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1.
Sci Rep ; 11(1): 21480, 2021 11 02.
Article En | MEDLINE | ID: mdl-34728744

Atmospheric levels of pollutants may reduce the UVB intensity at the earth's surface, with a subsequent reduction in cutaneous vitamin D synthesis. We investigated the association of various pollutants with UVB intensity on the ground. Four-year data obtained from four weather stations from across Kuwait were analyzed by median regression. Pollutants that were negatively associated with UVB were [ß (95% CI)]: benzene [- 2.61 (- 4.13, - 1.09)], ethyl-benzene [- 2.20 (- 3.15, - 1.25)], ozone [- 0.23 (- 0.28, - 0.17)], nitric oxide [- 0.11 (- 0.15, - 0.06)], sulfur dioxide [- 0.10 (- 0.17, - 0.04)] and particulate matter PM10 [- 0.002 (- 0.003, - 0.002)]. Pollutants that were negatively associated with the UVB/UVA ratio were [ß (95% CI)]: benzene [- 15.57 (- 24.94, - 6.20)], nitric oxide [- 0.53 (- 0.81, - 0.25)], ozone [- 0.38 (- 0.70, - 0.06)], and total hydrocarbon [- 0.02 (- 0.04, - 0.01)]. Furthermore, benzene and nitric oxide levels were higher in the morning and evening hours, which are the times of most solar exposure in this region due to high temperature during midday. In addition to other known factors, attenuation of UVB by these pollutants may contribute to lower vitamin D levels in populations. In addition to direct public health hazard, these pollutants may contribute to the very high prevalence of VDD in this region.


Air Pollutants/adverse effects , Hot Temperature , Particulate Matter/adverse effects , Ultraviolet Rays , Vitamin D/biosynthesis , Weather , Benzene/analysis , Humans , Kuwait , Nitric Oxide/analysis , Nitrogen Dioxide/analysis , Ozone/analysis , Sulfur Dioxide/analysis , Vitamin D/radiation effects , Vitamins/biosynthesis , Vitamins/radiation effects
2.
Lab Chip ; 21(21): 4071-4080, 2021 10 26.
Article En | MEDLINE | ID: mdl-34618882

Microbial cells represent a standard production host for various important biotechnological products. Production yields can be increased by optimising strains and growth conditions and understanding deviations in production rates over time or within the microbial population. We introduce here microfluidic cultivation chambers for highly parallel studies on microbial cultures, enabling continuous biosynthesis monitoring of the industrially relevant product by Escherichia coli cells. The growth chambers are defined by ring-valves that encapsulate a volume of 200 pL when activated. Bacterial cells, labelled with magnetic beads, are inoculated in a small magnetic trap, positioned in the centre of each chamber. Afterwards, the ring-valves are partially activated, allowing for exchange reagents, such as the addition of fresh media or specific inducers of biosynthesis, while the bacterial cells and their progeny are maintained inside. On this platform, we monitor the production of riboflavin (vitamin B2). We used different variants of a riboflavin-overproducing bacterial strain with different riboflavin production levels and could distinguish them on the level of individual micro-colonies. In addition, we could also observe differences in the bacterial morphology with respect to the production. The presented platform represents a flexible microfluidic tool for further studies of microbial cell factories.


Escherichia coli , Microfluidics , Riboflavin/biosynthesis , Vitamins/biosynthesis , Culture Media , Escherichia coli/genetics , Industrial Microbiology
3.
Sci Rep ; 11(1): 19648, 2021 10 04.
Article En | MEDLINE | ID: mdl-34608200

The gut microbiota has tremendous potential to affect the host's health, in part by synthesizing vitamins and generating nutrients from food that is otherwise indigestible by the host. 1,5-Anhydro-D-fructose (1,5-AF) is a monosaccharide with a wide range of bioactive potentials, including anti-oxidant, anti-inflammatory, and anti-microbial effects. Based on its potential benefits and minimal toxicity, it is anticipated that 1,5-AF will be used as a dietary supplement to support general health. However, the effects of 1,5-AF on the gut microbiota are yet to be clarified. Here, using an unbiased metagenomic approach, we profiled the bacterial taxa and functional genes in the caecal microbiota of mice fed a diet containing either 2% 1,5-AF or a reference sweetener. Supplementation with 1,5-AF altered the composition of the gut microbiota, enriching the proportion of Faecalibacterium prausnitzii. 1,5-AF also altered the metabolomic profile of the gut microbiota, enriching genes associated with nicotinamide adenine dinucleotide biosynthesis. These findings support the potential benefits of 1,5-AF, but further studies are required to clarify the impact of 1,5-AF on health and disease.


