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Foods (Basel, Switzerland) Apr 2024Staka is a traditional Greek sour cream made mostly from spontaneously fermented sheep milk or a mixture of sheep and goat milk. At the industrial scale, cream...
Study of the Microbiome of the Cretan Sour Cream Staka Using Amplicon Sequencing and Shotgun Metagenomics and Isolation of Novel Strains with an Important Antimicrobial Potential.
Staka is a traditional Greek sour cream made mostly from spontaneously fermented sheep milk or a mixture of sheep and goat milk. At the industrial scale, cream separators and starter cultures may also be used. Staka is sometimes cooked with flour to absorb most of the fat. In this study, we employed culture-based techniques, amplicon sequencing, and shotgun metagenomics to analyze the Staka microbiome for the first time. The samples were dominated by or spp. Most other bacteria were lactic acid bacteria (LAB) from the and genera or Gram-negative bacteria from the , , , -, and genera. , , or were the most prevalent genera in the samples, followed by other yeasts and molds like , , , , , or spp. Shotgun metagenomics allowed the species-level identification of , , , , , , , and . Binning of assembled shotgun reads followed by recruitment plot analysis of single reads could determine near-complete metagenome assembled genomes (MAGs). Culture-dependent and culture-independent analyses were in overall agreement with some distinct differences. For example, lactococci could not be isolated, presumably because they had entered a viable but not culturable (VBNC) state or because they were dead. Finally, several LAB, , and spp. isolates exhibited antimicrobial activities against oral or other pathogenic streptococci, and certain spoilage and pathogenic bacteria establishing their potential role in food bio-protection or new biomedical applications. Our study may pave the way for additional studies concerning artisanal sour creams to better understand the factors affecting their production and the quality.
PubMed: 38611432
DOI: 10.3390/foods13071129 -
PeerJ 2024Plant growth-promoting rhizobacteria (PGPR) have a specific symbiotic relationship with plants and rhizosphere soil. The purpose of this study was to evaluate the...
BACKGROUND
Plant growth-promoting rhizobacteria (PGPR) have a specific symbiotic relationship with plants and rhizosphere soil. The purpose of this study was to evaluate the effects of PGPR on blueberry plant growth, rhizospheric soil nutrients and the microbial community.
METHODS
In this study, nine PGPR strains, belonging to the genera , were selected and added into the soil in which the blueberry cuttings were planted. All the physiological indexes of the cuttings and all rhizospheric soil element contents were determined on day 6 after the quartic root irrigation experiments were completed. The microbial diversity in the soil was determined using high-throughput amplicon sequencing technology. The correlations between phosphorus solubilization, the auxin production of PGPR strains, and the physiological indexes of blueberry plants, and the correlation between rhizospheric microbial diversity and soil element contents were determined using the Pearson's correlation, Kendall's tau correlation and Spearman's rank correlation analysis methods.
RESULTS
The branch number, leaf number, chlorophyllcontentand plant height of the treated blueberry group were significantly higher than those of the control group. The rhizospheric soil element contents also increased after PGPR root irrigation. The rhizospheric microbial community structure changed significantly under the PGPR of root irrigation. The dominant phyla, except Actinomycetota, in the soil samples had the greatest correlation with phosphorus solubilization and the auxin production of PGPR strains. The branch number, leaf number, and chlorophyllcontent had a positive correlation with the phosphorus solubilization and auxin production of PGPR strains and soil element contents. In conclusion, plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with modification of the rhizospheric soil microbial community.
DISCUSSION
Plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with the modification of the rhizospheric soil microbial community. These data may help us to better understand the positive effects of PGPR on blueberry growth and the rhizosphere soil microenvironment, as well as provide a research basis for the subsequent development of a rhizosphere-promoting microbial fertilizer.
Topics: Soil; Blueberry Plants; Rhizosphere; Plants; Indoleacetic Acids; Phosphorus; Alphaproteobacteria
PubMed: 38426138
DOI: 10.7717/peerj.16992 -
Molecules (Basel, Switzerland) Feb 2024The blue crab (BC) is considered an invasive species colonizing Tunisian coasts since 2014. This work aims to explore its associated bacteria potential to produce...
