fungal microbiome of the species using the same specimens as models. Firstly, this strategy enabled us to explore cultivable microbial community differences across sexes and to ascertain the influence exerted by biological and environmental contexts of each host in its microbiota signature. Secondly, it permitted us to compare the culturomics and microbial profiling approaches and their ability to provide information on mongoose gut microbiota. In agreement with microbial profiling, culturomics showed that the core gut cultivable microbiota of the mongoose is dominated by Firmicutes and, as previously found, is able to distinguish sex- and age class-specific genera. Additional information could be obtained by culturomics, with six new genera unveiled. Richness indices and the Shannon index were concordant between culture-dependent and culture-independent approaches, highlighting significantly higher values when using microbial profiling. However, the Simpson index underlined higher values for the culturomics-generated data. These contrasting results were due to a differential influence of dominant and rare taxa on those indices. Beta diversity analyses of culturable microbiota showed similarities between adults and juveniles, but not in the data series originated from microbial profiling. Additionally, whereas the microbial profiling indicated that there were several bioenvironmental features related to the bacterial gut microbiota of the Egyptian mongoose, a clear association between microbiota and bioenvironmental features could not be established through culturomics. The discrepancies found between the data generated by the two methodologies and the underlying inferences, both in terms of β-diversity and role of bioenvironmental features, confirm that culture-independent, sequence-based methods have a higher ability to assess, at a fine scale, the influence of abiotic and biotic factors on the microbial community composition of mongoose’ gut. However, when used in a complementary perspective, this knowledge can be expanded by culturomics.

The Core Gut Microbiome of Black Soldier Fly (Hermetia illucens) Larvae Raised on Low-Bioburden Diets.

An organism’s gut microbiome handles most of the metabolic processes associated with food intake and digestion but can also strongly affect health and behavior. A stable microbial core community in the gut provides general metabolic competences for substrate degradation and is robust against extrinsic disturbances like changing diets or pathogens. Black Soldier Fly larvae (BSFL; Hermetia illucens) are well known for their ability to efficiently degrade a wide spectrum of organic materials. The ingested substrates build up the high fat and protein content in their bodies that make the larvae interesting for the animal feedstuff industry. In this study, we subjected BSFL to three distinct types of diets carrying a low bioburden and assessed the diets’ impact on larval development and on the composition of the bacterial and archaeal gut community. No significant impact on the gut microbiome across treatments pointed us to the presence of a predominant core community backed by a diverse spectrum of low-abundance taxa. Actinomyces spp., Dysgonomonas spp., and Enterococcus spp. as main members of this community provide various functional and metabolic skills that could be crucial for the thriving of BSFL in various environments. This indicates that the type of diet could play a lesser role in guts of BSFL than previously assumed and that instead a stable autochthonous collection of bacteria provides the tools for degrading of a broad range of substrates. Characterizing the interplay between the core gut microbiome and BSFL helps to understand the involved degradation processes and could contribute to further improving large-scale BSFL rearing.

Effects of hydrolyzed fish protein and autolyzed yeast as substitutes of fishmeal in the gilthead sea bream (Sparus aurata) diet, on fish intestinal microbiome

BackgroundThis study evaluated the effects of partial substitution of dietary fishmeal (FM) with either fish protein hydrolysate (FPH) or autolysed dried yeast (HiCell®, Biorigin, Brazil) on intestinal microbiota of gilthead sea bream (Sparus aurata). A total number of 720 fish of 122.18 ± 6.22 g were fed for 92 days with three different diets in triplicate (3 tanks/diet). A diet based on FM/vegetable meal was used as control. The other two diets were formulated by replacing FM with 5% of either FPH or HiCell®. To analyze the gut microbiota associated to autochthonous and allochthonous microbial communities, the Illumina MiSeq platform for sequencing of 16S rRNA gene and QIIME pipeline were used.ResultsA total number of 102 OTUs (operational taxonomic units) at 97% identity were identified in fish gut samples collected at the end of feeding trial. Fourteen OTUs constituted the core gut microbiota, i.e. those OTUs found in at least nine out of fifteen samples per group and shared regardless of the diet. Eight OTUs were assigned to Firmicutes represented by Lactobacillus, Staphylococcus, and Bacillus genera, and six to Proteobacteria phylum. Dietary dried yeast autolysate modulated the intestinal microbiota by promoting the growth of some beneficial bacteria. At order level, fish fed yeast showed an enrichment in Bacillales and Clostridiales as compared to the control group, whereas fish fed FPH showed a significantly lower amount of bacteria belonging to Alteromonadales and Enterobacteriales than the other two feeding groups. Although we did not observe any effect of 5% FM replacement with alternative nitrogen sources at phylum level, at lower taxonomical levels, the composition of gut microbiota, in terms of relative abundance of specific taxa, was significantly influenced by the dietary treatment.ConclusionsThe metabarcoding analysis revealed a clearly intestinal microbiota modulation in response to dietary autolyzed yeast. The abundance of some beneficial bacteria, i.e. indigestible carbohydrate degrading- and SCFA producing bacteria, was positively affected. Brewer’s yeast autolysate could be a valid alternative protein source to FM as well as a valid functional ingredient for aquafeed production.

