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Microbiology Spectrum Dec 2023Acetobacteraceae are one of the best known and most extensively studied groups of bacteria, which nowadays encompasses a variety of taxa that are very different from the...
Acetobacteraceae are one of the best known and most extensively studied groups of bacteria, which nowadays encompasses a variety of taxa that are very different from the vinegar-producing species defining the family. Our paper presents the most detailed phylogeny of all current taxa classified as , for which we propose a taxonomic revision. Several of such taxa inhabit some of the most extreme environments on the planet, from the deserts of Antarctica to the Sinai desert, as well as acidic niches in volcanic sites like the one we have been studying in Patagonia. Our work documents the progressive variation of the respiratory chain in early branching Acetobacteraceae into the different respiratory chains of acidophilic taxa such as and acetous taxa such as . Remarkably, several genomes retain remnants of ancestral photosynthetic traits and functional complexes. Thus, we propose that the common ancestor of was photosynthetic.
Topics: Acetobacteraceae; Phylogeny; RNA, Ribosomal, 16S; Acids; Antarctic Regions; DNA, Bacterial
PubMed: 37975678
DOI: 10.1128/spectrum.00575-23 -
Microorganisms Dec 2023Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive...
Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that species, such as and prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to (32-35%). In addition, a high proportion of sequences belonging to the genera and but not classified at the species level were found in the suluguni-like cheese. , as well as constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and , and represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the , and families (the order within ), 4 to (the phylum) and 2 to (the phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.
PubMed: 38276185
DOI: 10.3390/microorganisms12010016 -
PloS One 2023Lactobacilli and Acetobacter sp. are commercially important bacteria that often form communities in natural fermentations, including food preparations, spoilage, and in...
Lactobacilli and Acetobacter sp. are commercially important bacteria that often form communities in natural fermentations, including food preparations, spoilage, and in the digestive tract of the fruit fly Drosophila melanogaster. Communities of these bacteria are widespread and prolific, despite numerous strain-specific auxotrophies, suggesting they have evolved nutrient interdependencies that regulate their growth. The use of a chemically-defined medium (CDM) supporting the growth of both groups of bacteria would facilitate the identification of the molecular mechanisms for the metabolic interactions between them. While numerous CDMs have been developed that support specific strains of lactobacilli or Acetobacter, there has not been a medium formulated to support both genera. We developed such a medium, based on a previous CDM designed for growth of lactobacilli, by modifying the nutrient abundances to improve growth yield. We further simplified the medium by substituting casamino acids in place of individual amino acids and the standard Wolfe's vitamins and mineral stocks in place of individual vitamins and minerals, resulting in a reduction from 40 to 8 stock solutions. These stock solutions can be used to prepare several CDM formulations that support robust growth of numerous lactobacilli and Acetobacters. Here, we provide the composition and several examples of its use, which is important for tractability in dissecting the genetic and metabolic basis of natural bacterial species interactions.
Topics: Animals; Acetobacter; Lactobacillus; Drosophila melanogaster; Bacteria; Vitamins
PubMed: 37824485
DOI: 10.1371/journal.pone.0292585 -
BMC Ecology and Evolution Aug 2023Rodents form the largest order among mammals in terms of species diversity, and home range is the area where an individual normally moves during its normal daily...
BACKGROUND
Rodents form the largest order among mammals in terms of species diversity, and home range is the area where an individual normally moves during its normal daily activities. Information about rodent home ranges is paramount in the development of effective conservation and management strategies. This is because rodent home range varies within species and different habitats. In Uganda, tropical high altitude forests such as the Mabira Central Forest Reserve are experiencing continuous disturbance. However, information on rodent home range is lacking. Therefore, a two year Capture-Mark-Release (CMR) of rodents was conducted in the intact forest habitat: Wakisi, regenerating forest habitat: Namananga, and the depleted forest habitat: Namawanyi of Mabira Central Forest Reserve in order to determine the dominant rodent species, their home ranges, and factors affecting these home ranges. The home ranges were determined by calculating a minimum convex polygon with an added boundary strip of 5 m.
