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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 -
Frontiers in Microbiology 2021The genus is a significant group of bacteria which is invariably of great clinical and ecological importance. Previous studies have shown that the genus is...
The genus is a significant group of bacteria which is invariably of great clinical and ecological importance. Previous studies have shown that the genus is polyphyletic in nature. Our present study focused on generating a lucid understanding of the phylogenetic framework for the re-evaluation and reclassification of the genus Phylogenetic studies based on the 16S rRNA gene and 92 concatenated genes suggested that the genus is heterogeneous, forming seven major groups. Existing species were subjected to an array of genomic, phenotypic, and chemotaxonomic analyses in order to resolve the heterogeneity. Genomic similarity indices (DDH and ANI) indicated that the members were well-defined at the species level. The Percentage of Conserved Proteins (POCP) and the average Amino Acid Identity (AAI) values between the groups of the genus and other interspersing members of the family were below 65 and 70%, respectively. The pan-genome evaluation depicted that the pan-genome was an open type and the members shared 958 core genes. This claim of reclassification was equally supported by the phenotypic and chemotaxonomic differences between the groups. Thus, in this study, we propose to re-evaluate and reclassify the genus and propose six novel genera as gen. nov., gen. nov., gen. nov., gen. nov., gen. nov., and gen. nov.
PubMed: 34484138
DOI: 10.3389/fmicb.2021.677842 -
International Journal of Food... Jan 2016Yeast, lactic acid bacteria (LAB) and acetic acid bacteria (AAB) populations, isolated from cocoa bean heap and box fermentations in West Africa, have been investigated....
Molecular identification and physiological characterization of yeasts, lactic acid bacteria and acetic acid bacteria isolated from heap and box cocoa bean fermentations in West Africa.
Yeast, lactic acid bacteria (LAB) and acetic acid bacteria (AAB) populations, isolated from cocoa bean heap and box fermentations in West Africa, have been investigated. The fermentation dynamicswere determined by viable counts, and 106 yeasts, 105 LAB and 82 AAB isolateswere identified by means of rep-PCR grouping and sequencing of the rRNA genes. During the box fermentations, the most abundant species were Saccharomyces cerevisiae, Candida ethanolica, Lactobacillus fermentum, Lactobacillus plantarum, Acetobacter pasteurianus and Acetobacter syzygii, while S. cerevisiae, Schizosaccharomyces pombe, Hanseniaspora guilliermondii, Pichia manshurica, C. ethanolica, Hanseniaspora uvarum, Lb. fermentum, Lb. plantarum, A. pasteurianus and Acetobacter lovaniensis were identified in the heap fermentations. Furthermore, the most abundant species were molecularly characterized by analyzing the rep-PCR profiles. Strains grouped according to the type of fermentations and their progression during the transformation process were also highlighted. The yeast, LAB and AAB isolates were physiologically characterized to determine their ability to grow at different temperatures, as well as at different pH, and ethanol concentrations, tolerance to osmotic stress, and lactic acid and acetic acid inhibition. Temperatures of 45 °C, a pH of 2.5 to 3.5, 12% (v/v) ethanol and high concentrations of lactic and acetic acid have a significant influence on the growth of yeasts, LAB and AAB. Finally, the yeastswere screened for enzymatic activity, and the S. cerevisiae, H. guilliermondii, H. uvarumand C. ethanolica species were shown to possess several enzymes that may impact the quality of the final product.
Topics: Acetic Acid; Acetobacter; Africa, Western; Biodiversity; Cacao; Ethanol; Fermentation; Hanseniaspora; Lactic Acid; Limosilactobacillus fermentum; Lactobacillus plantarum; RNA, Ribosomal; RNA, Ribosomal, 16S; Saccharomyces cerevisiae; Yeasts
PubMed: 26425801
DOI: 10.1016/j.ijfoodmicro.2015.09.004 -
Analysis of cellulose synthesis in a high-producing acetic acid bacterium Komagataeibacter hansenii.Applied Microbiology and Biotechnology May 2023Bacterial cellulose (BC) represents a renewable biomaterial with unique properties promising for biotechnology and biomedicine. Komagataeibacter hansenii ATCC 53,582 is...
