Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies.

The advent of omic technology has made it possible to identify viable but unculturable micro-organisms in the gut. Therefore, application of multi-omic technologies in gut microbiome studies has become invaluable for unveiling a comprehensive interaction between these commensals in health and disease. Meanwhile, despite the successful identification of many microbial and host-microbial cometabolites that have been reported so far, it remains difficult to clearly identify the origin and function of some proteins and metabolites that are detected in gut samples. However, the application of single omic techniques for studying the gut microbiome comes with its own challenges which may be overcome if a number of different omics techniques are combined. In this review, we discuss our current knowledge about multi-omic techniques, their challenges and future perspective in this field of gut microbiome studies.

Bioinformatic mapping of a more precise Aspergillus niger degradome.

Aspergillus niger has the ability to produce a large variety of proteases, which are of particular importance for protein digestion, intracellular protein turnover, cell signaling, flavour development, extracellular matrix remodeling and microbial defense. However, the A. niger degradome (the full repertoire of peptidases encoded by the A. niger genome) available is not accurate and comprehensive. Herein, we have utilized annotations of A. niger proteases in AspGD, JGI, and version 12.2 MEROPS database to compile an index of at least 232 putative proteases that are distributed into the 71 families/subfamilies and 26 clans of the 6 known catalytic classes, which represents ~ 1.64% of the 14,165 putative A. niger protein content. The composition of the A. niger degradome comprises ~ 7.3% aspartic, ~ 2.2% glutamic, ~ 6.0% threonine, ~ 17.7% cysteine, ~ 31.0% serine, and ~ 35.8% metallopeptidases. One hundred and two proteases have been reassigned into the above six classes, while the active sites and/or metal-binding residues of 110 proteases were recharacterized. The probable physiological functions and active site architectures of these peptidases were also investigated. This work provides a more precise overview of the complete degradome of A. niger, which will no doubt constitute a valuable resource and starting point for further experimental studies on the biochemical characterization and physiological roles of these proteases.

Influence of fermented soy protein consumption on hypertension and gut microbial modulation in spontaneous hypertensive rats.

Plant proteins are known to possess important bioactive peptides and have a positive impact on gut microbial modulation. In this study, we studied the ability of a single dose of a fermented soy protein product (P-SPI) to reduce high blood pressure in spontaneous hypertensive rats (SHR) and how it modulates the gut microbiota after six weeks of feeding. SHRs were fed with P-SPI, Captopril or distilled water once, and their blood pressures were monitored from the first to twelfth-hour post-administration. Consumption of P-SPI significantly reduced systolic and diastolic blood pressures up to the sixth hour by 25 ± 4 mmHg and 40 ± 5 mmHg respectively. P-SPI consumption inhibited serum ACE activity, increased superoxide dismutase activity and nitric oxide levels and reduced malondialdehyde levels in serum. Analysis of fecal microbial 16S rRNA of hypertensive rats revealed a significant reduction in microbial richness and diversity in the gut, while P-SPI consumption improved microbial richness and increased diversity. Also, P-SPI feeding significantly reduced the Firmicutes/Bacteroidetes ratio, increased propionate- and H2S-producing bacteria and reduced Streptococcaceae and Erysipelotrichales levels. Our results show that P-SPI is a potential antihypertensive functional food which could remodel the altered gut microbiota of hypertensive patients.

The current strategies and parameters for the enhanced microbial production of 2,3-butanediol.

2,3-Butanediol (2,3-BD) is a propitious compound with many industrial uses ranging from rubber, fuels, and cosmetics to food additives. Its microbial production has especially attracted as an alternative way to the petroleum-based production. However, 2,3-BD production has always been hampered by low yields and high production costs. The enhanced production of 2,3-butanediol requires screening of the best strains and a systematic optimization of fermentation conditions. Moreover, the metabolic pathway engineering is essential to achieve the best results and minimize the production costs by rendering the strains to use efficiently low cost substrates. This review is to provide up-to-date information on the current strategies and parameters for the enhanced microbial production of 2,3-BD.

Antihypertensive peptides from whey proteins fermented by lactic acid bacteria.

