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Archives of Microbiology May 2022The search for sustainable development has increased interest in the improvement of technologies that use renewable energy sources. One of the alternatives in the...
The search for sustainable development has increased interest in the improvement of technologies that use renewable energy sources. One of the alternatives in the production of renewable energy comes from the use of waste including urban solids, animal excrement from livestock, and biomass residues from agro-industrial plants. These materials may be used in the production of biogas, making its production highly sustainable and environmentally friendly. The present study aimed to evaluate the cultivated and uncultivated microbial community from a substrate (starter) used as an adapter for biogas production in anaerobic digestion processes. 16S rDNA metabarcoding revealed the domain of bacteria belonging to the phyla Firmicutes, Bacteroidota, Chloroflexi and Synergistota. The methanogenic group was represented by the phyla Halobacterota and Euryarchaeota. Through 16S rRNA sequencing of isolates recovered from the starter culture, the genera Rhodococcus (Actinobacteria phylum), Vagococcus, Lysinibacillus, Niallia, Priestia, Robertmurraya, Proteiniclasticum (Firmicutes phylum), and Luteimonas (Proteobacteria phylum) were identified, genera that were not observed in the metabarcoding data. The volatile solids, volatile organic acids, and total inorganic carbon reached 659.10 g kg, 717.70 g kg, 70,005.0 g kg, respectively. The cultured groups are involved in the metabolism of sugars and other compounds derived from lignocellulosic material, as well as in anaerobic methane production processes. The results demonstrate that culture-dependent approaches, such as isolation and sequencing, and culture-independent studies, such as the Metabarcoding approach, are complementary methodologies that, when integrated provide robust and comprehensive information about the microbial communities involved in processes of the production of biogas in anaerobic digestion processes.
Topics: Anaerobiosis; Animals; Bacteria; Biofuels; Bioreactors; Methane; Microbiota; RNA, Ribosomal, 16S
PubMed: 35590017
DOI: 10.1007/s00203-022-02819-8 -
Environmental Research Feb 2023The disposal of healthcare waste without prior elimination of pathogens and hazardous contaminants has negative effects on the environment and public health. This study...
Evaluation of pre-treated healthcare wastes during COVID-19 pandemic reveals pathogenic microbiota, antibiotics residues, and antibiotic resistance genes against beta-lactams.
The disposal of healthcare waste without prior elimination of pathogens and hazardous contaminants has negative effects on the environment and public health. This study aimed to profile the complete microbial community and correlate it with the antibiotic compounds identified in microwave pre-treated healthcare wastes collected from three different waste operators in Peninsular Malaysia. The bacterial and fungal compositions were determined via amplicon sequencing by targeting the full-length 16S rRNA gene and partial 18S with full-length ITS1-ITS2 regions, respectively. The antibiotic compounds were characterized using high-throughput spectrometry. There was significant variation in bacterial and fungal composition in three groups of samples, with alpha- (p-value = 0.04) and beta-diversity (p-values <0.006 and < 0.002), respectively. FC samples were found to acquire more pathogenic microorganisms than FA and FV samples. Paenibacillus and unclassified Bacilli genera were shared among three groups of samples, meanwhile, antibiotic-resistant bacteria Proteus mirabilis, Enterococcus faecium, and Enterococcus faecalis were found in modest quantities. A total of 19 antibiotic compounds were discovered and linked with the microbial abundance detected in the healthcare waste samples. The principal component analysis demonstrated a positive antibiotic-bacteria correlation for genera Pseudomonas, Aerococcus, Comamonas, and Vagococcus, while the other bacteria were negatively linked with antibiotics. Nevertheless, deep bioinformatic analysis confirmed the presence of bla and penP which are associated with the production of class A beta-lactamase and beta-lactam resistance pathways. Microorganisms and contaminants, which serve as putative indicators in healthcare waste treatment evaluation revealed the ineffectiveness of microbial inactivation using the microwave sterilization method. Our findings suggested that the occurrence of clinically relevant microorganisms, antibiotic contaminants, and associated antibiotic resistance genes (ARGs) represent environmental and human health hazards when released into landfills via ARGs transmission.
Topics: Humans; Anti-Bacterial Agents; beta-Lactams; Genes, Bacterial; RNA, Ribosomal, 16S; Pandemics; COVID-19; Bacteria; Drug Resistance, Microbial; Microbiota
PubMed: 36565841
DOI: 10.1016/j.envres.2022.115139 -
Journal of the Science of Food and... Mar 2024Aquatic products are rich in nutrients and unique in flavor, and are popular among the public. However, aquatic products are extremely susceptible to quality degradation... (Review)
Review
Analysis of changes in volatile compounds and evolution in free fatty acids, free amino acids, nucleotides, and microbial diversity in tilapia (Oreochromis mossambicus) fillets during cold storage.
