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Genome Biology and Evolution Aug 2021Annotated genome sequences provide valuable insight into the functional capabilities of members of microbial communities. Nevertheless, most studies on the microbiome in...
Annotated genome sequences provide valuable insight into the functional capabilities of members of microbial communities. Nevertheless, most studies on the microbiome in animal guts use metagenomic data, hampering the assignment of genes to specific microbial taxa. Here, we make use of the readily culturable bacterial communities in the gut of the fruit fly Drosophila melanogaster to obtain draft genome sequences for 96 isolates from wild flies. These include 81 new de novo assembled genomes, assigned to three orders (Enterobacterales, Lactobacillales, and Rhodospirillales) with 80% of strains identified to species level using average nucleotide identity and phylogenomic reconstruction. Based on annotations by the RAST pipeline, among-isolate variation in metabolic function partitioned strongly by bacterial order, particularly by amino acid metabolism (Rhodospirillales), fermentation, and nucleotide metabolism (Lactobacillales) and arginine, urea, and polyamine metabolism (Enterobacterales). Seven bacterial species, comprising 2-3 species in each order, were well-represented among the isolates and included ≥5 strains, permitting analysis of metabolic functions in the accessory genome (i.e., genes not present in every strain). Overall, the metabolic function in the accessory genome partitioned by bacterial order. Two species, Gluconobacter cerinus (Rhodospirillales) and Lactiplantibacillus plantarum (Lactobacillales) had large accessory genomes, and metabolic functions were dominated by amino acid metabolism (G. cerinus) and carbohydrate metabolism (La. plantarum). The patterns of variation in metabolic capabilities at multiple phylogenetic scales provide the basis for future studies of the ecological and evolutionary processes shaping the diversity of microorganisms associated with natural populations of Drosophila.
Topics: Animals; Drosophila; Drosophila melanogaster; Gastrointestinal Microbiome; Metagenome; Phylogeny
PubMed: 34081101
DOI: 10.1093/gbe/evab127 -
Applied and Environmental Microbiology Sep 2022In industrial production, the precursor of l-ascorbic acid (L-AA, also referred to as vitamin C), 2-keto-l-gulonic acid (2-KLG), is mainly produced using a classic... (Review)
Review
In industrial production, the precursor of l-ascorbic acid (L-AA, also referred to as vitamin C), 2-keto-l-gulonic acid (2-KLG), is mainly produced using a classic two-step fermentation process performed by Gluconobacter oxydans, Bacillus megaterium, and Ketogulonicigenium vulgare. In the second step of the two-step fermentation process, the microbial consortium of and B. megaterium is used to achieve 2-KLG production. can transform l-sorbose to 2-KLG, but the yield of 2-KLG is much lower in the monoculture than in the coculture fermentation system. The relationship between the two strains is too diverse to analyze and has been a hot topic in the field of vitamin C fermentation. With the development of omics technology, the relationships between the two strains are well explained; nevertheless, the cell-cell communication is unclear. In this review, based on current omics results, the interactions between the two strains are summarized, and the potential cell-cell communications between the two strains are discussed, which will shed a light on the further understanding of synthetic consortia.
Topics: Ascorbic Acid; Fermentation; Gluconobacter oxydans; Microbial Interactions; Rhodobacteraceae; Sorbose; Sugar Acids; Vitamins
PubMed: 36073939
DOI: 10.1128/aem.01212-22 -
Frontiers in Oncology 2024The gut microbiota has been significantly associated with differentiated thyroid cancer (DTC). However, the causal relationship between the gut microbiota and DTC...
BACKGROUND
The gut microbiota has been significantly associated with differentiated thyroid cancer (DTC). However, the causal relationship between the gut microbiota and DTC remains unexplored.
METHODS
Genome-wide association study (GWAS) summary databases were utilized to select exposures and outcomes. The Mendelian randomization (MR) method was employed to investigate the causal relationship between the gut microbiota and DTC. A sensitivity analysis was performed to assess the reliability of the findings.
RESULTS
Four bacterial traits were associated with the risk of DTC: Class Mollicutes [odds ratio (OR) = 10.953, 95% confidence interval (95% CI): 2.333-51.428, = 0.002], Phylum Tenericutes (OR = 10.953, 95% CI: 2.333-51.428, = 0.002), Genus Eggerthella (OR = 3.219, 95% CI: 1.033-10.024, = 0.044), and Order Rhodospirillales (OR = 2.829, 95% CI: 1.096-7.299, = 0.032). The large 95% CI range for the Class Mollicutes and the Phylum Tenericutes may be attributed to the small sample size. Additionally, four other bacterial traits were negatively associated with DTC: Genus Eubacterium fissicatena group (OR = 0.381, 95% CI: 0.148-0.979, = 0.045), Genus Lachnospiraceae UCG008 (OR = 0.317, 95% CI: 0.125-0.801, = 0.015), Genus Christensenellaceae R-7 group (OR = 0.134, 95% CI: 0.020-0.886, = 0.037), and Genus Escherichia Shigella (OR = 0.170, 95% CI: 0.037-0.769, = 0.021).
