Phylogenetic and functional analysis of gut microbiota of a fungus-growing higher termite: Bacteroidetes from higher termites are a rich source of β-glucosidase genes

Effects of hematite on two types of dissolved organic compounds in lignocellulosic anaerobic hydrolysate: Lignin-derived aromatic compounds and denitrifying carbon sources

The utilization of anaerobic hydrolysate from agroforestry wastes is limited by dissolved lignin and aromatics, which have received insufficient attention despite their potential as excellent carbon sources for denitrification. This study aims to investigate the influence of hematite on lignin-derived aromatic compounds and denitrifying carbon sources, as well as to identify iron-reducing bacteria that utilize lignin-derived aromatic compounds as electron donors. The findings revealed that hematite facilitated the anaerobic fermentation of plant biomass, resulting in the production of small molecular organic acids. Moreover, biodegradation of lignin-derived aromatic compounds led to the formation of phenolic acids, while an increased generation of denitrifying carbon sources enhanced nitrogen removal efficiency by 13.84 %. Additionally, due to adsorption by hematite and subsequent microbial degradation, there was a significant improvement (40.32%) in color removal rate within denitrification effluent. Notably, Azonexus strains were hypothesized to be involved in Fe(Ⅲ) reduction coupled with aromatic compounds oxidation.

Tripartite Symbiotic Digestion of Lignocellulose in the Digestive System of a Fungus-Growing Termite

Fungus-growing termites are efficient in degrading and digesting plant substrates, achieved through the engagement of symbiotic gut microbiota and lignocellulolytic Termitomyces fungi cultivated for protein-rich food. Insights into where specific plant biomass components are targeted during the decomposition process are sparse. In this study, we performed several analytical approaches on the fate of plant biomass components and did amplicon sequencing of the 16S rRNA gene to investigate the lignocellulose digestion in the symbiotic system of the fungus-growing termite Odontotermes formosanus (Shiraki) and to compare bacterial communities across the different stages in the degradation process. We observed a gradual reduction of lignocellulose components throughout the process. Our findings support that the digestive tract of young workers initiates the degradation of lignocellulose but leaves most of the lignin, hemicellulose, and cellulose, which enters the fresh fungus comb, where decomposition primarily occurs. We found a high diversity and quantity of monomeric sugars in older parts of the fungus comb, indicating that the decomposition of lignocellulose enriches the old comb with sugars that can be utilized by Termitomyces and termite workers. Amplicon sequencing of the 16S rRNA gene showed clear differences in community composition associated with the different stages of plant biomass decomposition which could work synergistically with Termitomyces to shape the digestion process. IMPORTANCE Fungus-farming termites have a mutualist association with fungi of the genus Termitomyces and gut microbiota to support the nearly complete decomposition of lignocellulose to gain access to nutrients. This elaborate strategy of plant biomass digestion makes them ecologically successful dominant decomposers in (sub)tropical Old World ecosystems. We employed acid detergent fiber analysis, high-performance anion-exchange chromatography (HPAEC), high-performance liquid chromatography (HPLC), scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), pyrolysis gas chromatography-mass spectrometry (Py-GC-MS), and amplicon sequencing of the 16S rRNA gene to examine which lignocellulose components were digested and which bacteria were abundant throughout the decomposition process. Our findings suggest that although the first gut passage initiates lignocellulose digestion, the most prominent decomposition occurs within the fungus comb. Moreover, distinct bacterial communities were associated with different stages of decomposition, potentially contributing to the breakdown of particular plant components.

Screening and fermentation medium optimization of a strain favorable to Rice-fish Coculture

Rice-fish coculture (RF) is a small ecosystem in which microorganisms are widely distributed in the fish, water environment, soil, and plants. In order to study the positive effects of microorganisms on common carp and rice in the RF ecosystem, a total of 18 strains with growth-promoting ability were screened from common carp (Cyprinus carpio) gut contents, among which three strains had the ability to produce both DDP-IV inhibitors and IAA. The strain with the strongest combined ability, FYN-22, was identified physiologically, biochemically, and by 16S rRNA, and it was initially identified as Bacillus licheniformis. As the number of metabolites secreted by the strain under natural conditions is not sufficient for production, the FYN-22 fermentation medium formulation was optimized by means of one-factor-at-a-time (OFAT) experiments and response surface methodology (RSM). The results showed that, under the conditions of a soluble starch concentration of 10.961 g/l, yeast concentration of 2.366 g/l, NH₄Cl concentration of 1.881 g/l, and FeCl₃ concentration of 0.850 g/l, the actual measured number of FYN-22 spores in the fermentation broth was 1.913 × 10⁹ CFU/ml, which was 2.575-fold improvement over the pre-optimization value. The optimized fermentation solution was used for the immersion operation of rice seeds, and, after 14 days of incubation in hydroponic boxes, the FYN-22 strain was found to have a highly significant enhancement of 48.31% (p < 0.01) on the above-ground part of rice, and different degrees of effect on root length, fresh weight, and dry weight (16.73, 17.80, and 21.97%, respectively; p < 0.05). This study may provide new insights into the fermentation process of Bacillus licheniformis FYN-22 and its further utilization in RF systems.