Fructose/analogs & derivatives , Gastrointestinal Microbiome , Animals , Diet , Dietary Supplements , Fructose/metabolism , Fructose/pharmacology , Gastrointestinal Microbiome/drug effects , Metagenome , Metagenomics/methods , Mice , NAD/biosynthesis , Nutrients/biosynthesis , Vitamins/biosynthesis
4.
J Appl Microbiol ; 130(5): 1412-1424, 2021 May.
Article En | MEDLINE | ID: mdl-32955761

Lactic acid bacteria (LAB), widely used as starter cultures for the fermentation of a large variety of food, can improve the safety, shelf life, nutritional value and overall quality of the fermented products. In this regard, the selection of strains delivering health-promoting compounds is now the main objective of many researchers. Although most LAB are auxotrophic for several vitamins, it is known that certain strains have the capability to synthesize B-group vitamins. This is an important property since humans cannot synthesize most vitamins, and these could be obtained by consuming LAB fermented foods. This review discusses the use of LAB as an alternative to fortification by the chemical synthesis to increase riboflavin and folate concentrations in food. Moreover, it provides an overview of the recent applications of vitamin-producing LAB with anti-inflammatory/antioxidant activities against gastrointestinal tract inflammation. This review shows the potential uses of riboflavin and folates producing LAB for the biofortification of food, as therapeutics against intestinal pathologies and to complement anti-inflammatory/anti-neoplastic treatments.


Folic Acid/biosynthesis , Food, Fortified , Inflammatory Bowel Diseases/therapy , Lactobacillales/metabolism , Mucositis/therapy , Riboflavin/biosynthesis , Animals , Antioxidants/analysis , Fermentation , Fermented Foods , Folic Acid/analysis , Humans , Lactobacillales/isolation & purification , Riboflavin/analysis , Vitamins/analysis , Vitamins/biosynthesis
5.
Mol Plant ; 14(1): 40-60, 2021 01 04.
Article En | MEDLINE | ID: mdl-33271336

Micronutrient deficiencies include shortages of vitamins and minerals. They affect billions of people and are associated with long-range effects on health, learning ability, and huge economic losses. Biofortification of multiple micronutrients can play an important role in combating malnutrition. The challenge, however, is to balance plant growth with nutrient requirements for humans. Here, we summarize the major progress about vitamin biosynthesis and its response to the changing environment. We discuss the interactions among vitamins as well as possible strategies for vitamin biofortification. Finally, we propose to integrate new breeding technologies with metabolic pathway modification to facilitate the biofortification of crops, thereby alleviating the hidden hunger of target populations.


Biofortification , Hunger , Plants/metabolism , Vitamins/metabolism , Environment , Plant Breeding , Vitamins/biosynthesis
6.
Microb Cell Fact ; 19(1): 173, 2020 Sep 03.
Article En | MEDLINE | ID: mdl-32883293

Due to its clear inherited backgrounds as well as simple and diverse genetic manipulation systems, Bacillus subtilis is the key Gram-positive model bacterium for studies on physiology and metabolism. Furthermore, due to its highly efficient protein secretion system and adaptable metabolism, it has been widely used as a cell factory for microbial production of chemicals, enzymes, and antimicrobial materials for industry, agriculture, and medicine. In this mini-review, we first summarize the basic genetic manipulation tools and expression systems for this bacterium, including traditional methods and novel engineering systems. Secondly, we briefly introduce its applications in the production of chemicals and enzymes, and summarize its advantages, mainly focusing on some noteworthy products and recent progress in the engineering of B. subtilis. Finally, this review also covers applications such as microbial additives and antimicrobials, as well as biofilm systems and spore formation. We hope to provide an overview for novice researchers in this area, offering them a better understanding of B. subtilis and its applications.