CONCLUSION
These findings contribute to our understanding of the pathological mechanisms underlying DTC and provide novel insights for the clinical treatment of DTC.
PubMed: 38737897
DOI: 10.3389/fonc.2024.1375525 -
Scientific Reports May 2023Several raw materials have been used as partial supplements or entire replacements for the main ingredients of kombucha to improve the biological properties of the...
Several raw materials have been used as partial supplements or entire replacements for the main ingredients of kombucha to improve the biological properties of the resulting kombucha beverage. This study used pineapple peels and cores (PPC), byproducts of pineapple processing, as alternative raw materials instead of sugar for kombucha production. Kombuchas were produced from fusions of black tea and PPC at different ratios, and their chemical profiles and biological properties, including antioxidant and antimicrobial activities, were determined and compared with the control kombucha without PPC supplementation. The results showed that PPC contained high amounts of beneficial substances, including sugars, polyphenols, organic acids, vitamins, and minerals. An analysis of the microbial community in a kombucha SCOBY (Symbiotic Cultures of Bacteria and Yeasts) using next-generation sequencing revealed that Acetobacter and Komagataeibacter were the most predominant acetic acid bacteria. Furthermore, Dekkera and Bacillus were also the prominent yeast and bacteria in the kombucha SCOBY. A comparative analysis was performed for kombucha products fermented using black tea and a fusion of black tea and PPC, and the results revealed that the kombucha made from the black tea and PPC infusion exhibited a higher total phenolic content and antioxidant activity than the control kombucha. The antimicrobial properties of the kombucha products made from black tea and the PPC infusion were also greater than those of the control. Several volatile compounds that contributed to the flavor, aroma, and beneficial health properties, such as esters, carboxylic acids, phenols, alcohols, aldehydes, and ketones, were detected in kombucha products made from a fusion of black tea and PPC. This study shows that PPC exhibits high potential as a supplement to the raw material infusion used with black tea for functional kombucha production.
Topics: Tea; Ananas; Beverages; Yeasts; Antioxidants; Camellia sinensis; Phenols; Anti-Infective Agents; Acetobacteraceae; Fermentation
PubMed: 37188725
DOI: 10.1038/s41598-023-34954-7 -
Proceedings of the National Academy of... Feb 2022Bacteria are efficient colonizers of a wide range of secluded microhabitats, such as soil pores, skin follicles, or intestinal crypts. How the structural diversity of...
Bacteria are efficient colonizers of a wide range of secluded microhabitats, such as soil pores, skin follicles, or intestinal crypts. How the structural diversity of these habitats modulates microbial self-organization remains poorly understood, in part because of the difficulty to precisely manipulate the physical structure of microbial environments. Using a microfluidic device to grow bacteria in crypt-like incubation chambers of systematically varied lengths, we show that small variations in the physical structure of the microhabitat can drastically alter bacterial colonization success and resistance against invaders. Small crypts are uncolonizable; intermediately sized crypts can stably support dilute populations, while beyond a second critical length scale, populations phase separate into a dilute region and a jammed region. The jammed state is characterized by extreme colonization resistance, even if the resident strain is suppressed by an antibiotic. Combined with a flexible biophysical model, we demonstrate that colonization resistance and associated priority effects can be explained by a crowding-induced phase transition, which results from a competition between proliferation and density-dependent cell leakage. The emerging sensitivity to scale underscores the need to control for scale in microbial ecology experiments. Systematic flow-adjustable length-scale variations may serve as a promising strategy to elucidate further scale-sensitive tipping points and to rationally modulate the stability and resilience of microbial colonizers.
Topics: Acetobacter; Anti-Bacterial Agents; Bacteriological Techniques; Drug Resistance, Bacterial; Lab-On-A-Chip Devices; Tetracycline
PubMed: 35145031
DOI: 10.1073/pnas.2115496119 -
The Journal of Physical Chemistry. B Apr 2022Defining chemical properties of intracellular organelles is necessary to determine their function(s) as well as understand and mimic the reactions they host. However,...
