Designing probiotics with respect to the native microbiome

Early cryptococcosis infection in a liver transplant patient: A case report

Key Clinical Message

In order to early diagnose and prevent the infection dissemination in both suspected solid organ donors and recipients after transplantation, pretransplantation screening tests for rare etiologies like Cryptococcus neoformans should be necessitated, as they can affect many vital organs, especially the brain, liver, and lungs.

Abstract

Cryptococcosis is a systemic fungal infection mainly affecting immunocompromised patients. The infection is occasionally seen in 16-21 months after organ transplantation, while early involvement is uncommon within <30 days posttransplantation. In the present study, we reported an unusual case of cryptococcosis infection 21 days after transplantation, limited to the transplanted liver in a 60-year-old male. Treatment with an antifungal agent showed prompt improvement in his clinical condition.

Bugs as Drugs: Understanding the Linkage between Gut Microbiota and Cancer Treatment Microbiome in Cancer Therapy

BACKGROUND

The commensal microbiota is known to regulate host physiology. Dysbiosis or compromised Resilience in the microbial ecology is related to the impending risk of cancer. A potential link between cancer and microbiota is indicated by a lot of evidence.

OBJECTIVE

The current review explores in detail the various links leading to and /or facilitating oncogenesis, providing sound reasoning or a basis for its utilization as potential therapeutic targets. The present review emphasizes the existing knowledge of the microbiome in cancer and further elaborates on the factors like genetic modifications, effects of dietary components, and environmental agents that are considered to assess the direct and indirect effect of microbes in the process of oncogenesis and on the host's health. Strategies modulating the microbiome and novel biotherapeutics are also discussed. Pharmacomicrobiomics is one such niche accounting for the interplay between the microbiome, xenobiotic, and host responses is also looked upon.

METHODS

The literature search strategy for this review was conducted by following the methodology of the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA). The method includes the collection of data from different search engines like PubMed, ScienceDirect, SciFinder etc. to get coverage of relevant literature for accumulating appropriate information regarding microbiome, cancer, and their linkages.

RESULTS

These considerations are made to expand the existing literature on the role of gut microbiota on the host's health, the interaction between host and microbiota, and the reciprocal relationship between the microbiome and modified neoplastic cells.

CONCLUSION

Potential therapeutic implications of cancer microbiomes that are yet unexplored and have rich therapeutic dividends improving human health are discussed in detail in this review.

Next-generation probiotics: a promising approach towards designing personalized medicine

Second brain, forgotten organ, individual's identity card, and host's fingerprint are the few collective terms that are often used to describe the gut microbiome because of its variability, accountability, and its role in deciding the host's health. Also, the understanding of this host health-gut microbiota relationship can create an opportunity to control an individual's health by manipulating the gut microbiota composition. Several approaches like administration of probiotic, prebiotics, synbiotics, faecal microbiota transplantation have been tried to mitigate the dysbiosis originated ill effects. But the effects of these approaches are highly generic and non-specific. This creates the necessity to design personalized medicine that focuses on treatment of specific disease considering the individual specific gut microbiome. The health promoting commensals could be the new promising prophylactic and therapeutic agents for designing personalized medicine. These commensals are designated as next-generation probiotics (NGPs) and their unusual characteristics, unknown identity and special growth requirements have presented difficulties for researcher, industrial exploitation, and regulatory agencies. In this perspective, this review discusses the concept of NGPs, NGP candidates as tool for designing personalized medicine, designer probiotics as NGPs, required regulatory framework, and propose a road map to develop the NGP based product.

The effects of microgravity on the digestive system and the new insights it brings to the life sciences

BACKGROUND

Weightlessness is a component of the complex space environment. It exerts adverse effects on the human body, and may pose unknown challenges to the implementation of space missions. The regular function of the digestive system is an important checkpoint for astronauts to conduct missions. Simulated microgravity can recreate the changes experienced by the human body in a weightless environment in space to a certain extent, providing technical support for the exploration of its mechanism and a practical method for other scientific research.