In this study, whey proteins were fermented with 34 lactic acid bacteria for 48 h at 37 °C and their ability to inhibit angiotensin 1-converting enzyme (ACE) activity were compared. All the lactic acid bacteria displayed varying proteolytic abilities in whey. Their fermentates also displayed varying abilities to inhibit ACE in vitro. Seven fermentates showed strong ACE inhibitory abilities between 84.70 ± 0.67 and 52.40 ± 2.1% with IC50 values between 19.78 ± 1.73 and 2.13 ± 0.7 mg/ml. Pediococcus acidilactici SDL1414 showed the strongest ACE inhibitory activity of 84.7 ± 0.67% (IC50 = 19.78 ± 1.73 µg/ml). Mass spectrometry revealed that more than half (57.7%) of the low molecular weight peptides (< 7 kDa) in the P. acidilactici SDL1414 fermented samples were ACE inhibitory peptides. Our results show that P. acidilactici SDL1414 could be used as a starter culture in the dairy industry to develop antihypertensive functional foods for hypertension management.

Bile salt hydrolases: Structure and function, substrate preference, and inhibitor development.

The worldwide trend of limiting the use of antibiotic growth promoters (AGPs) in animal production creates challenges for the animal feed industry, thus necessitating the development of effective non-antibiotic alternatives to improve animal performance. Increasing evidence has shown that the growth-promoting effect of AGPs is highly correlated with the reduced activity of bile salt hydrolase (BSH, EC 3.5.1.24), an intestinal bacteria-producing enzyme that has a negative impact on host fat digestion and energy harvest. Therefore, BSH inhibitors may become novel, attractive alternatives to AGPs. Detailed knowledge of BSH substrate preferences and the wealth of structural data on BSHs provide a solid foundation for rationally tailored BSH inhibitor design. This review focuses on the relationship between structure and function of BSHs based on the crystal structure, kinetic data, molecular docking and comparative structural analyses. The molecular basis for BSH substrate recognition is also discussed. Finally, recent advances and future prospectives in the development of potent, safe, and cost-effective BSH inhibitors are described.

Human microbiome restoration and safety.

The human gut microbiome consists of many bacteria which are in symbiotic relationship with human beings. The gut microbial metabolism, as well as the microbial-host co-metabolism, has been found to greatly influence health and disease. Factors such as diet, antibiotic use and lifestyle have been associated with alterations in the gut microbial community and may result in several pathological conditions. For this reason, several strategies including fecal microbiota transplant and probiotic administration have been applied and proven to be feasible and effective in restoring the gut microbiota in humans. Yet, safety concerns such as potential health risks that may arise from such interventions and how these strategies are regulated need to be addressed. Also, it will be important to know if these microbiome restoration strategies can have a profound impact on health. This review provides an overview of our current knowledge of the microbiome restoration strategies and safety issues on how these strategies are regulated.

Current trends and perspectives of bioactive peptides.

The remarkable growth of therapeutic peptide development in the past decade has led to a large number of market approvals and the market value is expected to hit $25 billion by 2018. This significant market increase is driven by the increasing incidences of metabolic and cardiovascular diseases and technological advancements in peptide synthesis. For this reason, the search for bioactive peptides has also increased exponentially. Many bioactive peptides from food and nonfood sources have shown positive health effects yet, obstacles such as the need to implement efficient and cost-effective strategies for industrial scale production, good manufacturing practices as well as well-designed clinical trials to provide robust evidence for supporting health claims continue to exist. Several other factors such as the possibility of allergenicity, toxicity and the stability of biological functions of the peptides during gastrointestinal digestion would need to be addressed.

Bioactive Peptides.

The increased consumer awareness of the health promoting effects of functional foods and nutraceuticals is the driving force of the functional food and nutraceutical market. Bioactive peptides are known for their high tissue affinity, specificity and efficiency in promoting health. For this reason, the search for food-derived bioactive peptides has increased exponentially. Over the years, many potential bioactive peptides from food have been documented; yet, obstacles such as the need to establish optimal conditions for industrial scale production and the absence of well-designed clinical trials to provide robust evidence for proving health claims continue to exist. Other important factors such as the possibility of allergenicity, cytotoxicity and the stability of the peptides during gastrointestinal digestion would need to be addressed. This review discusses our current knowledge on the health effects of food-derived bioactive peptides, their processing methods and challenges in their development.