Bacillus subtilis/genetics , Bacillus subtilis/metabolism , Biocompatible Materials/metabolism , Biological Products/metabolism , Industrial Microbiology , Bacterial Proteins/biosynthesis , Enzymes/biosynthesis , Gene Expression Regulation, Bacterial , Genetic Engineering/methods , Recombinant Proteins , Vitamins/biosynthesis
7.
Adv Exp Med Biol ; 1268: 319-331, 2020.
Article En | MEDLINE | ID: mdl-32918226

Sunlight, in particular UV-B radiation, is an important factor for endogenous vitamin D production as 80-90% of the required vitamin D needs to be photosynthesized in the skin. The active form of vitamin D, vitamin D3 or calcitriol, binds to the ligand-activated transcription factor vitamin D receptor (VDR) for genomic and non-genomic effects. Recently, calcitriol and analogs have been shown to have antiproliferative effects in mouse and human BCC and SCC cell lines in vitro. As UV radiation plays a critical role in the photosynthesis of vitamin D, stringent sun protection, as recommended for xeroderma pigmentosum (XP) patients, may impact their vitamin D levels.XP is a rare autosomal recessive disorder with a worldwide prevalence of 1 in 1,000,000. XP can be divided into seven different complementation groups: XP-A to XP-G. The complementation groups correspond with the underlying gene defect. Defects in these genes lead to a defective nucleotide excision repair (NER), which is necessary to remove UV-induced DNA damage such as the UV photoproducts cyclobutane pyrimidine dimers (CPD) and 6-4 pyrimidine-pyrimidone (6-4 PP) dimer. Additionally, a variant form with a mutation in the translational polymerase η gene (PolH), also called XP variant (XPV), exists. Patients with XPV show a defect in translesion synthesis. Due to their inability to repair UV-induced lesions, XP patients exhibit an increased risk for UV-induced nonmelanoma skin cancer (NMSC) such as basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) as well as melanoma. Although no curative therapy for XP exists today, numerous options for the treatment and prophylaxis of skin cancer have become available.


Sunlight , Vitamin D , Xeroderma Pigmentosum , Animals , Humans , Ultraviolet Rays , Vitamin D/biosynthesis , Vitamins/biosynthesis , Xeroderma Pigmentosum/genetics , Xeroderma Pigmentosum/metabolism
8.
mBio ; 11(4)2020 07 14.
Article En | MEDLINE | ID: mdl-32665271

We investigated the requirement of 15 human butyrate-producing gut bacterial strains for eight B vitamins and the proteinogenic amino acids by a combination of genome sequence analysis and in vitro growth experiments. The Ruminococcaceae species Faecalibacterium prausnitzii and Subdoligranulum variabile were auxotrophic for most of the vitamins and the amino acid tryptophan. Within the Lachnospiraceae, most species were prototrophic for all amino acids and several vitamins, but biotin auxotrophy was widespread. In addition, most of the strains belonging to Eubacterium rectale and Roseburia spp., but few of the other Lachnospiraceae strains, were auxotrophic for thiamine and folate. Synthetic coculture experiments of five thiamine or folate auxotrophic strains with different prototrophic bacteria in the absence and presence of different vitamin concentrations were carried out. This demonstrated that cross-feeding between bacteria does take place and revealed differences in cross-feeding efficiency between prototrophic strains. Vitamin-independent growth stimulation in coculture compared to monococulture was also observed, in particular for F. prausnitzii A2-165, suggesting that it benefits from the provision of other growth factors from community members. The presence of multiple vitamin auxotrophies in the most abundant butyrate-producing Firmicutes species found in the healthy human colon indicates that these bacteria depend upon vitamins supplied from the diet or via cross-feeding from other members of the microbial community.IMPORTANCE Microbes in the intestinal tract have a strong influence on human health. Their fermentation of dietary nondigestible carbohydrates leads to the formation of health-promoting short-chain fatty acids, including butyrate, which is the main fuel for the colonic wall and has anticarcinogenic and anti-inflammatory properties. A good understanding of the growth requirements of butyrate-producing bacteria is important for the development of efficient strategies to promote these microbes in the gut, especially in cases where their abundance is altered. The demonstration of the inability of several dominant butyrate producers to grow in the absence of certain vitamins confirms the results of previous in silico analyses. Furthermore, establishing that strains prototrophic for thiamine or folate (butyrate producers and non-butyrate producers) were able to stimulate growth and affect the composition of auxotrophic synthetic communities suggests that the provision of prototrophic bacteria that are efficient cross feeders may stimulate butyrate-producing bacteria under certain in vivo conditions.