Amygdalin: A Review on Its Characteristics, Antioxidant Potential, Gastrointestinal Microbiota Intervention, Anticancer Therapeutic and Mechanisms, Toxicity, and Encapsulation

Bioactive amygdalin, found in high concentrations in bitter almonds, has been recognized as a symbol of the cyanogenic glycoside chemical organic substance, which was initially developed as a pharmaceutical for treating cancer after being hydrolyzed to hydrogen cyanide (HCN). Regrettably, research has shown that HCN can also damage normal cells, rendering it non-toxic to the human body. Extreme controversy surrounds both in vivo and in vitro studies, making its use risky. This review provides an extensive update on characteristics, antioxidant potential, gastrointestinal microbiota intervention, anticancer therapeutic, mechanisms, toxicity, and encapsulation of amygdalin. Antioxidant, anti-tumor, anti-fibrotic, antiatherosclerosis, anti-inflammatory, immunomodulatory, and analgesic characteristics, and the ability to improve digestive and reproductive systems, neurodegeneration, and cardiac hypertrophy are just some of the benefits of amygdalin. Studies verified the HCN-produced amygdalin to be harmful orally, but only at very high doses. Although intravenous treatment was less effective than the oral method, the oral route has a dose range of 0.6 to 1 g daily. Amygdalin’s toxicity depends heavily on the variety of bacteria in the digestive tract. Unfortunately, there is currently no foolproof method for determining the microbial consortium and providing a safe oral dosage for every patient. Amygdalin encapsulation in alginate-chitosan nanoparticles (ACNPs) is a relatively new area of research. Amygdalin has an enhanced cytotoxic effect on malignant cells, and ACNPs can be employed as an active drug-delivery system to release this compound in a regulated, sustained manner without causing any harm to healthy cells or tissues. In conclusion, a large area of research for a substance that might be the next step in cancer therapy is opened up due to unverified and conflicting data.

Pharmacokinetics and anti-liver fibrosis characteristics of amygdalin: Key role of the deglycosylated metabolite prunasin

BACKGROUND

Amygdalin (Amy) is a cyanoside and is one of the chief active ingredients in Persicae Semen, Armeniacae Semen Amarum, and Pruni Semen. Amy has extensive and remarkable pharmacological activities, including against anti-hepatic fibrosis. However, the pharmacokinetic and anti-liver fibrosis effects of Amy and its enzyme metabolite prunasin (Pru) in vivo have not been studied and compared, and studies on Pru are limited.

PURPOSE

To investigate the pharmacokinetic characteristics and anti-liver fibrosis effect of Amy and its metabolite Pru in vivo and in vitro, and elucidate whether the metabolism of Amy in vivo for Pru is activated.

METHODS

Pru was prepared from Amy via the enzymatic hydrolysis of β-glucosidase, and isolated by silica gel column chromatography. An efficient and sensitive ultrahigh-performance liquid chromatography-Q exactive hybrid quadrupole orbitrap high-resolution accurate mass spectrometry was developed and validated to determine simultaneously Amy and Pru in rat plasma after dosing intravenously and orally for pharmacokinetic studies. The affinities of Amy and Pru for β-glucosidase were compared by enzyme kinetic experiments to explain the possible reasons for the differences in pharmacokinetic behavior. In vitro, the inhibitory effects of Amy and Pru on hepatic stellate cell activation and macrophage inflammation on JS1 and RAW 264.7 cells were determined. In vivo, the ameliorative effects of Amy and Pru on liver fibrosis effects were comprehensively evaluated by CCl4-induced liver fibrosis model in mice.

RESULTS

The standard curves of Amy and Pru in rat plasma showed good linearity within the concentration range of 1.31-5000.00 ng/ml, with acceptable selectivity, carry-over, detection limit and quantification limits, intra- and inter-day precision, accuracy, matrix effect, and stability. The Cmax and AUC(0-∞) of Pru (Cmax = 1835.12 ± 268.09 ng/ml, AUC(0-∞) = 103,913.17 ± 14,202.48 ng•min/ml) were nearly 79.51- and 66.22-fold higher than those of Amy (Cmax = 23.08 ± 5.08 ng/ml, AUC(0-∞) = 1569.22 ± 650.62 ng•min/ml) after the oral administration of Amy. The oral bioavailability of Pru (64.91%) was higher than that of Amy (0.19%). The results of enzyme hydrolysis kinetics assay showed that the Vmax and Km of Pru were lower than those of Amy in commercial β-glucosidase and intestinal bacteria. In vitro cellular assays showed that Amy and Pru were comparable in inhibiting the NO production in the RAW264.7 cell supernatant and the mRNA expression of α-SMA and Col1A1 in JS1 cells. Amy and Pru were also showed comparable activity in ameliorating CCl4-induced liver fibrosis in mice.