Current Immunoassay Methods for the Rapid Detection of Aflatoxin in Milk and Dairy Products.

The presence of mycotoxins in foodstuff causes serious health problems to consumers and economically affects the food industry. Among the mycotoxins, aflatoxins are very toxic and highly carcinogenic contaminants which affect the safety of many foods, and therefore endanger human health. Aflatoxin M1 (AFM1 ) found in milk results from the biotransformation of aflatoxin B1 . Many efforts have been made to control the source of AFM1 from farmers to dairy product companies. However, AFM1 escapes ordinary methods of food treatment such as cooking, sterilization, and freezing, hence it appears in milk and dairy products. The presence of high levels of AFM1 constitutes an alarming threat as milk and dairy products contain essential nutrients for human health, especially for infants and children. For this reason, there is a pressing need for developing a fast and reliable screening method for detecting trace aflatoxins in food. Several analytical methods based on high-performance liquid chromatography (HPLC) and mass spectroscopy have been used for aflatoxin detection; however, they are expensive, time-consuming, and require many skills. Recently, immunoassay methods, including enzyme-linked immunosorbent assay (ELISA), immunosensors, and lateral flow immunoassay (LFIA), have been preferred for food analysis because of their improved qualities such as high sensitivity, simplicity, and capability of onsite monitoring. This paper reviews the new developments and applications of immunoassays for the rapid detection of AFM1 in milk.

Current Status and New Perspectives on Chitin and Chitosan as Functional Biopolymers.

The natural biopolymer chitin and its deacetylated product chitosan are found abundantly in nature as structural building blocks and are used in all sectors of human activities like materials science, nutrition, health care, and energy. Far from being fully recognized, these polymers are able to open opportunities for completely novel applications due to their exceptional properties which an economic value is intrinsically entrapped. On a commercial scale, chitosan is mainly obtained from crustacean shells rather than from the fungal and insect sources. Significant efforts have been devoted to commercialize chitosan extracted from fungal and insect sources to completely replace crustacean-derived chitosan. However, the traditional chitin extraction processes are laden with many disadvantages. The present review discusses the potential bioextraction of chitosan from fungal, insect, and crustacean as well as its superior physico-chemical properties. The different aspects of fungal, insects, and crustacean chitosan extraction methods and various parameters having an effect on the yield of chitin and chitosan are discussed in detail. In addition, this review also deals with essential attributes of chitosan for high value-added applications in different fields and highlighted new perspectives on the production of chitin and deacetylated chitosan from different sources with the concomitant reduction of the environmental impact.

The human microbiome and metabolomics: Current concepts and applications.

The mammalian gastrointestinal tract has co-developed with a large number of microbes in a symbiotic relationship over millions of years. Recent studies indicate that indigenous bacteria are intimate with the intestine and play essential roles in health and disease. In the quest to maintain a stable niche, these prokaryotes influence multiple host metabolic pathways, resulting from an interactive host-microbiota metabolic signaling and impacting strongly on the metabolic phenotypes of the host. Since dysbiosis of the gut bacteria result in alteration in the levels of certain microbial and host co-metabolites, identifying these markers could enhance early detection of diseases. Also, identification of these metabolic fingerprints could give us clues as to how to manipulate the microbiome to promote health or treat diseases. This review provides an overview of our current knowledge of the microbiome and metablomics, applications and the future perspectives.

Current Perspectives on Antihypertensive Probiotics.

Hypertension is a major risk factor for cardiovascular diseases. Optimizing blood pressure results in an overall health outcome. Over the years, the gut microbiota has been found to play a significant role in host metabolic processes, immunity, and physiology. Dietary strategies have therefore become a target for restoring disturbed gut microbiota to treat metabolic diseases. Probiotics and their fermented products have been shown in many studies to lower blood pressure by suppressing nitrogen oxide production in microphages, reducing reactive oxygen species, and enhancing dietary calcium absorption. Other studies have shown that hypertension could be caused by many factors including hypercholesterolemia, chronic inflammation, and inconsistent modulation of the renin-angiotensin system. This review discusses the antihypertensive roles of probiotics and their fermented products via the reduction of serum cholesterol levels, anti-inflammation, and inhibition of angiotensin-converting enzyme. The ability of recombinant probiotics to reduce high blood pressure has also been discussed.