Bacteria/genetics , Butyrates/metabolism , Fermentation , Microbiota , Vitamins/biosynthesis , Bacteria/metabolism , Clostridiales/genetics , Clostridiales/physiology , Colon/microbiology , Faecalibacterium prausnitzii/genetics , Faecalibacterium prausnitzii/physiology , Humans , Ruminococcus/genetics , Ruminococcus/physiology
9.
J Sci Food Agric ; 100(14): 5230-5238, 2020 Nov.
Article En | MEDLINE | ID: mdl-32519367

BACKGROUND: Black sweet corn as an edible fruit has various nutritional qualities. This study discusses changes in the vitamin C and E, folate, and carotenoid content during black sweet corn maturation, and also the effects of preharvest weather conditions and of related genes in multi-vitamin biosynthesis pathways. RESULTS: Most vitamin levels improved, especially vitamin C and carotenoid levels, while the folate content dropped rapidly. Transcript levels of most genes in folate biosynthesis showed trends that were similar to the content changes. VTC2 and GLDH, which are regulated by light, had high expression levels leading to an increase in ascorbate content during maturation. γ-Tocotrienol is the main vitamin E component, and HGGT, the key gene controlling the synthesis of tocotrienols, had a much higher expression level than other genes. Lutein and zeaxanthin were the dominant carotenoid components. A rapid reduction in the transcription level of LCYε could result in a lower lutein production rate . CONCLUSION: Black sweet corn has a high nutritional value and is rich in vitamins, including zeaxanthin, γ-tocotrienols, and ascorbic acid. The best harvest time is between 20-25 days after pollination (DAPs) when kernels had a good taste as well as relatively high vitamin levels. © 2020 Society of Chemical Industry.


Seeds/growth & development , Vitamins/biosynthesis , Zea mays/metabolism , Carotenoids/analysis , Carotenoids/metabolism , Color , Lutein/analysis , Lutein/metabolism , Seeds/chemistry , Seeds/metabolism , Tocotrienols/analysis , Tocotrienols/metabolism , Vitamins/analysis , Zea mays/chemistry , Zea mays/growth & development , Zeaxanthins/analysis , Zeaxanthins/metabolism
10.
FEMS Microbiol Lett ; 367(9)2020 05 01.
Article En | MEDLINE | ID: mdl-32275307

Lactic acid bacteria (LAB) can be used to increase the folate in foods by in situ fortification. Seventy LAB were screened for their ability to produce folate during growth in de Man, Rogosa and Sharpe/M17 broth. Lactobacillus casei, Lactobacillus plantarum, Lactobacillus paracasei subsp. paracasei, Lactobacillus rhamnosus, Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus, Lactococcus lactis subsp. lactis, Enterococcus faecium and Enterococcus lactis were able to synthetize folates in the medium, even if to a different extent. The 47 folate-producing strains were further analyzed by microbiological assay, for total, extra and intracellular folate. Enterococcus faecium VC223 and E. lactis BT161 were able to produce in cultural medium 123,625.74 ± 8.00 ng/ml and 384.22 ± 5.00 ng/ml of folate, respectively. Five strains were further examined for their ability to synthesize folate in cheese. The folate content increased with ripening up to by 54% after 30 d when L. casei VC199 was used and up to 108% and 113% after 60 d, with L. paracasei SE160 and E. lactis BT161 respectively exceeding 100 ng/100g. Results encourage the use of specific LAB to obtain natural folate bio-enriched dairy products improving folate intake.