METHODS AND MATERIALS

In the present study, we reviewed and discussed the latest research on the effects of weightlessness or simulated microgravity on the digestive system, as well as the current challenges and future expectations for progress in medical science and further space exploration.

RESULTS

A series of studies have investigated the effects of weightlessness on the human digestive system. On one hand, weightlessness and the changing space environment may exert certain adverse effects on the human body. Studies based on cells or animals have demonstrated the complex effects on the human digestive system in response to weightlessness. On the other hand, a microgravity environment also facilitates the ideation of novel concepts for research in the domain of life science.

CONCLUSION

The effects of weightlessness on the digestive system are considerably complicated. The emergence of methods that help simulate a weightless environment provides a more convenient alternative for assessing the impact and the mechanism underlying the effect of weightlessness on the human body. In addition, the simulated microgravity environment facilitates the ideation of novel concepts for application in regenerative medicine and other fields of life science.

Prophylactic effects of secretion metabolites of dairy lactobacilli through downregulation of ErbB-2 and ErbB-3 genes on colon cancer cells

Colon cancer is one of the most prevalent cancers, and intestinal microbial community plays a pivotal role in colorectal tumor genesis. Probiotics as live microorganisms may be able to exert an anticancer effect in colon cancer. The aim of this study was to isolate and identify Lactobacillus spp. from traditional dairy products with probiotic properties and to investigate their anticancer effects through ErbB-2 and ErbB-3 gene expression in colon cancer cells. The isolated lactobacilli from yogurt and cheese samples were molecularly identified by blasting of 16-23s rDNA region PCR sequenced products. The probiotic properties, including acid and bile tolerance, antimicrobial activity, and antibiotic susceptibility, were assayed. The proliferation inhibition effects of lactobacilli secretion metabolites with probiotic potential on colon cancer cell lines (HT-29 and caco-2) were analyzed using MTT assay. The real-time PCR was used for assessment of ErbB-2 and ErbB-3 gene expression after being treated with probiotics. Four species of bacteria with the most probiotic properties, including Lactobacillus casei, Lactobacillus paracasei, Lactobacillus rhamnosus, and Lactobacillus plantarum, were characterized and their effects on different human cell lines were taken into consideration. Total bacterial secretions significantly reduced the viability of HT-29 and caco-2 cancer cells compared with untreated controls. The metabolites secreted by bacteria downregulated the expression of ErbB-2 and ErbB-3 genes in colon cancer cells. The present study indicated that probiotic bacteria isolated from traditional dairy products exert anticancer effect on colon cancer cells through the downregulation of ErbB-2 and ErbB-3 gene expression.

Probiotics, mechanisms of action, and clinical perspectives for diarrhea management in children

Infectious diarrhea is the second most common cause of morbidity and mortality in children under 5 years of age in the underdeveloped areas of the world. Conventional treatment consists of rehydration, which may be coupled with antimicrobial agents in more severe bacterial infections or with antiprotozoal agents. In the last few decades, research on the use of probiotic strains, such as Lactobacillus rhamnosus GG ATCC 53013 (LGG), Lactobacillus reuteri DSM 17938 and Saccharomyces boulardii, has gained much attention to prevent and treat diarrheal diseases. However, they are rarely used in the clinical routine, perhaps because there are still gaps in the knowledge about the effective benefit to the patient in terms of the reduction of the duration of diarrhea and its prevention. Furthermore, only a few probiotic strains are safely indicated for usage in pediatric practice. This review summarizes the current knowledge on the antimicrobial mechanisms of probiotics on distinct enteropathogens and their role in stimulating host defense mechanisms against intestinal infections. In addition, we highlight the potential of probiotics for the treatment and prevention of diarrhea in children. We conclude that the use of probiotics is beneficial for both the treatment and prevention of diarrhea in children and that the identification of other candidate probiotics might represent an important advance to a greater reduction in hospital stays and to prevent infectious diarrhea in a larger portion of this population.