RESULTS
Overall, the most dominant rodent species were: Lophuromys stanleyi, Hylomyscus stella, Praomys jacksoni Mastomys natalensis, Lophuromys ansorgei, and Lemniscomys striatus. H. stella dominated the intact forest habitat, while L. stanleyi was the most dominant both in the regenerating and the depleted forest habitats. L. stanleyi had a larger home range in the depleted forest, and the regenerating forest habitats, respectively. In the regenerating forest habitat, M. natalensis had a larger home range size, followed by L. stanleyi, and L. striatus. While in the intact forest habitat, H. stella had the largest home range followed by P. jacksoni. H. stella, L. striatus, L. stanleyi, M. natalensis, and P. jacksoni were most dominant during the wet season while L. ansorgei was relatively more dominant during the dry season. L. ansorgei, and P. jacksoni had a larger home range in the dry season, and a lower home range in the wet season. H. stella, L. stanleyi, M. natalansis and L.striatus had larger home ranges in the wet season, and lower home ranges in the dry season. The home ranges of the dominant rodent species varied across the three habitats in Mabira central forest reserve ([Formula: see text], [Formula: see text]).
CONCLUSION
The significant variation in home ranges of the dominant rodent species in Mabira Central Forest Reserve depending on the type of habitat presupposes that the rodent management strategies in disturbed forest reserves should focus on the type of habitat.
Topics: Animals; Homing Behavior; Uganda; Forests; Acetobacteraceae; Murinae
PubMed: 37605119
DOI: 10.1186/s12862-023-02148-4 -
Frontiers in Microbiology 2023The microbiota of bulk tank raw milk is known to be closely related to that of microbial niches of the on-farm environment. Preserved forage types are partof this...
INTRODUCTION
The microbiota of bulk tank raw milk is known to be closely related to that of microbial niches of the on-farm environment. Preserved forage types are partof this ecosystem and previous studies have shown variations in their microbial ecology. However, little is known of the microbiota of forage ration combinations and the transfer rates of associated species to milk.
METHODS
We identified raw milk bacteria that may originate from forage rations encompassing either hay (H) or grass/legume silage uninoculated (GL) as the only forage type, or a combination of GL and corn silage uninoculated (GLC), or grass/legume and corn silage both inoculated (GLICI). Forage and milk samples collected in the fall and spring from 24 dairy farms were analyzed using 16S rRNA gene high-throughput sequencing following a treatment with propidium monoazide to account for viable cells.
RESULTS AND DISCUSSION
Three community types separating H, GL, and GLICI forage were identified. While the H community was co-dominated by , , , and , the GL and GLICI communities showed high proportions of and , respectively. Most of the GLC and GLICI rations were similar, suggesting that in the mixed forage rations involving grass/legume and corn silage, the addition of inoculant in one or both types of feed does not considerably change the microbiota. Raw milk samples were not grouped in the same way, as the GLC milk was phylogenetically different from that of GLICI across sampling periods. Raw milk communities, including the GLICI group for which cows were fed inoculated forage, were differentiated by and other Proteobacteria, instead of by lactic acid bacteria. Of the 113 amplicon sequence variants (ASVs) shared between forage rations and corresponding raw milk, bacterial transfer rates were estimated at 18 to 31%. Silage-based forage rations, particularly those including corn, share more ASVs with raw milk produced on corresponding farms compared to that observed in the milk from cows fed hay. These results show the relevance of cow forage rations as sources of bacteria that contaminate milk and serve to advance our knowledge of on-farm raw milk contamination.
PubMed: 38029116
DOI: 10.3389/fmicb.2023.1175663 -
Microbial Biotechnology Sep 2023The excessive consumption of alcohol results in a dysbiosis of the gut microbiota, which subsequently impairs the gut microbiota-brain/liver axes and induces cognitive...