The blue crab (BC) is considered an invasive species colonizing Tunisian coasts since 2014. This work aims to explore its associated bacteria potential to produce anionic exopolysaccharides (EPSs) in order to open up new ways of valorization. In this study, different BC samples were collected from the coastal area of Sfax, Tunisia. First, bacterial DNA was extracted from seven different fractions (flesh, gills, viscera, carapace scraping water, and three wastewaters from the production plant) and then sequenced using the metabarcoding approach targeting the V3-V4 region of the 16S rDNA to describe their microbiota composition. Metabarcoding data showed that the dominant bacterial genera were mainly , , and . In parallel, plate counting assays were performed on different culture media, and about 250 bacterial strains were isolated and identified by sequencing the 16S rDNA. EPS production by this new bacterial diversity was assessed to identify new compounds of biotechnological interest. The identification of the bacterial strains in the collection confirmed the dominance of spp. strains. Among them, 43 were identified as EPS producers, as revealed by Stains-all dye in agarose gel electrophoresis. A strain produced an EPS rich in both neutral sugars including rare sugars such as rhamnose and fucose and uronic acids. This original composition allows us to assume its potential for biotechnological applications and, more particularly, for developing innovative therapeutics. This study highlights bacterial strains associated with BC; they are a new untapped source for discovering innovative bioactive compounds for health and cosmetic applications, such as anionic EPS.
Topics: Animals; Brachyura; Bacteria; Microbiota; Sugars; DNA, Ribosomal; Polysaccharides, Bacterial
PubMed: 38398526
DOI: 10.3390/molecules29040774 -
Journal of Animal Science Jan 2023This study aimed to determine the efficacy of a bacterial 6-phytase (Buttiauxella spp.) supplemented beyond traditional dose levels based on jejunal mucosa-associated...
Efficacy of a bacterial 6-phytase supplemented beyond traditional dose levels on jejunal mucosa-associated microbiota, ileal nutrient digestibility, bone parameters, and intestinal health, and growth performance of nursery pigs.
This study aimed to determine the efficacy of a bacterial 6-phytase (Buttiauxella spp.) supplemented beyond traditional dose levels based on jejunal mucosa-associated microbiota, apparent ileal digestibility (AID), intestinal health and bone parameters, and growth performance of nursery pigs. Seventy-two weaned pigs (36 barrows and 36 gilts at 21 d of age with 5.8 ± 0.5 kg BW) were allotted to six treatments based on randomized complete block design with sex and initial BW as blocks and fed in three dietary phases (phase 1 for 14 d, phase 2 for 10 d, and phase 3 for 14 d). The treatments included a negative control (NC) diet without phytase formulated meeting nutrient requirements by NRC and the other five treatments were deficient in calcium (Ca) and phosphorus (P) by 0.12% with increasing levels of a bacterial 6-phytase (0, 500, 1,000, 2,000, and 5,000 FTU/kg feed). Titanium dioxide (0.4%) was added to phase 3 diets as an indigestible marker to measure AID of nutrients. On day 45, all pigs were euthanized to collect ileal digesta to measure AID, the third metacarpus to measure bone parameters, and jejunal mucosa to evaluate intestinal health and microbiota. Data were analyzed using the MIXED procedure for polynomial contrasts and the NLMIXED procedure for broken line analysis using the SAS 9.4. Broken line analysis demonstrated that 948 FTU/kg feed increased (P < 0.05) the ADG and the bone P content. Increasing phytase supplementation increased (linear, P < 0.05) AID of CP, bone P, and ash content. Increasing phytase supplementation reduced (P < 0.05) the fecal score during phases 2 and 3. Broken line analysis demonstrated that 1,889 FTU/kg feed increased (P < 0.05) bone breaking strength. Increasing phytase supplementation (PC vs. Phy) increased (P < 0.05) AID of ether extract (EE) and P. The supplementation of phytase at 2,000 FTU/kg feed tended (P = 0.087) to reduce the relative abundance of Prevotellaceae. In conclusion, the supplementation of a bacterial 6-phytase beyond traditional dose levels improved bone breaking strength, bone ash, and P content, AID of CP, EE, and P, and growth performance of nursery pigs with reduced relative abundance of Bacteroidetes specifically Prevotellaceae in the jejunal mucosa. Supplementation of a bacterial 6-phytase between 1,000 and 2,000 FTU/kg feed provided benefits associated with growth performance and bone parameters of nursery pigs.