Defining chemical properties of intracellular organelles is necessary to determine their function(s) as well as understand and mimic the reactions they host. However, the small size of bacterial and archaeal microorganisms often prevents defining local intracellular chemical conditions in a similar way to what has been established for eukaryotic organelles. This work proposes to use magnetite (FeO) nanocrystals contained in magnetosome organelles of magnetotactic bacteria as reporters of elemental composition, pH, and redox potential of a hypothetical environment at the site of formation of intracellular magnetite. This methodology requires combining recent single-cell mass spectrometry measurements together with elemental composition of magnetite in trace and minor elements. It enables a quantitative characterization of chemical disequilibria of 30 chemical elements between the intracellular and external media of magnetotactic bacteria, revealing strong transfers of elements with active influx or efflux processes that translate into elemental accumulation (Mo, Se, and Sn) or depletion (Sr and Bi) in the bacterial internal medium of up to seven orders of magnitude relative to the extracellular medium. Using this concept, we show that chemical conditions in magnetosomes are compatible with a pH of 7.5-9.5 and a redox potential of -0.25 to -0.6 V.
Topics: Bacteria; Ferrosoferric Oxide; Gram-Negative Bacteria; Magnetosomes; Magnetospirillum
PubMed: 35362974
DOI: 10.1021/acs.jpcb.2c00752 -
Bioengineered Dec 2021Bacterial cellulose (BC) is higher in demand due to its excellent properties which is attributed to its purity and nano size. is a model organism where BC production... (Review)
Review
Bacterial cellulose (BC) is higher in demand due to its excellent properties which is attributed to its purity and nano size. is a model organism where BC production has been studied in detail because of its higher cellulose production capacity. BC production mechanism shows involvement of a series of sequential reactions with enzymes for biosynthesis of cellulose. It is necessary to know the mechanism to understand the involvement of regulatory proteins which could be the probable targets for genetic modification to enhance or regulate yield of BC and to alter BC properties as well. For the industrial production of BC, controlled synthesis is desired so as to save energy, hence genetic manipulation opens up avenues for upregulating or controlling the cellulose synthesis in the bacterium by targeting genes involved in cellulose biosynthesis. In this review article genetic modification has been presented as a tool to introduce desired changes at genetic level resulting in improved yield or properties. There has been a lack of studies on genetic modification for BC production due to limited availability of information on whole genome and genetic toolkits; however, in last few years, the number of studies has been increased on this aspect as whole genome sequencing of several strains are being done. In this review article, we have presented the mechanisms and the targets for genetic modifications in order to achieve desired changes in the BC production titer as well as its characteristics.
Topics: Acetobacteraceae; Cellulose; Genetic Engineering; Nanostructures
PubMed: 34519629
DOI: 10.1080/21655979.2021.1968989 -
Frontiers in Immunology 2023The evolution of nutritional strategies to improve the gut health and microbiota profiles of early-weaned piglets is essential to reduce diarrhoea caused by weaning...
INTRODUCTION
The evolution of nutritional strategies to improve the gut health and microbiota profiles of early-weaned piglets is essential to reduce diarrhoea caused by weaning stress. Therefore, the aim of this study was to determine the effects of dietary supplementation of Qi-Weng-Huangbo powder, a traditional herbal medicine consisting of a mixture of , and extracts (PCE), on the growth performance, diarrhoea rate, immune function and intestinal health of weaned piglets.
METHODS
162 piglets were randomly assigned to the CON group (no PCE added), the PCEL group (300 mg/kg PCE) and the PCEH group (500 mg/kg PCE) at the end of the third week post farrowing. There were 9 replicates of each group with 6 pigs per replicate. The experiment lasted for 28 days and sampling was performed on the final day.
RESULTS
The results showed that the PCE diet increased the average daily gain (ADG) and final body weight (BW) compared to the CON group. Both supplemented doses of PCE reduced the faecal scores of piglets, and the diarrhoea rate in the PCEL group was significantly lower than that in the CON group. The application of PCE diets promoted the development of the spleen in piglets and up-regulated serum immunoglobulin concentrations to enhance immune function, which was also reflected in the down-regulated gene expression of the colonic TLR/MyD88/NF-κB pathway. Supplementation with PCE improved intestinal morphology, and all doses of PCE significantly increased villus height (VH) in the ileum, whereas colonic crypt depth (CD) was significantly lower in the PCEH group than in the CON group. The PCEH diet significantly increased the levels of valeric and isovaleric acid in the colon content. Dietary PCEH also improved the colonic microbial community profile, reflected by a significant increase in Shannon's index compared with CON group. The abundance of and was significantly increased in the PCEH group at the family level.
DISCUSSION
In conclusion, dietary PCE reduced diarrhoea rates, improved growth performance and enhanced immune function in weaned piglets. These improvements were potentially supported by altered ileum and colonic morphology, elevated colonic VFA levels, and modulation of colonic microbial profiles.