Bacterial cellulose (BC) represents a renewable biomaterial with unique properties promising for biotechnology and biomedicine. Komagataeibacter hansenii ATCC 53,582 is a well-characterized high-yield producer of BC used in the industry. Its genome encodes three distinct cellulose synthases (CS), bcsAB1, bcsAB2, and bcsAB3, which together with genes for accessory proteins are organized in operons of different complexity. The genetic foundation of its high cellulose-producing phenotype was investigated by constructing chromosomal in-frame deletions of the CSs and of two predicted regulatory diguanylate cyclases (DGC), dgcA and dgcB. Proteomic characterization suggested that BcsAB1 was the decisive CS because of its high expression and its exclusive contribution to the formation of microcrystalline cellulose. BcsAB2 showed a lower expression level but contributes significantly to the tensile strength of BC and alters fiber diameter significantly as judged by scanning electron microscopy. Nevertheless, no distinct extracellular polymeric substance (EPS) from this operon was identified after static cultivation. Although transcription of bcsAB3 was observed, expression of the protein was below the detection limit of proteome analysis. Alike BcsAB2, deletion of BcsAB3 resulted in a visible reduction of the cellulose fiber diameter. The high abundance of BcsD and the accessory proteins CmcAx, CcpAx, and BglxA emphasizes their importance for the proper formation of the cellulosic network. Characterization of deletion mutants lacking the DGC genes dgcA and dgcB suggests a new regulatory mechanism of cellulose synthesis and cell motility in K. hansenii ATCC 53,582. Our findings form the basis for rational tailoring of the characteristics of BC. KEY POINTS: • BcsAB1 induces formation of microcrystalline cellulose fibers. • Modifications by BcsAB2 and BcsAB3 alter diameter of cellulose fibers. • Complex regulatory network of DGCs on cellulose pellicle formation and motility.
Topics: Acetic Acid; Extracellular Polymeric Substance Matrix; Proteomics; Acetobacteraceae; Cellulose
PubMed: 36930278
DOI: 10.1007/s00253-023-12461-z -
BMC Microbiology Dec 2022The microbiome in the insect reproductive tract is poorly understood. Our previous study demonstrated the presence of Lactobacillus spp. in female moths, but their...
BACKGROUND
The microbiome in the insect reproductive tract is poorly understood. Our previous study demonstrated the presence of Lactobacillus spp. in female moths, but their distribution and function remain unclear. Lactobacillus spp. are known as the 'healthy' vaginal microbiome in humans.
RESULTS
Here, we studied the microbiome in the reproductive system (RS) and gut of Spodoptera frugiperda using 16S rDNA sequences. The obtained 4315 bacterial OTUs were classified into 61 phyla and 642 genera, with Proteobacteria, Firmicutes and Bacteroidota being the top three dominant phyla and Enterococcus and Asaia being dominant genera in most samples. Mating dramatically increased the abundance of pathogens or pathogenic functions in the gut, while in the RS, the change range was trivial. Taxonomy assignment identified thirteen Lactobacillus spp. in S. frugiperda, with Lactobacillus crustorum and Lactobacillus murinus showing high abundance. Three species found in S. frugiperda, namely L. reuteri, L. plantarum and L. brevis, have also been identified as human 'healthy' vaginal bacterial species. Lactobacillus spp. showed higher abundance in the RS of virgin females and lower abundance in the RS of virgin males and the gut of virgin females. Mating reduced their abundance in the RS of females but increased their abundance in the RS of males, especially in males mated with multiple females. The RS of virgin females and of multiple mated males were very similar in terms of composition and abundance of Lactobacillus species, with Lactobacillus crustorum showing much higher abundance in both tissues, potentially due to sexual transmission.
CONCLUSIONS
Lactobacillus spp. showed high abundance and diversity in the RS of female moths. The higher abundance of Lactobacillus spp. in the RS of female moths and the similarity of Lactobacillus species in female moths with human 'healthy' vaginal Lactobacillus spp. suggest that these bacterial strains are also an important microbiome in the RS of female moths.
Topics: Male; Animals; Humans; Female; Gastrointestinal Microbiome; Moths; Lactobacillus; Vagina; Acetobacteraceae
PubMed: 36536275
DOI: 10.1186/s12866-022-02724-6 -
BMC Microbiology Dec 2019Mass-rearing, domestication and gamma irradiation of tephritid fruit flies used in sterile insect technique (SIT) programmes can negatively impact fly quality and...
Diet and irradiation effects on the bacterial community composition and structure in the gut of domesticated teneral and mature Queensland fruit fly, Bactrocera tryoni (Diptera: Tephritidae).
BACKGROUND
Mass-rearing, domestication and gamma irradiation of tephritid fruit flies used in sterile insect technique (SIT) programmes can negatively impact fly quality and performance. Symbiotic bacteria supplied as probiotics to mass-reared fruit flies may help to overcome some of these issues. However, the effects of tephritid ontogeny, sex, diet and irradiation on their microbiota are not well known.
RESULTS
We have used next-generation sequencing to characterise the bacterial community composition and structure within Queensland fruit fly, Bactrocera tryoni (Froggatt), by generating 16S rRNA gene amplicon libraries derived from the guts of 58 individual teneral and mature, female and male, sterile and fertile adult flies reared on artificial larval diets in a laboratory or mass-rearing environment, and fed either a full adult diet (i.e. sugar and yeast hydrolysate) or a sugar only adult diet. Overall, the amplicon sequence read volume in tenerals was low and smaller than in mature adult flies. Operational taxonomic units (OTUs), belonging to the families Enterobacteriaceae (8 OTUs) and Acetobacteraceae (1 OTU) were most prevalent. Enterobacteriaceae dominated laboratory-reared tenerals from a colony fed a carrot-based larval diet, while Acetobacteraceae dominated mass-reared tenerals from a production facility colony fed a lucerne chaff based larval diet. As adult flies matured, Enterobacteriaceae became dominant irrespective of larval origin. The inclusion of yeast in the adult diet strengthened this shift away from Acetobacteraceae towards Enterobacteriaceae. Interestingly, irradiation increased 16S rRNA gene sequence read volume.