The excessive consumption of alcohol results in a dysbiosis of the gut microbiota, which subsequently impairs the gut microbiota-brain/liver axes and induces cognitive dysfunction and hepatic injury. This study aimed to investigate the potential effect of Acetobacter pasteurianus BP2201 in reducing the negative effects of alcohol consumption on cognitive function and liver health by modulating the gut microbiota-brain/liver axes. Treatment with A. pasteurianus BP2201 improved alcohol-induced hippocampal damage, suppressed neuroinflammation, promoted neuroprotein expression in the hippocampus and enhanced cognitive function. At the same time, A. pasteurianus BP2201 can also reduce serum lipid levels, relieve oxidative stress, inhibit TLR4/MyD88/NF-κB pathway, reduce the secretion of TNF-α and IL-1β, so as to improve alcoholic liver injury. Concomitantly, the treatment with A. pasteurianus BP2201 leads to a shift in the intestinal microbiota structure towards that of healthy individuals, inhibiting the proliferation of harmful bacteria and promoting the recovery of beneficial bacteria. In addition, it also improves brain cognitive dysfunction and liver health by affecting the gut microbiota-brain/liver axes by promoting the synthesis of relevant amino acids and the metabolism of nucleotide base components. These findings demonstrate the potential of regulating the gut microbiome and gut microbiota-brain/liver axes to mitigate alcohol-induced disease.
Topics: Mice; Animals; Gastrointestinal Microbiome; Liver; Ethanol; Acetobacter; Mice, Inbred C57BL; Dysbiosis
PubMed: 37354051
DOI: 10.1111/1751-7915.14303 -
Microbial Ecology Oct 2023Bacteria residing in the guts of pollinating insects play a key role in nutrient acquisition, digestion, and resistance to pests and diseases. Imbalances in microbial...
Bacteria residing in the guts of pollinating insects play a key role in nutrient acquisition, digestion, and resistance to pests and diseases. Imbalances in microbial flora in response to environmental change and stress can therefore impact insect health and resilience. This study is aimed at defining the core gut microbiome of the Australian native stingless bee, Tetragonula carbonaria, and exploring the impact of colony transplantation on gut health. The gut microbiomes of nine forager bees from natural (log) and manufactured (box) hives were examined via 16S rRNA gene amplicon sequencing. Some differences were observed at the ASV level between the microbiomes of log and box hive bees. However, a core microbiome, dominated by Lactobacillus spp., unclassified Acetobacteraceae spp., and Bombella spp., was maintained. Further, the inferred functional potential of the microbiomes was consistent across all individuals. This study highlights that although hive transplantation has an impact on the overall diversity of stingless bee gut microbiomes, it is unlikely to have a significant negative impact on the overall health and resilience of the colony.
Topics: Bees; Animals; Gastrointestinal Microbiome; Australia; RNA, Ribosomal, 16S; Microbiota; Urticaria
PubMed: 37088849
DOI: 10.1007/s00248-023-02222-w -
Biosensors Dec 2023Biosensors based on an oxygen electrode, a mediator electrode, and a mediator microbial biofuel cell (MFC) using the bacteria B-1280 were formed and tested to determine...
Biosensors based on an oxygen electrode, a mediator electrode, and a mediator microbial biofuel cell (MFC) using the bacteria B-1280 were formed and tested to determine the integral toxicity. bacteria exhibited high sensitivity to the toxic effects of phenol, 2,4-dinitrophenol, salicylic and trichloroacetic acid, and a number of heavy metal ions. The system " bacteria-ferrocene-graphite-paste electrode" was superior in sensitivity to biosensors formed using an oxygen electrode and MFC, in particular regarding heavy metal ions (EC of Cr, Mn and Cd was 0.8 mg/dm, 0.3 mg/dm and 1.6 mg/dm, respectively). It was determined that the period of stable functioning of electrochemical systems during measurements was reduced by half (from 30 to 15 days) due to changes in the enzyme system of microbial cells when exposed to toxicants. Samples of the products made from polymeric materials were analyzed using developed biosensor systems and standard biotesting methods based on inhibiting the growth of duckweed , reducing the motility of bull sperm, and quenching the luminescence of the commercial test system "Ecolum". The developed bioelectrocatalytic systems were comparable in sensitivity to commercial biosensors, which made it possible to correlate the results and identify, by all methods, a highly toxic sample containing diphenylmethane-4,4'-diisocyanate according to GC-MS data.