Molecular Identification and Probiotic Potential Characterization of Lactic Acid Bacteria Isolated from Human Vaginal Microbiota

Purpose: The increased demand for probiotics because of their health purposes provides the context for this study, which involves the molecular identification of lactic acid bacteria (LAB) obtained from the vaginal microbiota of healthy fertile women. The isolates were subjected for examination to prove their probiotic potential. In particular, the isolates were subjected to various tests, including acid/bile tolerance, antimicrobial activity, antibiotic susceptibility, Gram staining, and catalase enzyme activity assessment. Methods: Several methods were utilized for the molecular identification of the isolates, including ARDRA, (GTG)5-PCR fingerprinting, and the PCR sequencing of 16S-rDNA amplified fragments. Disc diffusion and well diffusion methods were used to assess antibiotic susceptibility and antibacterial activity of isolates. Tolerance to acid and bile was performed at pH 2.5 and 0.3% bile oxgall. Results: A total of 45 isolates of 88 separate organisms was selected. All of the isolates demonstrated an antibacterial effect on the exploited indicator microorganisms. All selected strains also maintained their viability at low-pH and high-bile salt conditions and exhibited abroad variation in their survival. Only the Enterococcus avium strain showed resistance to all 9 tested antibiotics. Based on the molecular identification and clustering, the 45 isolated bacteria were classified into three major groups of LAB: Enterococcus, Lactobacillus and Lactococcus. Conclusion: LAB are microorganisms that have a particularly important function in maintaining the health of the vaginal and gastrointestinal tract and in protecting it from infection by other pathogenic organisms. The isolates found to be a promising probiotic candidate by showed desirable characteristics. Therefore, strain DL3 can be used as natural food preservative with some more potential investigations.

Intestinal microbiota contributes to colonic epithelial changes in simulated microgravity mouse model

Exposure to microgravity leads to alterations in multiple systems, but microgravity-related changes in the gastrointestinal tract and its clinical significance have not been well studied. We used the hindlimb unloading (HU) mouse model to simulate a microgravity condition and investigated the changes in intestinal microbiota and colonic epithelial cells. Compared with ground-based controls (Ctrls), HU affected fecal microbiota composition with a profile that was characterized by the expansion of Firmicutes and decrease of Bacteroidetes. The colon epithelium of HU mice showed decreased goblet cell numbers, reduced epithelial cell turnover, and decreased expression of genes that are involved in defense and inflammatory responses. As a result, increased susceptibility to dextran sulfate sodium-induced epithelial injury was observed in HU mice. Cohousing of Ctrl mice with HU mice resulted in HU-like epithelial changes in Ctrl mice. Transplantation of feces from Ctrl to HU mice alleviated these epithelial changes in HU mice. Results indicate that HU changes intestinal microbiota, which leads to altered colonic epithelial cell homeostasis, impaired barrier function, and increased susceptibility to colitis. We further demonstrate that alteration in gastrointestinal motility may contribute to HU-associated dysbiosis. These animal results emphasize the necessity of evaluating astronauts' intestinal homeostasis during distant space travel.-Shi, J., Wang, Y., He, J., Li, P., Jin, R., Wang, K., Xu, X., Hao, J., Zhang, Y., Liu, H., Chen, X., Wu, H., Ge, Q. Intestinal microbiota contributes to colonic epithelial changes in simulated microgravity mouse model.

Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing

Prebiotics are selectively fermentable dietary compounds that result in changes in the composition and/or activity of the intestinal microbiota, thus conferring benefits upon host health. In veterinary medicine, commercially available products containing prebiotics have not been well studied with regard to the changes they trigger on the composition of the gut microbiota. This study evaluated the effect of a commercially available nutraceutical containing fructo-oligosaccharides (FOS) and inulin on the fecal microbiota of healthy cats and dogs when administered for 16 days. Fecal samples were collected at two time points before and at two time points during prebiotic administration. Total genomic DNA was obtained from fecal samples and 454-pyrosequencing was used for 16S rRNA gene bacterial profiling. The linear discriminant analysis (LDA) effect size (LEfSe) method was used for detecting bacterial taxa that may respond (i.e., increase or decrease in its relative abundance) to prebiotic administration. Prebiotic administration was associated with a good acceptance and no side effects (e.g., diarrhea) were reported by the owners. A low dose of prebiotics (50 mL total regardless of body weight with the end product containing 0.45% of prebiotics) revealed a lower abundance of Gammaproteobacteria and a higher abundance of Veillonellaceae during prebiotic administration in cats, while Staphylococcaceae showed a higher abundance during prebiotic administration in dogs. These differences were not sufficient to separate bacterial communities as shown by analysis of weighted UniFrac distance metrics. A predictive approach of the fecal bacterial metagenome using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) also did not reveal differences between the period before and during prebiotic administration. A second trial using a higher dose of prebiotics (3.2 mL/kg body weight with the end product containing 3.1% of prebiotics) was tested in dogs and revealed a lower abundance of Dorea (family Clostridiaceae) and a higher abundance of Megamonas and other (unknown) members of Veillonellaceae during prebiotic administration. Again, these changes were not sufficient to separate bacterial communities or predicted metabolic profiles according to treatment. A closer analysis of bacterial communities at all time-points revealed highly individualized patterns of variation. This study shows a high interindividual variation of fecal bacterial communities from pet cats and dogs, that these communities are relatively stable over time, and that some of this variation can be attributable to prebiotic administration, a phenomenon that may be affected by the amount of the prebiotic administered in the formulation. This study also provides insights into the response of gut bacterial communities in pet cats and dogs during administration of commercially available products containing prebiotics. More studies are needed to explore potentially beneficial effects on host health beyond changes in bacterial communities.

Engineered Probiotics: Applications and Biological Containment

Bioengineered probiotics represent the next generation of whole cell-mediated biotherapeutics. Advances in synthetic biology, genome engineering, and DNA sequencing and synthesis have enabled scientists to design and develop probiotics with increased stress tolerance and the ability to target specific pathogens and their associated toxins, as well as to mediate targeted delivery of vaccines, drugs, and immunomodulators directly to host cells. Herein, we review the most significant advances in the development of this field. We discuss the critical issue of biological containment and consider the role of synthetic biology in the design and construction of the probiotics of the future.

The search for a promising cell factory system for production of edible vaccine

Despite worldwide vaccination against devastating diseases for decades, millions of children in remote and impoverished regions of the globe die every year from vaccine-preventable infectious diseases. The reasons for incomplete coverage of vaccination programs are based in part on the relatively high costs of conventional vaccinations, including mass production, refrigeration, transportation, and training as well as funding personnel for their administration. Plant-based edible vaccines (PEVs) have been introduced as a revolutionary cost-effective vaccination modality. However, they suffer from major deficiencies that have restricted their application to bench-scale. This article discusses the deficiencies of PEVs and also provides concise overview on the health-promoting, biological and biotechnological features of spirulina (Arthrospira). In short, we envision that spirulina could be considered as a potential alternative biofactory system to the plants toward the production of edible vaccines in high-yield with low-costs that other hosts cannot yet offer.

Probiotic assessment of Enterococcus durans 6HL and Lactococcus lactis 2HL isolated from vaginal microflora

