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PLoS Biology Mar 2020The interplay between nutrition and the microbial communities colonizing the gastrointestinal tract (i.e., gut microbiota) determines juvenile growth trajectory....
The interplay between nutrition and the microbial communities colonizing the gastrointestinal tract (i.e., gut microbiota) determines juvenile growth trajectory. Nutritional deficiencies trigger developmental delays, and an immature gut microbiota is a hallmark of pathologies related to childhood undernutrition. However, how host-associated bacteria modulate the impact of nutrition on juvenile growth remains elusive. Here, using gnotobiotic Drosophila melanogaster larvae independently associated with Acetobacter pomorumWJL (ApWJL) and Lactobacillus plantarumNC8 (LpNC8), 2 model Drosophila-associated bacteria, we performed a large-scale, systematic nutritional screen based on larval growth in 40 different and precisely controlled nutritional environments. We combined these results with genome-based metabolic network reconstruction to define the biosynthetic capacities of Drosophila germ-free (GF) larvae and its 2 bacterial partners. We first established that ApWJL and LpNC8 differentially fulfill the nutritional requirements of the ex-GF larvae and parsed such difference down to individual amino acids, vitamins, other micronutrients, and trace metals. We found that Drosophila-associated bacteria not only fortify the host's diet with essential nutrients but, in specific instances, functionally compensate for host auxotrophies by either providing a metabolic intermediate or nutrient derivative to the host or by uptaking, concentrating, and delivering contaminant traces of micronutrients. Our systematic work reveals that beyond the molecular dialogue engaged between the host and its bacterial partners, Drosophila and its associated bacteria establish an integrated nutritional network relying on nutrient provision and utilization.
Topics: Acetobacter; Amino Acids; Animal Nutritional Physiological Phenomena; Animals; Drosophila melanogaster; Gastrointestinal Microbiome; Host Microbial Interactions; Lactobacillus; Larva; Metabolic Networks and Pathways; Micronutrients; Nutritional Requirements; Species Specificity
PubMed: 32196485
DOI: 10.1371/journal.pbio.3000681 -
The Journal of Experimental Biology Oct 2020Most research on the impact of the gut microbiome on animal nutrition is designed to identify the effects of single microbial taxa and single metabolites of microbial...
Most research on the impact of the gut microbiome on animal nutrition is designed to identify the effects of single microbial taxa and single metabolites of microbial origin, without considering the potentially complex network of interactions among co-occurring microorganisms. Here, we investigated how different microbial associations and their fermentation products affect host nutrition, using colonized with three gut microorganisms (the bacteria and , and the yeast ) in all seven possible combinations. Some microbial effects on host traits could be attributed to single taxa (e.g. yeast-mediated reduction of insect development time), while other effects were sex specific and driven by among-microbe interactions (e.g. male lipid content determined by interactions between the yeast and both bacteria). Parallel analysis of nutritional indices of microbe-free flies administered different microbial fermentation products (acetic acid, acetoin, ethanol and lactic acid) revealed a single consistent effect: that the lipid content of both male and female flies is reduced by acetic acid. This effect was recapitulated in male flies colonized with both yeast and , but not for any microbial treatment in females or males with other microbial complements. These data suggest that the effect of microbial fermentation products on host nutritional status is strongly context dependent, with respect to both the combination of associated microorganisms and host sex. Taken together, our findings demonstrate that among-microbe interactions can play a critically important role in determining the physiological outcome of host-microbiome interactions in and, likely, in other animal hosts.