CONCLUSION

The pharmacokinetic characteristics of Amy and Pru in rat plasma were significantly different. After the separate gavage of Amy and Pru, Amy was absorbed predominantly as it's metabolite Pru, whereas Pru was absorbed predominantly as a prototype. The anti-liver fibrosis effects of Amy and its deglycosylated metabolite Pru were comparable in vivo and in vitro. The deglycosylated activated metabolite Pru of Amy plays an important role in anti-liver fibrosis. These findings will facilitate the further exploitation of Amy and Pru.

Multipartite symbioses in fungus-growing termites (Blattodea: Termitidae, Macrotermitinae) for the degradation of lignocellulose

Fungus-growing termites are among the most successful herbivorous animals and improve crop productivity and soil fertility. A range of symbiotic organisms can be found inside their nests. However, interactions of termites with these symbionts are poorly understood. This review provides detailed information on the role of multipartite symbioses (between termitophiles, termites, fungi, and bacteria) in fungus-growing termites for lignocellulose degradation. The specific functions of each component in the symbiotic system are also discussed. Based on previous studies, we argue that the enzymatic contribution from the host, fungus, and bacteria greatly facilitates the decomposition of complex polysaccharide plant materials. The host-termitophile interaction protects the termite nest from natural enemies and maintains the stability of the microenvironment inside the colony.

Some characters of bacterial cellulases in goats' rumen elucidated by metagenomic DNA analysis and the role of fibronectin 3 module for endoglucanase function

Objective

Fibronectin 3 (FN3) and immunoglobulin like modules (Ig) are usually collocated beside modular cellulase catalytic domains. However, very few researches have investigated the role of these modules. In a previous study, we have sequenced and analyzed bacterial metagenomic DNA in Vietnamese goats’ rumen and found that cellulase-producing bacteria and cellulase families were dominant. In this study, the properties of modular cellulases and the role of a FN3 in unique endoglucanase belonging to glycosyl hydorlase (GH) family 5 were determined.

Methods

Based on Pfam analysis, the cellulases sequences containing FN3, Ig modules were extracted from 297 complete open reading frames (ORFs). The alkaline, thermostability, tertiary structure of deduced enzymes were predicted by AcalPred, TBI software, Phyre2 and Swiss models. Then, whole and truncated forms of a selected gene were expressed in Escherichia coli and purified by His-tag affinity column for assessment of FN3 ability to enhance enzyme activity, solubility and conformation.

Results

From 297 complete ORFs coding for cellulases, 148 sequences containing FN3, Ig were identified. Mostly FN3 appeared in 90.9% beta-glucosidases belonging to glycosyl hydrolase family 3 (GH3) and situated downstream of catalytic domains. The Ig was found upstream of 100% endoglucanase GH9. Rarely FN3 was seen to be situated downstream of X domain and upstream of catalytic domain endoglucanase GH5. Whole enzyme (called XFN3GH5 based on modular structure) and truncate forms FN3, XFN3, FN3GH5, GH5 were cloned in pET22b (+) and pET22SUMO to be expressed in single and fusion forms with a small ubiquitin-related modifier partner (S). The FN3, SFN3 increased GH5 solubility in FN3GH5, SFN3GH5. The SFN3 partly served for GH5 conformation in SFN3GH5, increased modules interaction and enzyme-soluble substrate affinity to enhance SXFN3GH5, SFN3GH5 activities in mixtures. Both SFN3 and SXFN3 did not anchor enzyme on filter paper but exfoliate and separate cellulose chains on filter paper for enzyme hydrolysis.

Conclusion

Based on these findings, the presence of FN3 module in certain cellulases was confirmed and it assisted for enzyme conformation and activity in both soluble and insoluble substrate.

Synergism between Hydramethylnon and Metarhizium anisopliae and Their Influence on the Gut Microbiome of Blattella germanica (L.)