CONCLUSIONS
Our findings suggest that bacterial populations in fruit flies experience significant bottlenecks during metamorphosis. Gut bacteria in teneral flies were less abundant and less diverse, and impacted by colony origin. In contrast, mature adult flies had selectively increased abundances for some gut bacteria, or acquired these bacteria from the adult diet and environment. Furthermore, irradiation augmented bacterial abundance in mature flies. This implies that either some gut bacteria were compensating for damage caused by irradiation or irradiated flies had lost their ability to regulate bacterial load. Our findings suggest that the adult stage prior to sexual maturity may be ideal to target for probiotic manipulation of fly microbiota to increase fly performance in SIT programmes.
Topics: Animal Feed; Animals; Bacteria; DNA, Bacterial; DNA, Ribosomal; Domestication; Female; Gastrointestinal Microbiome; High-Throughput Nucleotide Sequencing; Male; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, RNA; Tephritidae
PubMed: 31870300
DOI: 10.1186/s12866-019-1649-6 -
Journal of Bacteriology Jun 2016
Topics: Acetobacter; Caulobacter; Cyclic GMP; Fimbriae, Bacterial; Flagella; Locomotion; Phosphoric Diester Hydrolases
PubMed: 27179064
DOI: 10.1128/JB.00190-16 -
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 -
The Journal of Biological Chemistry Sep 2021Understanding the mechanism by which cellulases from bacteria, fungi, and protozoans catalyze the digestion of lignocellulose is important for developing cost-effective...
Understanding the mechanism by which cellulases from bacteria, fungi, and protozoans catalyze the digestion of lignocellulose is important for developing cost-effective strategies for bioethanol production. Cel7A from the fungus Trichoderma reesei is a model exoglucanase that degrades cellulose strands from their reducing ends by processively cleaving individual cellobiose units. Despite being one of the most studied cellulases, the binding and hydrolysis mechanisms of Cel7A are still debated. Here, we used single-molecule tracking to analyze the dynamics of 11,116 quantum dot-labeled TrCel7A molecules binding to and moving processively along immobilized cellulose. Individual enzyme molecules were localized with a spatial precision of a few nanometers and followed for hundreds of seconds. Most enzyme molecules bound to cellulose in a static state and dissociated without detectable movement, whereas a minority of molecules moved processively for an average distance of 39 nm at an average speed of 3.2 nm/s. These data were integrated into a three-state model in which TrCel7A molecules can bind from solution into either static or processive states and can reversibly switch between states before dissociating. From these results, we conclude that the rate-limiting step for cellulose degradation by Cel7A is the transition out of the static state, either by dissociation from the cellulose surface or by initiation of a processive run. Thus, accelerating the transition of Cel7A out of its static state is a potential avenue for improving cellulase efficiency.
Topics: Acetobacteraceae; Cellulose; Cellulose 1,4-beta-Cellobiosidase; Fungal Proteins; Hydrolysis; Hypocreales; Microscopy, Atomic Force; Microscopy, Fluorescence; Quantum Dots; Substrate Specificity
PubMed: 34339742
DOI: 10.1016/j.jbc.2021.101029 -
Advanced Science (Weinheim,... Jun 2021Bacterial cellulose (BC) has excellent material properties and can be produced sustainably through simple bacterial culture, but BC-producing bacteria lack the extensive...
Bacterial cellulose (BC) has excellent material properties and can be produced sustainably through simple bacterial culture, but BC-producing bacteria lack the extensive genetic toolkits of model organisms such as (). Here, a simple approach is reported for producing highly programmable BC materials through incorporation of engineered . The acetic acid bacterium is cocultured with engineered in droplets of glucose-rich media to produce robust cellulose capsules, which are then colonized by the upon transfer to selective lysogeny broth media. It is shown that the encapsulated can produce engineered protein nanofibers within the cellulose matrix, yielding hybrid capsules capable of sequestering specific biomolecules from the environment and enzymatic catalysis. Furthermore, capsules are produced which can alter their own bulk physical properties through enzyme-induced biomineralization. This novel system uses a simple fabrication process, based on the autonomous activity of two bacteria, to significantly expand the functionality of BC-based living materials.
Topics: Bioengineering; Capsules; Cellulose; Coculture Techniques; Culture Media; Escherichia coli; Gluconacetobacter; Nanofibers
PubMed: 34141524
DOI: 10.1002/advs.202004699