Cheese/microbiology , Folic Acid/biosynthesis , Food Microbiology , Lactobacillales/growth & development , Lactobacillales/metabolism , Enterococcus/growth & development , Enterococcus/metabolism , Lactobacillales/isolation & purification , Lactobacillus/growth & development , Lactobacillus/metabolism , Lactococcus/growth & development , Lactococcus/metabolism , Streptococcus/growth & development , Streptococcus/metabolism , Vitamins/biosynthesis
11.
Appl Microbiol Biotechnol ; 104(8): 3331-3337, 2020 Apr.
Article En | MEDLINE | ID: mdl-32112134

Recent studies have shown that inflammatory diseases are becoming more frequent throughout the world. The causes of these disorders are multifactorial and include genetic, immunological, and environmental factors, and intestinal microbiota dysbiosis. The use of beneficial microorganisms has shown to be useful in the prevention and treatment of disorders such as colitis, mucositis, and even colon cancer by their immune-stimulating properties. It has also been shown that certain vitamins, especially riboflavin and folate derivatives, have proven to be helpful in the treatment of these diseases. The application of vitamin-producing lactic acid bacteria, especially strains that produce folate and riboflavin together with immune-stimulating strains, could be used as adjunct treatments in patients suffering from a wide range of inflammatory diseases since they could improve treatment efficiency and prevent undesirable side effects in addition to their nutrition values. In this review, the most up to date information on the current knowledge and uses of vitamin-producing lactic acid bacteria is discussed in order to stimulate further studies in this field.


Inflammation/therapy , Inflammatory Bowel Diseases/therapy , Lactobacillales/metabolism , Probiotics/therapeutic use , Vitamins/biosynthesis , Animals , Anti-Inflammatory Agents/therapeutic use , Clinical Trials as Topic , Colitis/drug therapy , Folic Acid/biosynthesis , Humans , Inflammation/complications , Inflammatory Bowel Diseases/classification , Riboflavin/biosynthesis , Vitamin K
12.
Chem Commun (Camb) ; 56(18): 2787-2790, 2020 Mar 03.
Article En | MEDLINE | ID: mdl-32025667

Expanding the catalytic repertoire of ribozymes to include vitamin synthesis requires efficient labelling of RNA with the substrate of interest, prior to in vitro selection. For this purpose, we rationally designed and synthesized six GMP-conjugates carrying a synthetic pre-thiamine or biotin precursor and investigated their transcription incorporation properties by T7 RNA polymerase.


DNA-Directed RNA Polymerases/metabolism , Guanosine Monophosphate/biosynthesis , Viral Proteins/metabolism , Vitamins/biosynthesis , Biocatalysis , Biotin/chemistry , Biotin/metabolism , Guanosine Monophosphate/chemistry , Molecular Structure , Thiamine/chemistry , Thiamine/metabolism , Vitamins/chemistry
13.
Sci Rep ; 10(1): 652, 2020 01 20.
Article En | MEDLINE | ID: mdl-31959775

The keystone zooplankton Daphnia magna has recently been used as a model system for understanding host-microbiota interactions. However, the bacterial species present and functions associated with their genomes are not well understood. In order to understand potential functions of these species, we combined 16S rRNA sequencing and shotgun metagenomics to characterize the whole-organism microbiota of Daphnia magna. We assembled five potentially novel metagenome-assembled genomes (MAGs) of core bacteria in Daphnia magna. Genes involved in host colonization and immune system evasion were detected across the MAGs. Some metabolic pathways were specific to some MAGs, including sulfur oxidation, nitrate reduction, and flagellar assembly. Amino acid exporters were identified in MAGs identified as important for host fitness, and pathways for key vitamin biosynthesis and export were identified across MAGs. In total, our examination of functions in these MAGs shows a diversity of nutrient acquisition and metabolism pathways present that may benefit the host, as well as genomic signatures of host association and immune system evasion.


Daphnia/microbiology , Host Microbial Interactions , Metagenomics/methods , Microbiota/genetics , Amino Acids , Animals , Comamonadaceae , Daphnia/metabolism , Flagella/physiology , High-Throughput Nucleotide Sequencing , Microbiota/physiology , Nitrates/metabolism , Oxidation-Reduction , RNA, Ribosomal, 16S , Sulfur/metabolism , Vitamins/biosynthesis
14.
Yeast ; 37(4): 283-304, 2020 04.
Article En | MEDLINE | ID: mdl-31972058