Topics: Swine; Animals; Female; 6-Phytase; Digestion; Dietary Supplements; Diet; Intestinal Mucosa; Nutrients; Animal Feed
PubMed: 37115619
DOI: 10.1093/jas/skad134 -
Molecules (Basel, Switzerland) Feb 20232,4,6-Trinitrotoluene (TNT) is an aromatic pollutant that is difficult to be degraded in the natural environment. The screening of efficient degrading bacteria for...
2,4,6-Trinitrotoluene (TNT) is an aromatic pollutant that is difficult to be degraded in the natural environment. The screening of efficient degrading bacteria for bioremediation of TNT has received much attention from scholars. In this paper, transcriptome analysis of the efficient degrading bacterium sp. S19-1 revealed that the monooxygenase gene () was significantly up-regulated during TNT degradation. S-Δ (absence of gene in S19-1 mutant) degraded TNT 1.66-fold less efficiently than strain S19-1 (from 71.2% to 42.9%), and E- mutant (-expressing strain) increased the efficiency of TNT degradation 1.33-fold (from 52.1% to 69.5%) for 9 h at 180 rpm at 27 °C in LB medium with 1.4 µg·mL TNT. We predicted the structure of BuMO and purified recombinant BuMO (rBuMO). Its specific activity was 1.81 µmol·min·mg protein at pH 7.5 and 35 °C. The results of gas chromatography mass spectrometry (GC-MS) analysis indicated that 4-amino-2,6-dinitrotoluene (ADNT) is a metabolite of TNT biodegradation. We speculate that MO is involved in catalysis in the bacterial degradation pathway of TNT in TNT-polluted environment.
Topics: Biodegradation, Environmental; Trinitrotoluene; Mixed Function Oxygenases; Escherichia coli
PubMed: 36838956
DOI: 10.3390/molecules28041969 -
Systematic and Applied Microbiology Apr 2023While investigating the role of the rhizosphere in the development of Acute Oak Decline, bacterial strains belonging to the family Enterobacteriaceae were isolated from...
Description of Dryocola gen. nov. and two novel species, Dryocola boscaweniae sp. nov. and Dryocola clanedunensis sp. nov. isolated from the rhizosphere of native British oaks.
While investigating the role of the rhizosphere in the development of Acute Oak Decline, bacterial strains belonging to the family Enterobacteriaceae were isolated from rhizosphere soil following enrichment for the Enterobacterales. Partial sequencing of several housekeeping genes showed that these strains could not be assigned to an existing genus. Overall, 16 strains were investigated using a polyphasic approach to determine their taxonomic status. This involved phenotypic testing and fatty acid analysis paired with phylogenetic analyses of 16S rRNA and housekeeping gene sequences, as well as phylogenomic analysis of whole genome sequences. Phylogenomic and phylogenetic analyses consistently demonstrated that the 16 isolates could be separated into two distinct clusters in a monophyletic clade situated between the genera Cedecea and Buttiauxella. The two clusters could be genotypically and phenotypically differentiated from each other and from their closest neighbours. As such we propose the description of Dryocola boscaweniae gen. nov. sp. nov. (type strain H6W4 = CCUG 76177 = LMG 32610) and Dryocola clanedunesis sp. nov. (type strain H11S18 = CCUG 76181 = LMG 32611).