Topics: Acetobacter; Animals; Drosophila melanogaster; Female; Gastrointestinal Microbiome; Hanseniaspora; Male
PubMed: 33051361
DOI: 10.1242/jeb.227843 -
International Journal of Molecular... Mar 2021This article compares the properties of bacterial cellulose/fish collagen composites (BC/Col) after enzymatic and chemical cross-linking. In our methodology, two... (Comparative Study)
Comparative Study
This article compares the properties of bacterial cellulose/fish collagen composites (BC/Col) after enzymatic and chemical cross-linking. In our methodology, two transglutaminases are used for enzymatic cross-linking-one recommended for the meat and the other proposed for the fish industry-and pre-oxidated BC (oxBC) is used for chemical cross-linking. The structure of the obtained composites is characterized by scanning electron microscopy, thermogravimetric analysis, X-ray diffraction, and Fourier transform infrared spectroscopy, and their functional properties by mechanical and water barrier tests. While polymer chains in uncross-linked BC/Col are intertwined by H-bonds, new covalent bonds in enzymatically cross-linked ones are formed-resulting in increased thermal stability and crystallinity of the material. The C2-C3 bonds cleavage in D-glucose units, due to BC oxidation, cause secondary alcohol groups to vanish in favor of the carbonyl groups' formation, thus reducing the number of H-bonded OHs. Thermal stability and crystallinity of oxBC/Col remain lower than those of BC/Col. The BC/Col formation did not affect tensile strength and water vapor permeability of BC, but enzymatic cross-linking with TG improved them significantly.
Topics: Animals; Cellulose; Collagen; Cross-Linking Reagents; Enzymes; Fishes; Gluconacetobacter; Hydrogen Bonding; Microscopy, Electron, Scanning; Permeability; Polymers; Spectroscopy, Fourier Transform Infrared; Stress, Mechanical; Temperature; Tensile Strength; Thermogravimetry; X-Ray Diffraction
PubMed: 33805875
DOI: 10.3390/ijms22073346 -
Molecular Ecology Sep 2017Various bacterial taxa have been identified both in association with animals and in the external environment, but the extent to which related bacteria from the two...
Various bacterial taxa have been identified both in association with animals and in the external environment, but the extent to which related bacteria from the two habitat types are ecologically and evolutionarily distinct is largely unknown. This study investigated the scale and pattern of genetic differentiation between bacteria of the family Acetobacteraceae isolated from the guts of Drosophila fruit flies, plant material and industrial fermentations. Genome-scale analysis of the phylogenetic relationships and predicted functions was conducted on 44 Acetobacteraceae isolates, including newly sequenced genomes from 18 isolates from wild and laboratory Drosophila. Isolates from the external environment and Drosophila could not be assigned to distinct phylogenetic groups, nor are their genomes enriched for any different sets of genes or category of predicted gene functions. In contrast, analysis of bacteria from laboratory Drosophila showed they were genetically distinct in their universal capacity to degrade uric acid (a major nitrogenous waste product of Drosophila) and absence of flagellar motility, while these traits vary among wild Drosophila isolates. Analysis of the competitive fitness of Acetobacter discordant for these traits revealed a significant fitness deficit for bacteria that cannot degrade uric acid in culture with Drosophila. We propose that, for wild populations, frequent cycling of Acetobacter between Drosophila and the external environment prevents genetic differentiation by maintaining selection for traits adaptive in both the gut and external habitats. However, laboratory isolates bear the signs of adaptation to persistent association with the Drosophila host under tightly defined environmental conditions.
Topics: Acetobacteraceae; Adaptation, Biological; Animals; Drosophila; Ecology; Genetics, Population; Genome, Bacterial; Phylogeny
PubMed: 28667798
DOI: 10.1111/mec.14232 -
International Journal of Systematic and... Jul 2021Two novel Gram-staining-negative, aerobic, cocci-shaped, non-motile, non-spore forming, pink-pigmented bacteria designated strains T6 and T18, were isolated from a...
Two novel Gram-staining-negative, aerobic, cocci-shaped, non-motile, non-spore forming, pink-pigmented bacteria designated strains T6 and T18, were isolated from a biocrust (biological soil crust) sample from the vicinity of the Tabernas Desert (Spain). Both strains were catalase-positive and oxidase-negative, and grew under mesophilic, neutrophilic and non-halophilic conditions. According to the 16S rRNA gene sequences, strains T6 and T18 showed similarities with CGMCC 1.10758 and CP2C (98.11 and 98.55% gene sequence similarity, respectively). The DNA G+C content was 69.80 and 68.96% for strains T6 and T18, respectively; the average nucleotide identity by blast (ANIb) and digital DNA-DNA hybridization (dDDH) values confirmed their adscription to two novel species within the genus . The predominant fatty acids were summed feature 8 (Cω7Cω6), C, C 2-OH and summed feature 3 (Cω7Cω6). According to he results of the polyphasic study, strains T6 and T18 represent two novel species in the genus (which currently includes only three species), for which names sp. nov. (type strain T6 = CECT 30228=DSM 112073) and sp. nov. (type strain T18=CECT 30229=DSM 112074) are proposed, respectively.