The Indian gut microbiota-Is it unique?

Colonization of the gut by microbes depends on a number of factors including age, diet, genetic makeup, gender, geographic location, and health status of an individual. India is a megadiverse country and includes 4 biodiversity hot spots. These features, along with the transitioning Indian sociodemographic profile, make the gut microbiota of Indian subjects an interesting area to study. In this review, we critically discuss the present status of the gut microbiome in the Indian population and its difference from other populations. We also discuss the aberrations in the available study designs that could introduce heterogeneity. An ideal study to evaluate the core gut microbiota of healthy Indians should involve a large homogeneous population across the country and use the same technology and data analytics tools. The "Landscape of Gut Microbiome-Pan India Exploration" (LogMPIE) is such a study that confirmed the most predominant organisms in Indians to be Prevotella copri and Faecalibacterium prausnitzii.

Changes in the gut microbiota of wild mice according to environment

BackgroundThe gut microbiota is closely linked with the health and disease status of hosts. This could be affected by multifactorial factors, among which environmental factors have a great effect on the gut microbiota, which is the cause of different phenotypes in mice. Here, we investigated the changes in the gut microbiota of wild mice according to habitat and diet.Methods and ResultsForty‐nine Mus musculus were captured from fields that were separated by rivers, roads, and mountains in Korea. Sixteen representative wild mice were transferred to laboratory animal facilities and their gut microbiota was analyzed at 2–4 weeks intervals up to 20 weeks. At the phylum level, 16 phyla were identified; among them, four phyla (Firmicutes, Bacteroidetes, Epsilonbacteraeota, and Proteobacteria) comprised the core gut microbiota and accounted for about 98% of the total microbiota. In alpha diversity, the number of observed OTUs and richness significantly reduced, while the evenness significantly increased. In beta diversity, the distribution of the gut microbiota initially differed depending on the habitat of wild mice. However, as wild mice adapted to laboratory animal facilities, the gut microbiota clustered together in the PCoA plot and the volatility of beta diversity also showed distinct differences. Furthermore, the relative abundance of Staphylococcus (p < 0.01) and Alistipes (p < 0.05) tended to increase at the genus level.ConclusionsDue to the variety of wild environments in which wild mice are exposed, wild mice have a greater diversity and distribution of the gut microbiota than mice exposed to constant environments. As wild mice adapted to a constant environment, the gut microbial diversity decreased and the distribution of the gut microbiota became constant. This study provides a new approach, gut microbiota analysis, in the assessment of environmental exposure in wild mice, which is limited based on phenotyping and genotyping.Support or Funding InformationThis research was supported by the National Research Foundation of Korea (NRF‐2018R1A2B6002396) and the Korea Mouse Phenotyping Project (2016M3A9D5A01952417) of the Ministry of Science, ICT and Future Planning.

Deciphering the Bifidobacterial Populations within the Canine and Feline Gut Microbiota.

During the course of evolution, dogs and cats have been subjected to extensive domestication, becoming the principal companion animals for humans. For this reason, their health care, including their intestinal microbiota, is considered of considerable importance. However, the canine and feline gut microbiota still represent a largely unexplored research area. In the present work, we profiled the microbiota of 23 feline fecal samples by 16S rRNA gene and bifidobacterial internally transcribed spacer (ITS) approaches and compared this information with previously reported data from 138 canine fecal samples. The obtained data allowed the reconstruction of the core gut microbiota of the above-mentioned samples coupled with their classification into distinct community state types at both genus and species levels, identifying Bacteroides, Fusobacterium, and Prevotella 9 as the main bacterial components of the canine and feline gut microbiota. At the species level, the intestinal bifidobacterial gut communities of dogs and cats differed in terms of both species number and composition, as emphasized by a covariance analysis. Together, our findings show that the intestinal populations of cats and dogs are similar in terms of genus-level taxonomical composition, while at the bifidobacterial species level, clear differences were observed, indicative of host-specific colonization behavior by particular bifidobacterial taxa.IMPORTANCE Currently, domesticated dogs and cats are the most cherished companion animals for humans, and concerns about their health and well-being are therefore important. In this context, the gut microbiota plays a crucial role in maintaining and promoting host health. However, despite the social relevance of domesticated dogs and cats, their intestinal microbial communities are still far from being completely understood. In this study, the taxonomical composition of canine and feline gut microbiota was explored at genus and bifidobacterial species levels, allowing classification of these microbial populations into distinct gut community state types at either of the two investigated taxonomic levels. Furthermore, the reconstruction of core gut microbiota coupled with covariance network analysis based on bifidobacterial internally transcribed spacer (ITS) profiling revealed differences in the bifidobacterial compositions of canine and feline gut microbiota, suggesting that particular bifidobacterial species have developed a selective ability to colonize a specific host.