Simple Summary

The widespread use of insecticides has cause extensive resistance in German cockroach (Blattella germanica) populations globally. Biological control has the potential to mitigate insecticide resistance, and Metarhizium anisopliae, an entomopathogenic fungus, alone and in combination with various insecticides has shown good effects against cockroaches. This experiment compared the cumulative mortality after infecting B. germanica with M. anisopliae conidia by per os infection and topical dorsal infection. To probe the mechanisms that underlie the synergism between M. anisopliae and hydramethylnon, we conducted dose-response assays with cockroaches fed combinations of them and characterized the gut microbiome of treated cockroaches. The results showed that the mortality of per os infection was lower than that of topical dorsal infection. In addition, the combination of M. anisopliae and hydramethylnon had a synergistic effect. The gut microbiome was also altered by hydramethylnon treatment. Therefore, we speculate that one of the mechanism underlying this synergism is that hydramethylnon promotes the survival of M. anisopliae in the harsh gut environment and enhances its virulence on German cockroaches by altering the gut microbiome. This may help to develop new types of bio-control glue baits for the control of cockroaches.

Abstract

(1) Background: The widespread use of insecticides has cause extensive resistance in German cockroach (Blattella germanica) populations globally. Biological control has the potential to mitigate insecticide resistance, and Metarhizium anisopliae (Meschn.) Sorokin, an entomopathogenic fungus, alone and in combination with various insecticides, has shown good effects against cockroaches. (2) Methods: This experiment compared the cumulative mortality after infecting B. germanica with M. anisopliae conidia by two routes, per os and topical application. To probe the mechanisms that underlie the synergism between M. anisopliae and hydramethylnon, we conducted dose–response assays with cockroaches fed combinations of M. anisopliae and hydramethylnon and characterized the gut microbiomes of the treated cockroaches. (3) Results: The study showed that the mortality with per os infection was lower than that with topical application. In addition, the combination of M. anisopliae and hydramethylnon had a synergistic effect in 16 treatments. The gut microbiome was also altered by hydramethylnon treatment. The abundance of Parabacteroides and Enterococcus declined with the hydramethylnon and combination treatments, which are known to have anti-inflammatory and antifungal activities. The abundance of Alistipes, which is a fungal cell wall component, significantly increased in these treatments. (4) Conclusions: Therefore, we speculate that the major mechanism underlying this synergism is hydramethylnon promoting the survival of M. anisopliae in the harsh gut environment and enhancing its virulence for German cockroaches by altering the gut microbiome. This may provide a method for the fight against B. germanica and lay the foundation for the development of new baits.

Diversity and Composition of the Gut Microbiota in the Developmental Stages of the Dung Beetle Copris incertus Say (Coleoptera, Scarabaeidae)

Dung beetles are holometabolous insects that feed on herbivorous mammal dung and provide services to the ecosystem including nutrient cycling and soil fertilization. It has been suggested that organisms developing on incomplete diets such as dungs require the association with microorganisms for the synthesis and utilization of nutrients. We describe the diversity and composition of the gut-microbiota during the life cycle of the dung beetle Copris incertus using 16S rRNA gene sequencing. We found that C. incertus gut contained a broad diversity of bacterial groups (1,699 OTUs and 302 genera). The taxonomic composition varied during the beetle life cycle, with the predominance of some bacterial genera in a specific developmental stage (Mothers: Enterobacter and Serratia; Eggs: Nocardioides and Hydrogenophaga; Larval and pupal stages: Dysgonomonas and Parabacteroides; offspring: Ochrobactrum). The beta diversity evidenced similarities among developmental stages, clustering (i) the adult stages (mother, male and female offsprings), (ii) intermediate developmental (larvae and pupa), and (iii) initial stage (egg). Microbiota differences could be attributed to dietary specialization or/and morpho-physiological factors involved in the transition from a developmental stage to the next. The predicted functional profile (PICRUSt2 analysis) for the development bacterial core of the level 3 categories, indicated grouping by developmental stage. Only 36 categories were significant in the SIMPER analysis, including the metabolic categories of amino acids and antibiotic synthesis, which were enriched in the larval and pupal stages; both categories are involved in the metamorphosis process. At the gene level, we found significant differences only in the KOs encoding functions related to nitrogen fixation, uric acid metabolism, and plant cell wall degradation for all developmental stages. Nitrogen fixation and plant cell wall degradation were enriched in the intermediate stages and uric acid metabolism was enriched in mothers. The data reported here suggested the influence of the maternal microbiota in the composition and diversity of the gut microbiota of the offspring.