Topics: Sequence Analysis, DNA; Quercus; Rhizosphere; Phylogeny; RNA, Ribosomal, 16S; Bacterial Typing Techniques; DNA, Bacterial; Nucleic Acid Hybridization; Enterobacteriaceae; Fatty Acids
PubMed: 36689899
DOI: 10.1016/j.syapm.2023.126399 -
Microorganisms Nov 2022Tomatoes are among the most consumed vegetables worldwide and represent a source of health-beneficial substances. Our study represents the first investigating the...
Tomatoes are among the most consumed vegetables worldwide and represent a source of health-beneficial substances. Our study represents the first investigating the peel-associated epiphytic bacteria of red and purple (anthocyanin-rich) tomatoes subjected to organic and conventional farming systems. was the dominant phylum (relative abundances 79-91%) in all experimental conditions. represented a large fraction (39.3-47.5%) of the communities, with and as the most represented genera. The core microbiota was composed of 59 operational taxonomic units (OTUs), including the majority of the most abundant ones. The occurrence of the most abundant OTUs differed among the experimental conditions. OTU 1 (), OTU 2 (), and OTU 6 () were higher in red and purple tomatoes grown under organic farming. OTU 5 () had the highest abundance in red tomatoes subjected to organic farming. OTU 3 () was among the major OTUs in red tomatoes under both farming conditions. OTU 7 () and OTU 8 () had abundances ≥1% only in red tomatoes grown under conventional farming. PCA and clustering analysis highlighted a high similarity between the bacterial communities of red and purple tomatoes grown under organic farming. Furthermore, the bacterial communities of purple tomatoes grown under organic farming showed the lowest diversity and evenness. This work paves the way to understand the role of nutritional superior tomato genotypes, combined with organic farming, to modulate the presence of beneficial/harmful bacteria and supply healthier foods within a sustainable agriculture.
PubMed: 36422310
DOI: 10.3390/microorganisms10112240 -
Interactions of semiconductor Cd-based quantum dots and Cd with gut bacteria isolated from wild fry.PeerJ 2022With the rapid development of nanotechnology, more and more nanoproducts are being released into the environment where they may both pose ecological risks and be toxic...
BACKGROUND
With the rapid development of nanotechnology, more and more nanoproducts are being released into the environment where they may both pose ecological risks and be toxic to living organisms. The ecotoxicological impact of quantum dots (QDs), a class of nanoparticles (NPs), on aquatic organisms is becoming an emerging issue, this due to their nano-specific properties, to the physico-chemical transformation in the environment and to the possible release of toxic metals from their structure such as Cd.
METHODS
In this work, (i) spectroscopic measurements of commercially available Cd-based QDs (CdSe/ZnS-COOH) were made at various pH values (5.0 and 7.0) to study their interactions (at a concentration of 4 nm) with various strains of Gram-positive and Gram-negative gut bacteria after short-term exposure and (ii) the antibacterial efficacy of QDs and Cd (at a concentration 0.09-3.56 mM) against gut bacteria isolated from wild freshwater fry was studied at different temperatures (15 °C and 25 °C) and pH values (5.0 and 7.0) by applying a well-established disc diffusion assay.
RESULTS
Twenty-six gut bacterial isolates from wild fry were identified as spp., , , , , sp., sp., sp., and sp. Cd-based (CdSe/ZnS-COOH) QDs at a concentration of 4 nm were found to be stable in aqueous media (with pH 7.0) or starting to form aggregates (at pH 5.0), thus, apparently, did not release heavy metals (HMs) into the media over 48 h in conditions of light or dark and did not show antibacterial efficacy on the gut bacteria isolated from wild fry after short-term (9 h and 48 h) incubations. Cd was found to produce significant dose-dependent toxic effects on bacterial growth, and the size of the inhibition zones on some of the tested strains significantly correlated with temperature. The most sensitive and the most resistant to Cd were the Gram-positive bacteria, for which the minimum inhibitory concentration (MIC) values of Cd were 0.09-0.27 mM and 3.11-3.29 mM respectively and varied significantly between the tested temperatures (15 °C and 25 °C). The MIC values of Cd for the Gram-negative bacteria (18 out of 22 strains) ranged from 0.44 to 0.71 mM and did not differ significantly between the tested temperatures. Among the selected Gram-positive and Gram-negative strains, those with the higher sensitivity towards Cd also revealed relatively stronger signals of QDs photoluminescence (PL) when transferred after incubation into fresh medium without QDs. In addition, the formation of endogenous metalloporphyrins observed spectroscopically in some bacterial strains indicates certain differences in metabolic activity that may play a protective role against potential oxidative damage.