Topics: Animals; Swine; Powders; Qi; Weaning; Diet; Diarrhea; Immunity
PubMed: 38187371
DOI: 10.3389/fimmu.2023.1342852 -
Applied and Environmental Microbiology Mar 2022Poly(hydroxybutyrate--hydroxyhexanoate) [P(HB--HHx)] and poly(hydroxybutyrate--hydroxyvalerate-hydroxyhexanoate) [P(HB--HV--HHx)] demonstrate interesting mechanical and...
Poly(hydroxybutyrate--hydroxyhexanoate) [P(HB--HHx)] and poly(hydroxybutyrate--hydroxyvalerate-hydroxyhexanoate) [P(HB--HV--HHx)] demonstrate interesting mechanical and thermal properties as well as excellent biocompatibility, making them suitable for multiple applications and notably biomedical purposes. The production of such polymers was described in Rhodospirillum rubrum, a purple nonsulfur bacteria in a nutrient-lacking environment where the HHx synthesis is triggered by the presence of hexanoate in the medium. However, the production of P(HB--HHx) under nutrient-balanced growth conditions in has not been described so far, and the assimilation of hexanoate is poorly documented. In this study, we used proteomic analysis and a mutant fitness assay to demonstrate that hexanoate assimilation involve β-oxidation and the ethylmalonyl-coenzyme A (CoA) (EMC) and methylbutanoyl-CoA (MBC) pathways, both being anaplerotic pathways already described in . Polyhydroxyalkanoate (PHA) production is likely to involve the fatty acid synthesis pathway. Concerning the polymer composition, HB is the main component of the polymer, probably as acetyl-CoA and butyryl-CoA are intermediates of hexanoate assimilation pathways. When no essential nutrient is lacking in the medium, the synthesis of PHA seems to help maintain the redox balance of the cell. In this framework, we showed that the fixation of CO is required to sustain the growth. An increase in the proportion of HHx in the polymer was observed when redox stress was engendered in the cell under bicarbonate-limiting growth conditions. The addition of isoleucine or valerate in the medium also increased the HHx content of the polymer and allowed the production of a terpolymer of P(HB--HV--HHx). The use of purple bacteria, which can assimilate volatile fatty acids, for biotechnological applications has increased, since they reduce the production costs of added-value compounds such as PHA. P(HB--HHx) and P(HB--HV--HHx) have demonstrated interesting properties, notably for biomedical applications. In a nutrient-lacking environment, is known to synthesize such polymers when hexanoate is used as the carbon source. However, their production in in non-nutrient-lacking growth conditions has not been described so far, and the assimilation of hexanoate is poorly documented. As the carbon source and its assimilation directly impact the polymer composition, we studied under non-nutrient-lacking growth conditions the assimilation pathway of hexanoate and PHA production in Proteomic analysis and mutant fitness assays allowed us to explain PHA production and composition. An increase in HHx content of the polymer and production of P(HB--HV--HHx) was possible using the knowledge gained on metabolism under hexanoate growth conditions.
Topics: Biotechnology; Hydroxybutyrates; Polyhydroxyalkanoates; Proteomics; Rhodospirillum rubrum
PubMed: 35080906
DOI: 10.1128/AEM.01586-21 -
ACS Biomaterials Science & Engineering Jul 2021Microcapsules made of synthetic polymers are used for the release of cargo in agriculture, food, and cosmetics but are often difficult to be degraded in the environment....
Microcapsules made of synthetic polymers are used for the release of cargo in agriculture, food, and cosmetics but are often difficult to be degraded in the environment. To diminish the environmental impact of microcapsules, we use the biofilm-forming ability of bacteria to grow cellulose-based biodegradable microcapsules. The present work focuses on the design and optimization of self-grown bacterial cellulose capsules. In contrast to their conventionally attributed pathogenic role, bacteria and their self-secreted biofilms represent a multifunctional class of biomaterials. The bacterial strain used in this work, , is able to survive and proliferate in various environmental conditions by forming biofilms as part of its lifecycle. Cellulose is one of the main components present in these self-secreted protective layers and is known for its outstanding mechanical properties. Provided enough nutrients and oxygen, these bacteria and the produced cellulose are able to self-assemble at the interface of any given three-dimensional template and could be used as a novel stabilization concept for water-in-oil emulsions. Using a microfluidic setup for controlled emulsification, we demonstrate that bacterial cellulose capsules can be produced with tunable size and monodispersity. Furthermore, we show that successful droplet stabilization and bacterial cellulose formation are functions of the bacteria concentration, droplet size, and surfactant type. The obtained results represent the first milestone in the production of self-assembled biodegradable cellulose capsules to be used in a vast range of applications such as flavor, fragrance, agrochemicals, nutrients, and drug encapsulation.
Topics: Capsules; Cellulose; Emulsions; Gluconacetobacter xylinus; Polymers
PubMed: 34190548
DOI: 10.1021/acsbiomaterials.1c00399