Exploring the effect of plant substrates on bacterial community structure in termite fungus-combs

Fungus-cultivating termites are successful herbivores largely rely on the external symbiotic fungus-combs to decompose plant polysaccharides. The comb harbors both fungi and bacteria. However, the complementary roles and functions of the bacteria are out of the box. To this purpose, we look into different decomposition stages of fungus-combs using high-throughput sequencing of the 16S rRNA gene to examine bacterial community structure. We also explored the bacterial response to physicochemical indexes (such as moisture, ash content and organic matter) and plant substrates (leaves or branches or mix food). Some specific families such as Lachnospiraceae, Ruminococcaceae, and Peptostreptococcaceae may be involved in lignocellulose degradation, whereas Burkholderiaceae may be associated with aromatic compounds degradation. We observed that as the comb mature there is a shift of community composition which may be an adjustment of specific bacteria to deal with different lignocellulosic material. Our results indicated that threshold amount of physicochemical indexes are beneficial for bacterial diversity but too high moisture, low organic matter and high ash content may reduce their diversity. Furthermore, the average highest bacterial diversity was recorded from the comb built by branches followed by mix food and leaves. Besides, this study could help in the use of bacteria from the comb of fungus-cultivating termites in forestry and agricultural residues making them easier to digest as fodder.

Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes

In this study, we used shotgun metagenomic sequencing to characterise the microbial metabolic potential for lignocellulose transformation in the gut of two colonies of Argentine higher termite species with different feeding habits, Cortaritermes fulviceps and Nasutitermes aquilinus. Our goal was to assess the microbial community compositions and metabolic capacity, and to identify genes involved in lignocellulose degradation. Individuals from both termite species contained the same five dominant bacterial phyla (Spirochaetes, Firmicutes, Proteobacteria, Fibrobacteres and Bacteroidetes) although with different relative abundances. However, detected functional capacity varied, with C. fulviceps (a grass-wood-feeder) gut microbiome samples containing more genes related to amino acid metabolism, whereas N. aquilinus (a wood-feeder) gut microbiome samples were enriched in genes involved in carbohydrate metabolism and cellulose degradation. The C. fulviceps gut microbiome was enriched specifically in genes coding for debranching- and oligosaccharide-degrading enzymes. These findings suggest an association between the primary food source and the predicted categories of the enzymes present in the gut microbiomes of each species. To further investigate the termite microbiomes as sources of biotechnologically relevant glycosyl hydrolases, a putative GH10 endo-β-1,4-xylanase, Xyl10E, was cloned and expressed in Escherichia coli. Functional analysis of the recombinant metagenome-derived enzyme showed high specificity towards beechwood xylan (288.1 IU/mg), with the optimum activity at 50 °C and a pH-activity range from 5 to 10. These characteristics suggest that Xy110E may be a promising candidate for further development in lignocellulose deconstruction applications.

Effect of Streptomyces probiotics on the gut microbiota of Litopenaeus vannamei challenged with Vibrio parahaemolyticus

This study assessed the intestinal microbiota of juveniles of the White shrimp Litopenaus vannamei, whose feed was enriched with three probiotic formulations: Streptomyces sp. RL8 (RL8); a mix of Lactobacillus graminis and Streptomyces spp. RL8 and N7 (Lac-Strep); and a mix of Bacillus spp. and Streptomyces spp. RL8 and N7 (Bac-Strep). The analysis was performed by sequencing the V3 region of the 16S rRNA gene of treated animals and the control group before and after Vibrio parahaemolyticus challenge. After challenge, the highest Shannon diversity indexes corresponded to RL8 and Bac-Strep (3.94 ± 0.11 and 3.39 ± 0.3, respectively) and the lowest to the control group (2.58 ± 0.26). The most abundant phyla before and after challenge were Proteobacteria, Actinobacteria, and Bacteroidetes. The principal component analysis and Statistical Analysis of Metagenomic Profiles (STAMP) showed that the gut microbiota of the groups RL8 and Bac-Strep after challenge was different from the other experimental groups, which was characterized by a higher bacterial diversity, as well as a significant stimulation of the Bacteriovorax population and other antimicrobial producing genera that protected shrimp from infection.

Understanding the roles of surface proteins in regulation of Lactobacillus pentosus HC-2 to immune response and bacterial diversity in midgut of Litopenaeus vannamei

The interactions of microbiota in the intestines play an important role in promoting or maintaining the health of hosts. The present study aim to investigate the effects of the surface proteins of Lactobacillus pentosus HC-2 on the immune response and the bacterial composition of Litopenaeus vannamei, thus, the immune-related genes, surface condition, HC-2 numbers and the bacteria diversity in midgut were explored after shrimp feeding the normal HC-2 and 5 M -  lithium chloride (LiCl) treated HC-2 for four weeks. Obvious improvements in the intestinal surface were observed in R group than the control group and L group. qPCR analysis demonstrated that the selected immune-related genes of lysozyme, proPO, LGBP, PEN-3α, crustin, and lvLec were significantly up-regulated in group R than in group L. Meanwhile, in the challenge test, shrimp in R group received 72% relative percent survival, which was significantly higher than the L group (RPS = 9%). The bacteria composition analysis showed that the abundance of Proteobacteria were significantly higher in group R and L than in group C, and the Bacteroidetes were significantly higher in group C than in group R and L, whereas the numbers of Chloroflexi were significantly higher in group R than in group C and L. The bacterial community difference analysis revealed that the harmful bacteria such as genus of Vibrio, Tenacibaculu and Thalassobius were decreased and the beneficial bacterium as Ruegeria and Lactobacillus were increased in R group, whereas this phenomenon were not found in L group. Taken together, above results indicating that the surface proteins were indispensable for L. pentosus HC-2 adhesion and colonization in shrimp intestines to improve intestine condition, enhance immune response, competitively exclude the pathogens, and promote the beneficial bacteria growth to protect the shrimp from pathogens infection. The findings in this work will help to promote the understanding of the roles of probiotics in shrimp intestines displaying probiotic-function by regulating the intestinal bacteria.