Topics: Acetobacteraceae; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Desert Climate; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pigmentation; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Spain
PubMed: 34292142
DOI: 10.1099/ijsem.0.004837 -
Acta Crystallographica. Section F,... Mar 2018Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a key enzyme in homofermentative metabolism where ethanol is the major product. PDCs are thiamine pyrophosphate- and Mg...
Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a key enzyme in homofermentative metabolism where ethanol is the major product. PDCs are thiamine pyrophosphate- and Mg ion-dependent enzymes that catalyse the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. As this enzyme class is rare in bacteria, current knowledge of bacterial PDCs is extremely limited. One approach to further the understanding of bacterial PDCs is to exploit the diversity provided by evolution. Ancestral sequence reconstruction (ASR) is a method of computational molecular evolution to infer extinct ancestral protein sequences, which can then be synthesized and experimentally characterized. Through ASR a novel PDC was generated, designated ANC27, that shares only 78% amino-acid sequence identity with its closest extant homologue (Komagataeibacter medellinensis PDC, GenBank accession No. WP_014105323.1), yet is fully functional. Crystals of this PDC diffracted to 3.5 Å resolution. The data were merged in space group P321, with unit-cell parameters a = b = 108.33, c = 322.65 Å, and contained two dimers (two tetramer halves) in the asymmetric unit. The structure was solved by molecular replacement using PDB entry 2wvg as a model, and the final R values were R = 0.246 (0.3671 in the highest resolution bin) and R = 0.319 (0.4482 in the highest resolution bin). Comparison with extant bacterial PDCs supports the previously observed correlation between decreased tetramer interface area (and number of interactions) and decreased thermostability.
Topics: Acetobacteraceae; Amino Acid Sequence; Catalytic Domain; Crystallization; Crystallography, X-Ray; Models, Molecular; Protein Conformation; Pyruvate Decarboxylase
PubMed: 29497023
DOI: 10.1107/S2053230X18002819 -
Scientific Reports Nov 2022Bacterial nanocellulose (BC) is a highly versatile biopolymer currently pursued as a material of choice in varied themes of biomedical and material science research...
Bacterial nanocellulose (BC) is a highly versatile biopolymer currently pursued as a material of choice in varied themes of biomedical and material science research fields. With the aim to extend the biotechnological applications, the genetic tractability of the BC producers within the Komagataeibacter genus and its potential as an alternative host chassis in synthetic biology have been extensively studied. However, such studies have been largely focused on the model Komagataeibacter spp. Here, we present a novel K. intermedius strain capable of utilizing glucose, and glycerol sources for biomass and BC synthesis. Genome assembly identified one bacterial cellulose synthetase (bcs) operon containing the complete gene set encoding the BC biogenesis machinery (bcsI) and three additional copies (bcsII-IV). Investigations on the genetic tractability confirmed plasmid transformation, propagation of vectors with pBBR1 and p15A origin of replications and constitutive and inducible induction of recombinant protein in K. intermedius ENS15. This study provides the first report on the genetic tractability of K. intermedius, serving as starting point towards future genetic engineering of this strain.
Topics: Acetobacteraceae; Genetic Engineering; Synthetic Biology; Biomass
PubMed: 36443480
DOI: 10.1038/s41598-022-24735-z -
Carbohydrate Polymers Jun 2020Hydroxyapatite-associated bacterial cellulose (BC/HA) is a promising composite for biomedical applications. However, this hybrid composite has some limitations due to...
Hydroxyapatite-associated bacterial cellulose (BC/HA) is a promising composite for biomedical applications. However, this hybrid composite has some limitations due to its low in vivo degradability. The objective of this work was to oxidize BC and BC/HA composites for different time periods to produce 2,3 dialdehyde cellulose (DAC). The BC and oxidized BC (OxBC) membranes were mineralized to obtain the hybrid materials (BC/HA and OxBC/HA) and their physico-chemical, degradability, and bioactivity properties were studied. The results showed that OxBC/HA was more bioactive and degradable than BC/HA, which isa function of the degree of BC oxidation. High glucose levels in the BC degradation were observed as a function of oxidation degree, and other products, such as butyric acid and acetic acid resulted from DAC degradation. Therefore, this chemical modification reaction favors BC degradation, making it a good biodegradable and bioactive material with a potential for bone regeneration applications.