Egyptian Mongoose (Herpestes ichneumon) Gut Microbiota: Taxonomical and Functional Differences across Sex and Age Classes.

The Egyptian mongoose (Herpestes ichneumon) is a medium-size carnivore that, in Europe, is restricted to Iberia. The bio-ecology of this species remains to be elucidated in several dimensions, including gut microbiota that is nowadays recognized as a fundamental component of mammals. In this work, we investigated the gut microbiota of this herpestid by single-molecule real-time sequencing of twenty paired male (n = 10) and female (n = 10) intestinal samples. This culture-independent approach enabled microbial profiling based on 16S rDNA and investigation of taxonomical and functional features. The core gut microbiome of the adult subpopulation was dominated by Firmicutes, Fusobacteria, Actinobacteria, and Proteobacteria. Eight genera were uniquely found in adults and five in non-adults. When comparing gut bacterial communities across sex, four genera were exclusive of females and six uniquely found in males. Despite these compositional distinctions, alpha- and beta-diversity analyses showed no statistically significant differences across sex or between adult and non-adult specimens. However, when function was inferred, males presented a significantly higher abundance of amino acid and citrate cycle metabolic pathways, compared to the significant overrepresentation in females of galactose metabolic pathways. Additionally, adults exhibited a significantly higher abundance of cationic antimicrobial peptide resistance pathways, while non-adults bared a significant overrepresentation of two-component systems associated with antibiotic synthesis, flagellin and biofilm production, and chemotaxis control. This study adds new insights into the mongoose bio-ecology palette, highlighting taxonomical and functional microbiome dissimilarities across sex and age classes, possibly related to primary production resources and life-history traits that impact on behavior and diet.

Characterization of the Gut Microbiota of the Antarctic Heart Urchin (Spatangoida) Abatus agassizii.

Abatus agassizii is an irregular sea urchin species that inhabits shallow waters of South Georgia and South Shetlands Islands. As a deposit-feeder, A. agassizii nutrition relies on the ingestion of the surrounding sediment in which it lives barely burrowed. Despite the low complexity of its feeding habit, it harbors a long and twice-looped digestive tract suggesting that it may host a complex bacterial community. Here, we characterized the gut microbiota of specimens from two A. agassizii populations at the south of the King George Island in the West Antarctic Peninsula. Using a metabarcoding approach targeting the 16S rRNA gene, we characterized the Abatus microbiota composition and putative functional capacity, evaluating its differentiation among the gut content and the gut tissue in comparison with the external sediment. Additionally, we aimed to define a core gut microbiota between A. agassizii populations to identify potential keystone bacterial taxa. Our results show that the diversity and the composition of the microbiota, at both genetic and predicted functional levels, were mostly driven by the sample type, and to a lesser extent by the population location. Specific bacterial taxa, belonging mostly to Planctomycetacia and Spirochaetia, were differently enriched in the gut content and the gut tissue, respectively. Predictive functional profiles revealed higher abundance of specific pathways, as the sulfur cycle in the gut content and the amino acid metabolism, in the gut tissue. Further, the definition of a core microbiota allowed to obtain evidence of specific localization of bacterial taxa and the identification of potential keystone taxa assigned to the Desulfobacula and Spirochaeta genera as potentially host selected. The ecological relevance of these keystone taxa in the host metabolism is discussed.

Biodegradation of Polyethylene and Polystyrene by Greater Wax Moth Larvae (Galleria mellonella L.) and the Effect of Co-diet Supplementation on the Core Gut Microbiome.

Plastics waste and microplastics including polyethylene (PE) and polystyrene (PS) have been an environmental concern for years. Recent research has revealed that larvae of Galleria mellonella are capable of biodegrading low density PE film. In this study, we tested the feasibility of enhancing larval survival and the effect of supplementing the co-diet on plastic degradation by feeding the larvae beeswax or wheat bran as a co-diet. Significant mass loss of plastic was observed over a 21-day period, i.e., with respective consumption of 0.88 and 1.95 g by 150 larvae fed only either PS or PE. The formation of C═O and C-O containing functional groups and long chain fatty acids as the metabolic intermediates of plastics in the residual polymers indicated depolymerization and biodegradation. Supplementing beeswax and bran increased the survival rates but decreased the consumption of plastic. The changes in the gut microbiome revealed that Bacillus and Serratia were significantly associated with the PS and PE diets. Beeswax and bran showed different shaping effects on the core gut microbiome of larvae fed the PE and PS. These results suggest that supplementing the co-diet affected the physiological properties of the larvae and plastic biodegradation and shaped the core gut microbiome.