The accumulation, histopathology, and intestinal microorganism effects of waterborne cadmium on Carassius auratus gibelio

Cadmium (Cd) is known to be a potentially toxic heavy metals to the fish health and growth. Carassius auratus gibelio (C. a. gibelio) specimens were exposed to waterborne Cd (0, 0.05, 0.10, 0.15, and 0.20 mg/L CdCl₂) for 14 days. Cd accumulation, liver and intestine histopathology, and intestinal microorganism were investigated in the present study. The results indicated that Cd accumulation in the gill, liver, intestine, and muscle gradually decreased as Cd concentration increased. The gill accumulated higher amounts of Cd than other tissues. The histopathology of liver and intestine underwent changes with different Cd concentrations, including hepatocyte hypertrophy, aggregation of blood cells, sinusoids, lipidosis, necrosis of hepatic tissues, the erosion of villi, necrosis in the mucosal layer, the appearance of vacuoles in the lamina propria, hyperplasia, and swelling of goblet cells. Moreover, the core gut microbiota existed in the intestinal microorganism and did not change as Cd concentration increased. However, the diversity of intestinal microorganism was significantly reduced compared with that of the control sample. The present results indicated that C. a. gibelio exposed to Cd suffered toxicity, and Cd could affect the biodiversity of the intestinal microbiota of C. a. gibelio.

Comparative analysis of the intestinal bacterial community and expression of gut immunity genes in the Chinese Mitten Crab (Eriocheir sinensis)

Remarkably little information is available about the interaction between the gut microbiota and intestinal immunity in fish and crustaceans. In our study, we used Illumina MiSeq sequencing and real-time quantitative PCR to compare the microbial community and immunity genes expression in the foregut, midgut and hindgut of Chinese mitten crab (Eriocheir sinensis). Our results indicated that the community richness of the midgut is higher than in the foregut or the hindgut, although the bacterial diversity in the hindgut is higher. The predominant phyla were Tenericutes and Firmicutes in the foregut, Tenericutes and Proteobacteria in the midgut and Proteobacteria, Tenericutes and Bacteroidetes in the hindgut. When compared with the midgut, the expression of antimicrobial peptides (AMPs) were significantly elevated in the hindgut (P < 0.05), and the gene expression of EsRelish (IMD pathway) was higher than the Toll signaling pathway genes. Actinobacteria and Lactobacillus had negative correlationship with the expression of AMPs, although Acinetobacter, Bacteroides, Flavobacterium can up-regulate the expression of AMP genes. Collectively, our data indicate that microbiota are site-specific within the digestive tracts of crabs and the bacterial community and intestinal immunity have a close relationship in E. sinensis.

Cellulases from Thermophiles Found by Metagenomics

Cellulases are a heterogeneous group of enzymes that synergistically catalyze the hydrolysis of cellulose, the major component of plant biomass. Such reaction has biotechnological applications in a broad spectrum of industries, where they can provide a more sustainable model of production. As a prerequisite for their implementation, these enzymes need to be able to operate in the conditions the industrial process requires. Thus, cellulases retrieved from extremophiles, and more specifically those of thermophiles, are likely to be more appropriate for industrial needs in which high temperatures are involved. Metagenomics, the study of genes and gene products from the whole community genomic DNA present in an environmental sample, is a powerful tool for bioprospecting in search of novel enzymes. In this review, we describe the cellulolytic systems, we summarize their biotechnological applications, and we discuss the strategies adopted in the field of metagenomics for the discovery of new cellulases, focusing on those of thermophilic microorganisms.