Topics: Male; Animals; Cattle; Polymers; Semen; Metals, Heavy; Biosensing Techniques; Gluconobacter oxydans; Ions; Oxygen
PubMed: 38131771
DOI: 10.3390/bios13121011 -
Cell Reports Apr 2024Microbial invasions underlie host-microbe interactions resulting in pathogenesis and probiotic colonization. In this study, we explore the effects of the microbiome on...
Microbial invasions underlie host-microbe interactions resulting in pathogenesis and probiotic colonization. In this study, we explore the effects of the microbiome on microbial invasion in Drosophila melanogaster. We demonstrate that gut microbes Lactiplantibacillus plantarum and Acetobacter tropicalis improve survival and lead to a reduction in microbial burden during infection. Using a microbial interaction assay, we report that L. plantarum inhibits the growth of invasive bacteria, while A. tropicalis reduces this inhibition. We further show that inhibition by L. plantarum is linked to its ability to acidify its environment via lactic acid production by lactate dehydrogenase, while A. tropicalis diminishes the inhibition by quenching acids. We propose that acid from the microbiome is a gatekeeper to microbial invasions, as only microbes capable of tolerating acidic environments can colonize the host. The methods and findings described herein will add to the growing breadth of tools to study microbe-microbe interactions in broad contexts.
Topics: Animals; Drosophila melanogaster; Microbiota; Acetobacter; Gastrointestinal Microbiome; Lactobacillus plantarum; Hydrogen-Ion Concentration; Lactic Acid
PubMed: 38583152
DOI: 10.1016/j.celrep.2024.114087 -
ACS Applied Bio Materials Sep 2023There is a growing interest in developing natural hydrogel-based scaffolds to culture cells in a three-dimensional (3D) millieu that better mimics the cells'...
There is a growing interest in developing natural hydrogel-based scaffolds to culture cells in a three-dimensional (3D) millieu that better mimics the cells' microenvironment. A promising approach is to use hydrogels from animal tissues, such as decellularized extracellular matrices; however, they usually exhibit suboptimal mechanical properties compared to native tissue and their composition with hundreds of different protein complicates to elucidate which stimulus triggers cell's responses. As simpler scaffolds, type I collagen hydrogels are used to study cell behavior in mechanobiology even though they are also softer than native tissues. In this work, type I collagen is mixed with bacterial nanocellulose fibers (BCf) to develop reinforced scaffolds with mechanical properties suitable for 3D cell culture. BCf were produced from blended pellicles biosynthesized from . Then, BCf were mixed with concentrated collagen from rat-tail tendons to form composite hydrogels. Confocal laser scanning microscopy and scanning electron microscopy images confirmed the homogeneous macro- and microdistribution of both natural polymers. Porosity analysis confirmed that BCf do not disrupt the scaffold structure. Tensile strength and rheology measurements demonstrated the reinforcement action of BCf (43% increased stiffness) compared to the collagen hydrogel while maintaining the same viscoelastic response. Additionally, this reinforcement of collagen hydrogels with BCf offers the possibility to mix cells before gelation and then proceed to the culture of the 3D cell scaffolds. We obtained scaffolds with human bone marrow-derived mesenchymal stromal cells or human fibroblasts within the composite hydrogels, allowing a homogeneous 3D viable culture for at least 7 days. A smaller surface shrinkage in the reinforced hydrogels compared to type I collagen hydrogels confirmed the strengthening of the composite hydrogels. These collagen hydrogels reinforced with BCf might emerge as a promising platform for 3D organ modeling, tissue-engineering applications, and suitable to conduct fundamental mechanobiology studies.
Topics: Humans; Animals; Rats; Collagen Type I; Cell Culture Techniques, Three Dimensional; Fibroblasts; Gluconacetobacter xylinus; Hydrogels
PubMed: 37669535
DOI: 10.1021/acsabm.3c00126