Development of highly sensitive electrochemical genosensor based on multiwalled carbon nanotubes-chitosan-bismuth and lead sulfide nanoparticles for the detection of pathogenic Aeromonas.

In this paper, we reported the construction of new high sensitive electrochemical genosensor based on multiwalled carbon nanotubes-chitosan-bismuth complex (MWCNT-Chi-Bi) and lead sulfide nanoparticles for the detection of pathogenic Aeromonas. Lead sulfide nanoparticles capped with 5'-(NH2) oligonucleotides thought amide bond was used as signalizing probe DNA (sz-DNA) and thiol-modified oligonucleotides sequence was used as fixing probe DNA (fDNA). The two probes hybridize with target Aeromonas DNA (tDNA) sequence (fDNA-tDNA-szDNA). The signal of hybridization is detected by differential pulse voltammetry (DPV) after electrodeposition of released lead nanoparticles (PbS) from sz-DNA on the surface of glass carbon electrode decorated with MWCNT-Chi-Bi, which improves the deposition and traducing electrical signal. The optimization of incubation time, hybridization temperature, deposition potential, deposition time and the specificity of the probes were investigated. Our results showed the highest sensibility to detect the target gene when compared with related biosensors and polymerase chain reaction (PCR). The detection limit for this biosensor was 1.0×10(-14) M. We could detect lower than 10(2) CFU mL(-1) of Aeromonas in spiked tap water. This method is rapid and sensitive for the detection of pathogenic bacteria and would become a potential application in biomedical diagnosis, food safety and environmental monitoring.

The perspective on cholesterol-lowering mechanisms of probiotics.

The use of probiotics as food components combats not only cardiovascular diseases but also many gastrointestinal tract disorders. Their health benefits along with their increased global market have interested scientists for better formulation and appropriate administration to the consumers. However, the lack of clear elucidation of their cholesterol-lowering mechanisms has complicated their proper dosage and administration to the beneficiaries. In this review, proposed mechanisms of cholesterol reduction such as deconjugation of bile via bile salt hydrolase activity, binding of cholesterol to probiotic cellular surface and incorporation into their cell membrane, production of SCFAs from oligosaccharides, coprecipitation of cholesterol with deconjugated bile, and cholesterol conversion to coprostanol have been discussed. Also, hypocholesterolemic effects on human- and animal-trial results, commonly used probiotics and synbiotics with effect on serum cholesterol regulation, types of bile salt hydrolase genes, and substrate specificities have been discussed.

Enhanced conidial thermotolerance and field efficacy of Beauveria bassiana by saccharides.

Insecticide efficacy of Beauveria bassiana conidia was improved by optimizing the concentrations of conidial heat-protective saccharides (glucose, sucrose, maltose, trehalose, α-lactose, and mannitol) using response surface methodology. Two field trials in tea gardens were carried out to control leafhopper (Empoasca vitis) by spraying B. bassiana conidia together with the optimized saccharides (0.26 g glucose, 0.28 g lactose, 0.24 g mannitol per ml). In the field studies, B. bassiana conidia were applied to control Empoasca vitis with and without saccharides and compared with bifenthrin, a pyrethroid insecticide. With the optimal concentrations of saccharides, the conidial germination rate reached 72% and the control efficacy of the saccharides group (65.7%) was equal to the bifenthrin group (69.4%), which improved by about 55%.

Enhanced production techniques, properties and uses of coenzyme Q10.

Coenzyme Q10 (CoQ10) is an essential component of the respiratory chain which produces ATP. It is formed from the conjugation of a benzoquinone ring with a hydrophobic isoprenoid chain. Efforts on the production of CoQ10 by microorganisms focus on the development of potent strains by conventional mutagenesis and metabolic engineering especially in Escherichia coli, analysis and modification of the key metabolic pathways and optimization of fermentation strategies. CoQ10 has excellent antioxidant properties and is beneficial in the treatment of several human diseases. The present review covers the current strategies used to improve and/or engineer CoQ10 production in microbes, the yields obtained in light of the current knowledge on the biosynthesis of this molecule. It also highlights the medical effects of CoQ10.