Effects of the Gut microbiota on Amygdalin and its use as an anti-cancer therapy: Substantial review on the key components involved in altering dose efficacy and toxicity

Conventional and Alternative Medicine (CAM) is popularly used due to side-effects and failure of approved methods, for diseases like Epilepsy and Cancer. Amygdalin, a cyanogenic diglycoside is commonly administered for cancer with other CAM therapies like vitamins and seeds of fruits like apricots and bitter almonds, due to its ability to hydrolyse to hydrogen cyanide (HCN), benzaldehyde and glucose. Over the years, several cases of cyanide toxicity on ingestion have been documented. In-vitro and in-vivo studies using various doses and modes of administration, like IV administration studies that showed no HCN formation, point to the role played by the gut microbiota for the commonly seen poisoning on consumption. The anaerobic Bacteriodetes phylum found in the gut has a high β-glucosidase activity needed for amygdalin hydrolysis to HCN. However, there are certain conditions under which these HCN levels rise to cause toxicity. Case studies have shown toxicity on ingestion of variable doses of amygdalin and no HCN side-effects on consumption of high doses. This review shows how factors like probiotic and prebiotic consumption, other CAM therapies, obesity, diet, age and the like, that alter gut consortium, are responsible for the varying conditions under which toxicity occurs and can be further studied to set-up conditions for safe oral doses. It also indicates ways to delay or quickly treat cyanide toxicity due to oral administration and, reviews conflicts on amygdalin's anti-cancer abilities, dose levels, mode of administration and pharmacokinetics that have hindered its official acceptance at a therapeutic level.

Screening of multimeric β-xylosidases from the gut microbiome of a higher termite, Globitermes brachycerastes

Termite gut microbiome is a rich reservoir for glycoside hydrolases, a suite of enzymes critical for the degradation of lignocellulosic biomass. To search for hemicellulases, we screened 12,000 clones from a fosmid gut library of a higher termite, Globitermes brachycerastes. As a common Southeastern Asian genus, Globitermes distributes predominantly in tropical rain forests and relies on the lignocellulases from themselves and bacterial symbionts to digest wood. In total, 22 positive clones with β-xylosidase activity were isolated, in which 11 representing different restriction fragment length polymorphism (RFLP) patterns were pooled and subjected to 454 pyrosequencing. As a result, eight putative β-xylosidases were cloned and heterologously expressed in Escherichia coli BL21 competent cells. After purification using Ni-NTA affinity chromatography, recombinant G. brachycerastes symbiotic β-xylosidases were characterized enzymatically, including their pH and temperature optimum. In addition to β-xylosidase activity, four of them also exhibited either β-glucosidase or α-arabinosidases activities, suggesting the existence of bifunctional hemicellulases in the gut microbiome of G. brachycerastes. In comparison to multimeric protein engineering, the involvement of naturally occurring multifunctional biocatalysts streamlines the genetic modification procedures and simplifies the overall production processes. Alternatively, these multimeric enzymes could serve as the substitutes for β-glucosidase, β-xylosidase and α-arabinosidase to facilitate a wide range of industrial applications, including food processing, animal feed, environment and waste management, and biomass conversion.

Two new gene clusters involved in the degradation of plant cell wall from the fecal microbiota of Tunisian dromedary

Dromedaries are capable of digesting plant cell wall with high content of lignocellulose of poor digestibility. Consequently, their intestinal microbiota can be a source of novel carbohydrate-active enzymes (CAZymes). To the best of our knowledge, no data are available describing the biochemical analysis of enzymes in dromedary intestinal microbiota. To investigate new hydrolytic enzymes from the dromedary gut, a fosmid library was constructed using metagenomic DNA from feces of non-domestic adult dromedary camels living in the Tunisian desert. High-throughput functional screening of 13756 clones resulted in 47 hit clones active on a panel of various chromogenic and non-chromogenic glycan substrates. Two of them, harboring multiple activities, were retained for further analysis. Clone 26H3 displayed activity on AZO-CM-cellulose, AZCL Carob galactomannan and Tween 20, while clone 36A23 was active on AZCL carob galactomannan and AZCL barley β-glucan. The functional annotation of their sequences highlighted original metagenomic loci originating from bacteria of the Bacteroidetes/Chlorobi group, involved in the metabolization of mannosides and β-glucans thanks to a complete battery of endo- and exo-acting glycoside hydrolases, esterases, phosphorylases and transporters.

The effects of acute strenuous exercise on the faecal microbiota in Standardbred racehorses

While exercise has been found to change the faecal microbiome (FM) in laboratory animals exposed over weeks, no studies have identified immediate changes in the FM associated with short spans of intense exercise, ~5 min. The purpose of this study was to test the hypothesis that acute intense exercise would alter the FM in horses. Each horse performed two rounds of testing undergoing both a graded exercise test (GXT) and a parallel standing control (SC) trial before (GXT1 and SC1) and after (GXT2 and SC2) 12 weeks of exercise training. Rectal faecal samples were taken 24 h before and after testing. Bacterial community analysis was done by sequencing the 16s rRNA (V3-V4) region via Illumina Miseq. The relative abundance of the genus Clostridium significantly decreased in SC1 (P<0.05), with a concurrent decrease in the Shannon diversity index at the species level (P<0.05). At both the genus and species levels the principle coordinate analysis (PCoA) showed significant separation when the samples collected before SC1 were compared to those collected after SC1 (P<0.05). Interestingly, we found that Fusicatenibacter saccharivorans, a bacteria found to be decreased in ulcerative colitis patients, and Treponema zioleckii, a bacteria found to degrade fructan in sheep rumen, were significantly decreased when the samples collected before SC1 were compared to those collected after SC1 (P<0.05). None of the changes observed in SC1 happened in SC2 (P>0.05). Our results indicate that very intense acute exercise does not alter the faecal microbiome of the Standardbred race horse and that 12 weeks of exercise training does not alter that response.