Chemically defined media for yeast cultivation (CDMY) were developed to support fast growth, experimental reproducibility, and quantitative analysis of growth rates and biomass yields. In addition to mineral salts and a carbon substrate, popular CDMYs contain seven to nine B-group vitamins, which are either enzyme cofactors or precursors for their synthesis. Despite the widespread use of CDMY in fundamental and applied yeast research, the relation of their design and composition to the actual vitamin requirements of yeasts has not been subjected to critical review since their first development in the 1940s. Vitamins are formally defined as essential organic molecules that cannot be synthesized by an organism. In yeast physiology, use of the term "vitamin" is primarily based on essentiality for humans, but the genome of the Saccharomyces cerevisiae reference strain S288C harbours most of the structural genes required for synthesis of the vitamins included in popular CDMY. Here, we review the biochemistry and genetics of the biosynthesis of these compounds by S. cerevisiae and, based on a comparative genomics analysis, assess the diversity within the Saccharomyces genus with respect to vitamin prototrophy.


Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Vitamins/biosynthesis , Biomass , Biotin/biosynthesis , Inositol/biosynthesis , Niacin/biosynthesis , Pantothenic Acid/biosynthesis , Pyridoxine/biosynthesis , Reproducibility of Results , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Thiamine/biosynthesis
15.
Appl Microbiol Biotechnol ; 104(3): 935-951, 2020 Feb.
Article En | MEDLINE | ID: mdl-31838543

Fat-soluble vitamins are vitamins that are insoluble in water, soluble in fat, and organic solvents; they are found in minute amount in various foods. Fat-soluble vitamins, including vitamins A, D, E, and K, have been widely used in food, cosmetics, health care products, and pharmaceutical industries. Fat-soluble vitamins are currently produced via biological and chemical synthesis. In recent years, fat-soluble vitamin production by biotechnological routes has been regarded as a very promising approach. Based on biosynthetic pathways, considerable advances of α-tocopherol and ß-carotenes have been achieved in transgenic plants and microalgae. Microbial fermentation, as an alternative method for the production of vitamin K and ß-carotenes, is attracting considerable attention because it is an environment friendly process. In this review, we address the function and applications of fat-soluble vitamins, and an overview of current developments in the production of fat-soluble vitamins in transgenic plants, microalgae, and microorganisms. We focus on the metabolic and process engineering strategies for improving production of fat-soluble vitamins, and we hope this review can be useful for the people who are interested in the production of fat-soluble vitamins by biotechnological routes.


Fats/chemistry , Metabolic Engineering , Vitamins/biosynthesis , Biosynthetic Pathways , Biotechnology , Fermentation , Solubility , Vitamin A/biosynthesis , Vitamin D/biosynthesis , Vitamin E/biosynthesis , Vitamin K/biosynthesis
16.
Genome Biol Evol ; 12(1): 3647-3655, 2020 01 01.
Article En | MEDLINE | ID: mdl-31841132

Brown algae are important primary producers and ecosystem engineers in the ocean, and Ectocarpus has been established as a laboratory model for this lineage. Like most multicellular organisms, Ectocarpus is associated with a community of microorganisms, a partnership frequently referred to as holobiont due to the tight interconnections between the components. Although genomic resources for the algal host are well established, its associated microbiome is poorly characterized from a genomic point of view, limiting the possibilities of using these types of data to study host-microbe interactions. To address this gap in knowledge, we present the annotated draft genome sequences of seventy-two cultivable Ectocarpus-associated bacteria. A screening of gene clusters related to the production of secondary metabolites revealed terpene, bacteriocin, NRPS, PKS-t3, siderophore, PKS-t1, and homoserine lactone clusters to be abundant among the sequenced genomes. These compounds may be used by the bacteria to communicate with the host and other microbes. Moreover, detoxification and provision of vitamin B pathways have been observed in most sequenced genomes, highlighting potential contributions of the bacterial metabolism toward host fitness and survival. The genomes sequenced in this study form a valuable resource for comparative genomic analyses and evolutionary surveys of alga-associated bacteria. They help establish Ectocarpus as a model for brown algal holobionts and will enable the research community to produce testable hypotheses about the molecular interactions within this complex system.