Topics: Acetic Acid; Acetobacteraceae; Body Fluids; Bone Regeneration; Butyric Acid; Cellulose; Durapatite; Glucose; Oxidation-Reduction; Tissue Engineering
PubMed: 32241452
DOI: 10.1016/j.carbpol.2020.116174 -
PloS One 2021Sickle Cell Disease (SCD) is an inherited blood disorder that leads to hemolytic anemia, pain, organ damage and early mortality. It is characterized by polymerized...
BACKGROUND
Sickle Cell Disease (SCD) is an inherited blood disorder that leads to hemolytic anemia, pain, organ damage and early mortality. It is characterized by polymerized deoxygenated hemoglobin, rigid sickle red blood cells and vaso-occlusive crises (VOC). Recurrent hypoxia-reperfusion injury in the gut of SCD patients could increase tissue injury, permeability, and bacterial translocation. In this context, the gut microbiome, a major player in health and disease, might have significant impact. This study sought to characterize the gut microbiome in SCD.
METHODS
Stool and saliva samples were collected from healthy controls (n = 14) and SCD subjects (n = 14). Stool samples were also collected from humanized SCD murine models including Berk, Townes and corresponding control mice. Amplified 16S rDNA was used for bacterial composition analysis using Next Generation Sequencing (NGS). Pairwise group analyses established differential bacterial groups at many taxonomy levels. Bacterial group abundance and differentials were established using DeSeq software.
RESULTS
A major dysbiosis was observed in SCD patients. The Firmicutes/Bacteroidetes ratio was lower in these patients. The following bacterial families were more abundant in SCD patients: Acetobacteraceae, Acidaminococcaceae, Candidatus Saccharibacteria, Peptostreptococcaceae, Bifidobacteriaceae, Veillonellaceae, Actinomycetaceae, Clostridiales, Bacteroidacbactereae and Fusobacteriaceae. This dysbiosis translated into 420 different operational taxonomic units (OTUs). Townes SCD mice also displayed gut microbiome dysbiosis as seen in human SCD.
CONCLUSION
A major dysbiosis was observed in SCD patients for bacteria that are known strong pro-inflammatory triggers. The Townes mouse showed dysbiosis as well and might serve as a good model to study gut microbiome modulation and its impact on SCD pathophysiology.
Topics: Adult; Anemia, Sickle Cell; Animals; Bacteria; Case-Control Studies; Dysbiosis; Female; Gastrointestinal Microbiome; Humans; Male; Mice; Middle Aged; Young Adult
PubMed: 34432825
DOI: 10.1371/journal.pone.0255956 -
Genome Biology and Evolution Jan 2019Symbiosis is now recognized as a driving force in evolution, a role that finds its ultimate expression in the variety of associations bonding insects with microbial... (Comparative Study)
Comparative Study
Symbiosis is now recognized as a driving force in evolution, a role that finds its ultimate expression in the variety of associations bonding insects with microbial symbionts. These associations have contributed to the evolutionary success of insects, with the hosts acquiring the capacity to exploit novel ecological niches, and the symbionts passing from facultative associations to obligate, mutualistic symbioses. In bacterial symbiont of insects, the transition from the free-living life style to mutualistic symbiosis often resulted in a reduction in the genome size, with the generation of the smallest bacterial genomes thus far described. Here, we show that the process of genome reduction is still occurring in Asaia, a group of bacterial symbionts associated with a variety of insects. Indeed, comparative genomics of Asaia isolated from different mosquito species revealed a substantial genome size and gene content reduction in Asaia from Anopheles darlingi, a South-American malaria vector. We thus propose Asaia as a novel model to study genome reduction dynamics, within a single bacterial taxon, evolving in a common biological niche.
Topics: Acetobacteraceae; Animals; Culicidae; Female; Genome Size; Genome, Bacterial; Symbiosis
PubMed: 30476071
DOI: 10.1093/gbe/evy255