Exercise training-induced changes in the gut microbiota of Standardbred racehorses

Exercise has a significant effect on different physiological systems in the body of human and animals. Only limited numbers of published studies in laboratory animals or humans have shown the effect of exercise on the gut microbiota, and no studies have shown this effect in horses. In this study, 8 horses (4 mares, 4 geldings) were exercise trained for 12 weeks, and 4 additional mares were used as a parallel seasonal control. To identify bacterial community changes over time for both groups, rectal faecal samples were collected, DNA was extracted, and the 16S rRNA gene (V3-V4) was sequenced using the Illumina Miseq platform. One-way ANOVA, Shannon diversity index, and Principal Coordinate Analysis (PCoA) were used to identify differences between and among samples. The exercise training group showed significant changes in the levels of Bacteroidetes, Proteobacteria, and Spirochaetes phyla (P<0.05), while there were no changes in the gut microbiota of the seasonal control group through the three months of the study (P>0.05). Moreover, with training two genera significantly changed in their relative abundance over time, namely Clostridium and Dysgonomonas (P<0.05). Dysgonomonas spp. was significantly changed in abundance during the exercise training period (P<0.05). Also Treponema spp. showed significant changes during the exercise training period (P<0.05). Shannon diversity index was decreased (P<0.05) in the exercise group at the beginning of the study, but then returned to pre-training levels. PCoA showed significant separation between time points of the exercise training group as far as the levels of genera and species (P<0.05) represented. Our results show that exercise training influences the gut microbiota, especially at the beginning of training.

The Gut Microbiomes of Two Pachysoma MacLeay Desert Dung Beetle Species (Coleoptera: Scarabaeidae: Scarabaeinae) Feeding on Different Diets

Micro-organisms inhabiting animal guts benefit from a protected and nutrient-rich environment while assisting the host with digestion and nutrition. In this study we compare, for the first time, the bacterial and fungal gut communities of two species of the small desert dung beetle genus Pachysoma feeding on different diets: the detritivorous P. endroedyi and the dry-dung-feeding P. striatum. Whole-gut microbial communities from 5 individuals of each species were assessed using 454 pyrosequencing of the bacterial 16S rRNA gene and fungal ITS gene regions. The two bacterial communities were significantly different, with only 3.7% of operational taxonomic units shared, and displayed intra-specific variation. The number of bacterial phyla present within the guts of P. endroedyi and P. striatum individuals ranged from 6-11 and 4-7, respectively. Fungal phylotypes could only be detected within the gut of P. striatum. Although the role of host phylogeny in Pachysoma microbiome assembly remains unknown, evidence presented in this study suggests that host diet may be a deterministic factor.

Heterologous Expression and Characterization of a GH3 β-Glucosidase from Thermophilic Fungi Myceliophthora thermophila in Pichia pastoris

A novel β-glucosidase of glycoside hydrolase (GH) family 3 from Myceliophthora thermophila (mtbgl3b) was successfully expressed in Pichia pastoris. The full-length gene consists of 2613 bp nucleotides encoding a protein of 870 amino acids. MtBgl3b showed maximum activity at pH 5.0 and remained more than 70 % relative activity at 3.5-6.0. The enzyme displayed the highest activity at 60 °C and kept about 90 % relative activity for 50-65 °C; besides, the enzyme showed psychrophilic trait and remains 51 % relative activity at 40 °C. MtBgl3b exhibited good stability over a wide pH range of 3.0-10.0 and was thermostable at 60 and 65 °C. The enzyme displayed highest activity towards p-nitrophenyl-β-D-glucopyranoside (pNPG), followed by p-nitrophenyl-D-cellobioside (pNPC), cellotetraose, cellotriose, cellobiose, and gentiobiose. When using 10 % cellobiose (w/v) as the substrate, the enzyme showed transglycosylation activity to produce the cellotriose. The kinetic parametric of K m and V max were 2.78 mM and 927.9 μM mg(-1) min(-1), respectively. Finally, the reaction mode of the enzyme and the substrates were analyzed by molecular docking approach.