Genome, Bacterial , Phaeophyceae/microbiology , Bacteria/genetics , Bacteria/isolation & purification , Bacteria/metabolism , Phylogeny , Secondary Metabolism/genetics , Symbiosis , Vitamins/biosynthesis
17.
Appl Environ Microbiol ; 86(3)2020 01 21.
Article En | MEDLINE | ID: mdl-31757822

Akkermansia muciniphila is a mucin-degrading bacterium found in the gut of most humans and is considered a "next-generation probiotic." However, knowledge of the genomic and physiological diversity of human-associated Akkermansia sp. strains is limited. Here, we reconstructed 35 metagenome-assembled genomes and combined them with 40 publicly available genomes for comparative genomic analysis. We identified at least four species-level phylogroups (AmI to AmIV), with distinct functional potentials. Most notably, we identified genes for cobalamin (vitamin B12) biosynthesis within the AmII and AmIII phylogroups. To verify these predictions, 10 Akkermansia strains were isolated from adults and screened for vitamin B12 biosynthesis genes via PCR. Two AmII strains were positive for the presence of cobalamin biosynthesis genes, while all 9 AmI strains tested were negative. To demonstrate vitamin B12 biosynthesis, we measured the production of acetate, succinate, and propionate in the presence and absence of vitamin supplementation in representative strains of the AmI and AmII phylogroups, since cobalamin is an essential cofactor in propionate metabolism. Results showed that the AmII strain produced acetate and propionate in the absence of supplementation, which is indicative of vitamin B12 biosynthesis. In contrast, acetate and succinate were the main fermentation products for the AmI strains when vitamin B12 was not supplied in the culture medium. Lastly, two bioassays were used to confirm vitamin B12 production by the AmII phylogroup. This novel physiological trait of human-associated Akkermansia strains may affect how these bacteria interact with the human host and other members of the human gut microbiome.IMPORTANCE There is significant interest in the therapeutic and probiotic potential of the common gut bacterium Akkermansia muciniphila However, knowledge of both the genomic and physiological diversity of this bacterial lineage is limited. Using a combination of genomic, molecular biological, and traditional microbiological approaches, we identified at least four species-level phylogroups with differing functional potentials that affect how these bacteria interact with both their human host and other members of the human gut microbiome. Specifically, we identified and isolated Akkermansia strains that were able to synthesize vitamin B12 The ability to synthesize this important cofactor broadens the physiological capabilities of human-associated Akkermansia strains, fundamentally altering our understanding of how this important bacterial lineage may affect human health.


Genome, Bacterial , Verrucomicrobia/genetics , Vitamin B 12/biosynthesis , Vitamins/biosynthesis , Child , Child, Preschool , Genomics , Humans , Verrucomicrobia/metabolism , Vitamin B 12/genetics , Vitamins/genetics
18.
ISME J ; 14(1): 259-273, 2020 01.
Article En | MEDLINE | ID: mdl-31624345

Many insects depend on obligate mutualistic bacteria to provide essential nutrients lacking from their diet. Most aphids, whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera aphidicola to supply essential amino acids and B vitamins. However, in some aphid species, provision of these nutrients is partitioned between Buchnera and a younger bacterial partner, whose identity varies across aphid lineages. Little is known about the origin and the evolutionary stability of these di-symbiotic systems. It is also unclear whether the novel symbionts merely compensate for losses in Buchnera or carry new nutritional functions. Using whole-genome endosymbiont sequences of nine Cinara aphids that harbour an Erwinia-related symbiont to complement Buchnera, we show that the Erwinia association arose from a single event of symbiont lifestyle shift, from a free-living to an obligate intracellular one. This event resulted in drastic genome reduction, long-term genome stasis, and co-divergence with aphids. Fluorescence in situ hybridisation reveals that Erwinia inhabits its own bacteriocytes near Buchnera's. Altogether these results depict a scenario for the establishment of Erwinia as an obligate symbiont that mirrors Buchnera's. Additionally, we found that the Erwinia vitamin-biosynthetic genes not only compensate for Buchnera's deficiencies, but also provide a new nutritional function; whose genes have been horizontally acquired from a Sodalis-related bacterium. A subset of these genes have been subsequently transferred to a new Hamiltonella co-obligate symbiont in one specific Cinara lineage. These results show that the establishment and dynamics of multi-partner endosymbioses can be mediated by lateral gene transfers between co-ocurring symbionts.