Topics: Quantum Dots; Cadmium; Bacteria; Semiconductors; Anti-Bacterial Agents; Gram-Negative Bacteria
PubMed: 36128199
DOI: 10.7717/peerj.14025 -
Biology May 2022In this study, we used high-throughput sequencing technologies (sequencing of V3-V4 hypervariable regions of 16S rRNA gene) to investigate for the first time the...
In this study, we used high-throughput sequencing technologies (sequencing of V3-V4 hypervariable regions of 16S rRNA gene) to investigate for the first time the microbiota of Latxa ewe raw milk and the bacterial shifts that occur during the production and ripening of Idiazabal cheese. Results revealed several bacterial genera not reported previously in raw ewe milk and cheese, such as and . Both the cheese making and ripening processes had a significant impact on bacterial communities. Overall, the growth of lactic acid bacteria (LAB) (, , , , and ) was promoted, whereas that of non-desirable and environmental bacteria was inhibited (such as and ). However, considerable differences were observed among producers. It is noteworthy that the starter LAB () predominated up to 30 or 60 days of ripening and then, the growth of non-starter LAB (, , and ) was promoted. Moreover, in some cases, bacteria related to the production of volatile compounds (such as , and ) also showed notable abundance during the first few weeks of ripening. Overall, the results of this study enhance our understanding of microbial shifts that occur during the production and ripening of a raw ewe milk-derived cheese (Idiazabal), and could indicate that the practices adopted by producers have a great impact on the microbiota and final quality of this cheese.
PubMed: 35625497
DOI: 10.3390/biology11050769 -
Molecules (Basel, Switzerland) May 2022Acetyl xylan esterases (AXEs) are enzymes capable of hydrolysing the acetyl bonds in acetylated xylan, allowing for enhanced activity of backbone-depolymerizing enzymes....
Acetyl xylan esterases (AXEs) are enzymes capable of hydrolysing the acetyl bonds in acetylated xylan, allowing for enhanced activity of backbone-depolymerizing enzymes. Bioprospecting novel AXE is essential in designing enzyme cocktails with desired characteristics targeting the complete breakdown of lignocellulose. In this article, we report the characterisation of a novel AXE identified as Gene_id_40363 in the metagenomic library analysed from the gut microbiota of the common black slug. The conserved domain description was identified with an NCBI BLASTp search using the translated nucleotide sequence as a query. The activity of the recombinant enzyme was tested on various synthetic substrates and acetylated substrates. The protein sequence matched the conserved domain described as putative hydrolase and aligned closely to an uncharacterized esterase from , hence the designation as BaAXE. BaAXE showed low sequence similarity among characterized CE family proteins with an available 3D structure. BaAXE was active on 4-nitrophenyl acetate, reporting a specific activity of 78.12 U/mg and a Km value of 0.43 mM. The enzyme showed optimal activity at 40 °C and pH 8 and showed high thermal stability, retaining over 40% activity after 2 h of incubation from 40 °C to 100 °C. BaAXE hydrolysed acetyl bonds, releasing acetic acid from acetylated xylan and β-D-glucose pentaacetate. BaAXE has great potential for biotechnological applications harnessing its unique characteristics. In addition, this proves the possibility of bioprospecting novel enzymes from understudied environments.
Topics: Acetylesterase; Animals; Gastrointestinal Microbiome; Gastropoda; Substrate Specificity; Xylans
PubMed: 35566348
DOI: 10.3390/molecules27092999