Thermostability of Probiotics and Their α -Galactosidases and the Potential for Bean Products.

Soybeans and other pulses contain oligosaccharides which may cause intestinal disturbances such as flatulence. This study was undertaken to investigate α -galactosidase-producing probiotics added to frozen foods which can survive warming treatments used in thawing and consumption of the pulses. The maximum α -galactosidase activity (1.26 U/mg protein) was found in Bifidobacterium breve S46. Lactobacillus casei had the highest α -galactosidase thermostability among the various strains, with D values of 35, 29, and 9.3 minutes at 50°C, 55°C, and 60°C, respectively. The enzyme activity was less affected than viable cells by heating. However, the D values of two bacterial enzymes were lower than those of three commercial α -galactosidase-containing products. Freshly grown cells and their enzymes were more stable than the rehydrated cultures and their enzymes. Practical Application. Enzymes and cultures can be added to foods in order to enhance the digestibility of carbohydrates in the gastrointestinal tract. However since many foods are warmed, it is important that the thermostability of the enzymes be assessed. This paper provides data on the stability of α -galactosidase, which could potentially be added to food matrices containing stachyose or raffinose, such as beans.

Expression and characterization of an extremely thermostable ß-glycosidase (mannosidase) from the hyperthermophilic archaeon Pyrococcus furiosus DSM3638.

Genomic analysis of the hyperthermophilic archaeon Pyrococcus furiosus revealed the presence of an open reading frame (ORF PF0356) similar to the enzymes in glycoside hydrolase family 1. This ß-glycosidase, designated PFTG (P. furiosus thermostable glycosidase), was cloned and expressed in Escherichia coli. The expressed enzyme was purified by heat treatment and Ni-NTA affinity chromatography. The gene was composed of 1,452 bp encoding 483 amino acids for a protein with a predicted molecular mass of 56,326 Da. The temperature and pH optima were 100°C and 5.0 in sodium citrate buffer, respectively. The substrate specificity of PFTG suggests that it possesses characteristics of both ß-galactosidase and ß-mannosidase activities. However, through kinetic studies by ITC (Isothermal Titration Colorimetry) which is very sensitive method for enzyme kinetics, PF0356 enzyme revealed the highest catalytic efficiency toward p-nitrophenyl-ß-d-mannopyranoside (3.02 k(cat)/K(m)) and mannobiose (4.32 k(cat)/K(m)). The enzyme showed transglycosylation and transgalactosylation activities toward cellobiose, lactose and mannooligosaccharides that could produce GOS (galactooligosaccharides) and MOS (maltooligosaccharides). This novel hyperthermostable ß-glycosidase may be useful for food and pharmaceutical applications.

Recombinant protein production in a variety of Nicotiana hosts: a comparative analysis.

Although many different crop species have been used to produce a wide range of vaccines, antibodies, biopharmaceuticals and industrial enzymes, tobacco has the most established history for the production of recombinant proteins. To further improve the heterologous protein yield of tobacco platforms, transient and stable expression of four recombinant proteins (i.e. human erythropoietin and interleukin-10, an antibody against Pseudomonas aeruginosa, and a hyperthermostable α-amylase) was evaluated in numerous species and cultivars of Nicotiana. Whereas the transient level of recombinant protein accumulation varied significantly amongst the different Nicotiana plant hosts, the variety of Nicotiana had little practical impact on the recombinant protein concentration in stable transgenic plants. In addition, this study examined the growth rate, amount of leaf biomass, total soluble protein levels and the alkaloid content of the various Nicotiana varieties to establish the best plant platform for commercial production of recombinant proteins. Of the 52 Nicotiana varieties evaluated, Nicotiana tabacum (cv. I 64) produced the highest transient concentrations of recombinant proteins, in addition to producing a large amount of biomass and a relatively low quantity of alkaloids, probably making it the most effective plant host for recombinant protein production.