Aphids/microbiology , Buchnera/genetics , Erwinia/genetics , Gene Transfer, Horizontal , Symbiosis/genetics , Animals , Vitamins/biosynthesis
19.
Appl Microbiol Biotechnol ; 103(11): 4633-4648, 2019 Jun.
Article En | MEDLINE | ID: mdl-30972463

Clostridium autoethanogenum and Clostridium ljungdahlii are physiologically and genetically very similar strict anaerobic acetogens capable of growth on carbon monoxide as sole carbon source. While exact nutritional requirements have not been reported, we observed that for growth, the addition of vitamins to media already containing yeast extract was required, an indication that these are fastidious microorganisms. Elimination of complex components and individual vitamins from the medium revealed that the only organic compounds required for growth were pantothenate, biotin and thiamine. Analysis of the genome sequences revealed that three genes were missing from pantothenate and thiamine biosynthetic pathways, and five genes were absent from the pathway for biotin biosynthesis. Prototrophy in C. autoethanogenum and C. ljungdahlii for pantothenate was obtained by the introduction of plasmids carrying the heterologous gene clusters panBCD from Clostridium acetobutylicum, and for thiamine by the introduction of the thiC-purF operon from Clostridium ragsdalei. Integration of panBCD into the chromosome through allele-coupled exchange also conveyed prototrophy. C. autoethanogenum was converted to biotin prototrophy with gene sets bioBDF and bioHCA from Desulfotomaculum nigrificans strain CO-1-SRB, on plasmid and integrated in the chromosome. The genes could be used as auxotrophic selection markers in recombinant DNA technology. Additionally, transformation with a subset of the genes for pantothenate biosynthesis extended selection options with the pantothenate precursors pantolactone and/or beta-alanine. Similarly, growth was obtained with the biotin precursor pimelate combined with genes bioYDA from C. acetobutylicum. The work raises questions whether alternative steps exist in biotin and thiamine biosynthesis pathways in these acetogens.


Clostridium/growth & development , Clostridium/metabolism , Metabolic Engineering/methods , Metabolic Networks and Pathways/genetics , Vitamins/biosynthesis , Clostridium/genetics , Culture Media/chemistry , Desulfotomaculum/genetics , Gene Expression , Genes, Bacterial , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
20.
Crit Rev Food Sci Nutr ; 59(3): 506-527, 2019.
Article En | MEDLINE | ID: mdl-28945458

In the past, the beneficial effects of fermented foods on health were unknown, and so people primarily used fermentation to preserve foods, enhance shelf life, and improve flavour. Fermented foods became an important part of the diet in many cultures, and over time fermentation has been associated with many health benefits. Because of this, the fermentation process and the resulting fermented products have recently attracted scientific interest. In addition, microorganisms contributing to the fermentation process have recently been associated with many health benefits, and so these microorganisms have become another focus of attention. Lactic acid bacteria (LAB) have been some of the most studied microorganisms. During fermentation, these bacteria synthesize vitamins and minerals, produce biologically active peptides with enzymes such as proteinase and peptidase, and remove some non-nutrients. Compounds known as biologically active peptides, which are produced by the bacteria responsible for fermentation, are also well known for their health benefits. Among these peptides, conjugated linoleic acids (CLA) have a blood pressure lowering effect, exopolysaccharides exhibit prebiotic properties, bacteriocins show anti-microbial effects, sphingolipids have anti-carcinogenic and anti-microbial properties, and bioactive peptides exhibit anti-oxidant, anti-microbial, opioid antagonist, anti-allergenic, and blood pressure lowering effects. As a result, fermented foods provide many health benefits such as anti-oxidant, anti-microbial, anti-fungal, anti-inflammatory, anti-diabetic and anti-atherosclerotic activity. However, some studies have shown no relationship between fermented foods and health benefits. Therefore, this paper aims to investigate the health effects of fermented foods.


Fermented Foods , Health Promotion , Anti-Infective Agents/analysis , Anti-Inflammatory Agents/analysis , Antifungal Agents/analysis , Antioxidants/analysis , Atherosclerosis/prevention & control , Beer , Cultured Milk Products/analysis , Diet , Fermentation , Fermented Foods/analysis , Fruit , Humans , Hypoglycemic Agents/analysis , Lactobacillales/metabolism , Meat Products , Minerals/metabolism , Probiotics , Vegetables , Vitamins/biosynthesis , Wine
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