The distal intestinal microbiome of hybrids of Hainan black goats and Saanen goats.

Intestinal microbiota performed numerous important functions during digestion. The first filial generation (F1) hybrids of Hainan black goats and Saanen goats had different traits, black goats (BG) and white goats (WG), which also brought different production performance. We explored the difference of gut microbiota between black goats and white goats that both belonged to the first filial generation (F1) hybrids. In general, the alpha diversity of the black goat group was significantly higher than the white goat group. The species richness had no significant difference, while the species evenness of BG was higher than WG. Bacteroides, Oscillospira, Alistipes, Ruminococcus, Clostridium and Oscillibacter, as the core gut microbial genera, all had high abundance in BG and WG group. Only the Bacteroides and Bacteroidaceae 5-7N15 were the different genera between the BG and WG group, of which Bacteroides overlapped with the core genera and enriched in the WG group. Besides, PICRUSt analysis showed that there was a high abundance in the secondary metabolic pathways including membrane transport, replication and repair, carbohydrate metabolism and amino acid metabolism. We found the intestinal microbial species of black goats and white goats were very similar for living in the identical growing environment and feeding conditions, but there was still a slight difference in the content. On the one hand, it was proved that the small effect of genotype and the great effect of diet affected the intestinal microbiota together. On the other hand, it was also proved that these different traits of first filial generation (F1) hybrids may not related to gut microbiota and only because of different genotype. Moreover, characterization of the gut microbiota in BG and WG will be useful in goats gut microbiota research.

Division of labor in honey bee gut microbiota for plant polysaccharide digestion

Bees acquire carbohydrates from nectar and lipids; and amino acids from pollen, which also contains polysaccharides including cellulose, hemicellulose, and pectin. These potential energy sources could be degraded and fermented through microbial enzymatic activity, resulting in short chain fatty acids available to hosts. However, the contributions of individual microbiota members to polysaccharide digestion have remained unclear. Through analysis of bacterial isolate genomes and a metagenome of the honey bee gut microbiota, we identify that Bifidobacterium and Gilliamella are the principal degraders of hemicellulose and pectin. Both Bifidobacterium and Gilliamella show extensive strain-level diversity in gene repertoires linked to polysaccharide digestion. Strains from honey bees possess more such genes than strains from bumble bees. In Bifidobacterium, genes encoding carbohydrate-active enzymes are colocated within loci devoted to polysaccharide utilization, as in Bacteroides from the human gut. Carbohydrate-active enzyme-encoding gene expressions are up-regulated in response to particular hemicelluloses both in vitro and in vivo. Metabolomic analyses document that bees experimentally colonized by different strains generate distinctive gut metabolomic profiles, with enrichment for specific monosaccharides, corresponding to predictions from genomic data. The other 3 core gut species clusters (Snodgrassella and 2 Lactobacillus clusters) possess few or no genes for polysaccharide digestion. Together, these findings indicate that strain composition within individual hosts determines the metabolic capabilities and potentially affects host nutrition. Furthermore, the niche specialization revealed by our study may promote overall community stability in the gut microbiomes of bees.

High-throughput sequencing reveals the core gut microbiota of the mud crab (Scylla paramamosain) in different coastal regions of southern China

BackgroundScylla paramamosain is a commercially important mud crab. The microbiota is a community that inhabits the crab intestine, and is important for physiological functional and host health.ResultsProteobacteria, Firmicutes, Bacteroidetes, Tenericutes, Spirochaetae and Fusobacteria were the dominant phyla of the 36 representative phyla. Eleven genera of the 820 representative genera were considered as core gut microbiota and were distributed in the five dominant phyla. The core genus of the Proteobacteria included Arcobacter, Photobacterium, Vibrio, Shewanella and Desulfovibrio. The other four phyla contained one or two genera. Male and female crab samples had two different core genera, (male samples: Psychrilyobacter & Lactococcus; female samples: Clostridium_sensu_stricto_11 and Candidatus_Bacilloplasma).ConclusionsThis is the first time core intestinal microbiota have been identified in crab from nine coastal regions of southern China. This study provides sequencing data related to the gut microbiota of S. paramamosain, and may contribute to probiotic development for S. paramamosain aquaculture industries.