Forty-five lactic acid bacteria (LAB) were isolated from the vaginal specimens of healthy fertile women, and the identities of the bacteria were confirmed by sequencing of their 16S rDNA genes. Among these bacteria, only four isolates were able to resist and survive in low pH, bile salts and simulated in vitro digestion conditions. Lactococcus lactis 2HL, Enterococcus durans 6HL, Lactobacillus acidophilus 36YL and Lactobacillus plantarum 5BL showed the best resistance to these conditions. These strains were evaluated further to assess their ability to adhere to human intestinal Caco-2 cells. Lactococcus lactis 2HL and E. durans 6HL were the most adherent strains. In vitro tests under neutralized pH proved the antimicrobial activity of both strains. Results revealed that the growth of Escherichia coli O26, Staphylococcus aureus and Shigella flexneri was suppressed by both LAB strains. The antibiotic susceptibility tests showed that these strains were sensitive to all nine antibiotics: vancomycin, tetracycline, ampicillin, penicillin, gentamicin, erythromycin, clindamycin, sulfamethoxazole and chloramphenicol. These data suggest that E. durans 6HL and Lactococcus lactis 2HL could be examined further for their useful properties and could be developed as new probiotics.

Probiotic potential and biotherapeutic effects of newly isolated vaginal Lactobacillus acidophilus 36YL strain on cancer cells

Lactobacillus acidophilus is categorized as a probiotic strain because of its beneficial effects in human health and prevention of disease transmission. This study is aimed to characterize the probiotic potential of L. acidophilus 36YL originally isolated from the vagina of healthy and fertile Iranian women. The L. acidophilus 36YL strain was identified using 16S rDNA gene sequencing and characterized by biochemical methodologies, such as antibiotics susceptibility, antimicrobial activity, and acid and bile resistance. The bioactivity of the secretion of this strain on four human cancer cell lines (AGS, HeLa, MCF-7, and HT-29) and one normal cell line (HUVEC) was evaluated by cytotoxicity assay and apoptosis analysis. This newly isolated strain was found to exhibit notable probiotic properties, such as admirable antibiotic susceptibility, good antimicrobial activity, and favorable resistance to acid and bile salt. The results of bioactivity assessment demonstrated acceptable anticancer effects on the four tested cancer cell lines and negligible side effects on the assayed normal cell line. Our findings revealed that the anticancer effect of L. acidophilus 36YL strain secretions depends on the induction of apoptosis in cancer cells. L. acidophilus 36YL strain is considered as a nutraceutical alternative or a topical medication with a potential therapeutic index because of the absence of cytotoxicity to normal cells, but effective toxicity to cancer cell lines.

Lactobacillus with probiotic potential from homemade cheese in Azerbijan

INTRODUCTION

Lactobacillus is believed to be beneficial in human health, thus the search for isolation and identification of friendly human bacteria from traditional fermented foods is important in medicine. One of the dairy products, traditional cheese as a highly-consumed dairy product could be a valuable source of these friendly edible germs.

METHODS

In this research, home-made cheese from Lankaran, Jalil Abad and Salian regions in Azerbaijan was characterized for the presence of Lactobacilli with probiotic potential. The bacterial suspension was enriched and screened for acid and bile resistances. Then, the isolates were subjected to antibiotic resistance and antibacterial effects against convenient pathogenic bacteria. The isolates were identified by 16s rDNA sequencing.

RESULTS

The results clearly revealed two probiotics with higher homology to Lactobacillus planetarum and Lactobacillus fermentum.

CONCLUSION

No antibiotic resistance was detected in any of the potentially probiotic lactobacilli isolates in these regions, where people continue to follow a life-style that is largely traditional, with traditional medications.

Shrinkage of the human core microbiome and a proposal for launching microbiome biobanks

ABSTRACT: 

The Human Microbiome Project (HMP) revealed the significance of the gut microbiome in promoting health. Disruptions in microbiome composition are associated with the pathogenesis of numerous diseases. The indigenous microflora has co-evolved with humans for millions of years and humans have preserved the inherited microbiomes through consumption of fermented foods and interactions with environmental microbes. Through modernization, traditional foods were abandoned, native food starters were substituted with industrial products, vaccines and antibiotics were used, extreme hygiene measures were taken, the rate of cesarean section increased, and breast feeding changed into formula. These factors have reduced human exposure to microbial symbionts and led to shrinkage of the core microbiome. Reduction in microbiome biodiversity can compromise the human immune system and predispose individuals to several modern diseases. This article suggests launching microbiome biobanks for archiving native microbiomes, supervising antibiotic use, probiotic design and native starter production, as well as advertising a revisit to native lifestyles.

Bioengineered probiotics, a strategic approach to control enteric infections

Enteric infections account for high morbidity and mortality and are considered to be the fifth leading cause of death at all ages worldwide. Seventy percent of all enteric infections are foodborne. Thus significant efforts have been directed toward the detection, control and prevention of foodborne diseases. Many antimicrobials including antibiotics have been used for their control and prevention. However, probiotics offer a potential alternative intervention strategy owing to their general health beneficial properties and inhibitory effects against foodborne pathogens. Often, antimicrobial probiotic action is non-specific and non-discriminatory or may be ineffective. In such cases, bioengineered probiotics expressing foreign gene products to achieve specific function is highly desirable. In this review we summarize the strategic development of recombinant bioengineered probiotics to control enteric infections, and to examine how scientific advancements in the human microbiome and their immunomodulatory effects help develop such novel and safe bioengineered probiotics.

Adaptation of bifidobacteria to the gastrointestinal tract and functional consequences

Members of the genus Bifidobacterium are considered to be important constituents of the microbiota of animals, from insects to mammals. They are gut commensals extensively used by the food industry as probiotic microorganisms, since some strains have been shown to have specific beneficial effects. However, the molecular processes underlying their functional capacities to promote a healthy status in the host, as well as those involved in survival, colonization and persistence of bifidobacteria in the gut, are far from being completely understood. This review summarizes the current knowledge on the mechanisms used by bifidobacteria to cope with gastrointestinal factors and to adapt to them, and discusses the advantages of the adaptive traits acquired by these microorganisms as a consequence of their interactions with the gastrointestinal tract environment, as well as the impact of such adaptations in the functional characteristics of bifidobacteria.

The microbiome: the forgotten organ of the astronaut’s body – probiotics beyond terrestrial limits

Space medicine research has drawn immense attention toward provision of efficient life support systems during long-term missions into space. However, in extended missions, a wide range of diseases may affect astronauts. In space medicine research, the gastrointestinal microbiome and its role in maintaining astronauts’ health has received little attention. We would like to draw researchers’ attention to the significant role of microbiota. Because of the high number of microorganisms in the human body, man has been called a ‘supra-organism’ and gastrointestinal flora has been referred to as ‘a virtual organ of the human body’. In space, the lifestyle, sterility of spaceship and environmental stresses can result in alterations in intestinal microbiota, which can lead to an impaired immunity and predispose astronauts to illness. This concern is heightened by increase in virulence of pathogens in microgravity. Thus, design of a personal probiotic kit is recommended to improve the health status of astronauts.

Screening and genetic manipulation of green organisms for establishment of biological life support systems in space

Curiosity has driven humankind to explore and conquer space. However, today, space research is not a means to relieve this curiosity anymore, but instead has turned into a need. To support the crew in distant expeditions, supplies should either be delivered from the Earth, or prepared for short durations through physiochemical methods aboard the space station. Thus, research continues to devise reliable regenerative systems. Biological life support systems may be the only answer to human autonomy in outposts beyond Earth. For construction of an artificial extraterrestrial ecosystem, it is necessary to search for highly adaptable super-organisms capable of growth in harsh space environments. Indeed, a number of organisms have been proposed for cultivation in space. Meanwhile, some manipulations can be done to increase their photosynthetic potential and stress tolerance. Genetic manipulation and screening of plants, microalgae and cyanobacteria is currently a fascinating topic in space bioengineering. In this commentary, we will provide a viewpoint on the realities, limitations and promises in designing biological life support system based on engineered and/or selected green organism. Special focus will be devoted to the engineering of key photosynthetic enzymes in pioneer green organisms and their potential use in establishment of transgenic photobioreactors in space.