BACKGROUND
Aquatic products are rich in nutrients and unique in flavor, and are popular among the public. However, aquatic products are extremely susceptible to quality degradation during storage, of which odor deterioration is the most obvious and influential aspect. Odor deterioration in aquatic products is widespread and severely affects overall flavor and quality. In this study, odor deterioration and flavor-related quality degradation of tilapia during cold storage are discussed, focusing on the changes in volatile compounds and the evolution of free fatty acids (FFAs), free amino acids (FAAs), nucleotides, and microbial diversity.
RESULTS
A total of 63 volatile compounds were detected by gas chromatography-mass spectrometry, including 11 hydrocarbons, 10 alcohols, 6 aldehydes, 8 ketones, 6 esters, 9 aromatics, 3 phenols, and 10 other compounds. Microbial diversity analysis revealed that Acinetobacter, Psychrobacter, Vagococcus, and Myroides were the main dominant species of tilapia at the end of cold storage and predicted that microorganisms could influence the flavor of tilapia by participating in important metabolic pathways. Meanwhile, the evolution of FFAs, FAAs, and nucleotides also had a significant impact on odor deterioration, as evidenced by the contribution of unsaturated fatty acids (such as oleic acid and linoleic acid), Lys, and off-flavor nucleotides (HxR and Hx) to the undesirable flavor. Oxidation of oleic acid and linoleic acid resulted in changes in aldehydes, with Lys, HxR, and Hx being key flavor precursors and off-flavor contributors.
CONCLUSION
This study contributes to a comprehensive overview of odor deterioration and the evolution of flavor-related quality in tilapia during cold storage, providing new insights into the regulation of overall flavor and quality. © 2023 Society of Chemical Industry.
Topics: Animals; Food Storage; Fatty Acids, Nonesterified; Amino Acids; Tilapia; Aldehydes; Linoleic Acids; Oleic Acids; Volatile Organic Compounds
PubMed: 38050785
DOI: 10.1002/jsfa.13188 -
International Journal of Food... Feb 2022Quantification of lactic acid bacteria (LAB) is essential to control quality of seafood products like cold-smoked salmon (CSS). In the present study, we report the...
Quantification of lactic acid bacteria (LAB) is essential to control quality of seafood products like cold-smoked salmon (CSS). In the present study, we report the design and optimization of a dual-labelled TaqMan ™ probe targeting the V7 region of 16S rRNA gene for the detection of LAB in CSS. This quantitative PCR (qPCR) assays is useful for the simultaneous detection of the ten LAB genera communally encountered in CSS as Aerococcus, Carnobacterium, Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Macrococcus, Streptococcus, Vagococcus and Weissella. The specificity of this method was demonstrated against 14 genera (44 isolates, 35 species) of Gram-positive bacteria and 19 genera of Gram-negative (40 isolates, 34 species). Calibration of the method was performed in CSS matrix using a mix of equimolar cultured solution of five LAB. Quantification with the qPCR method range from 3.5 to 8.5 Log CFU/g in CSS matrix, covering 5 orders of magnitude. On these artificially contaminated CSS slices, PCR method results correlated successfully (R = 0.9945) with the conventional enumeration on Elliker medium. In addition, the new method was successful on commercial CSS from five different origins with a quantification range from 3.7 Log CFU/g to 8.0 Log CFU/g. This one-step quantitative methodology is proposed as a rapid and complementary tool of the cultural methods to investigate the LAB microbiota and biodiversity of CSS.
Topics: Animals; Colony Count, Microbial; Food Microbiology; Lactobacillales; Lactobacillus; RNA, Ribosomal, 16S; Real-Time Polymerase Chain Reaction; Salmon; Seafood
PubMed: 34959088
DOI: 10.1016/j.ijfoodmicro.2021.109504 -
Microbiology Spectrum Dec 2022The linezolid resistance mediated by has exhibited an increasing trend among Gram-positive bacteria, which greatly limits the treatment options for severe bacterial...
The linezolid resistance mediated by has exhibited an increasing trend among Gram-positive bacteria, which greatly limits the treatment options for severe bacterial infections. However, the prevalence of was usually underestimated based on the existing screening methods. In this study, we used a traditional method and an improved method that included a high-salinity condition treatment after enrichment to screen for -carrying bacteria from stool samples from 1,018 healthy donors in Hangzhou, China. The fecal carriage rate of -carrying bacteria was 19.25% when screened by the improved method (196/1,018), which was much higher than that of the traditional method at 5.89% (60/1,018). Enterococci were the majority of the -positive isolates, while five nonenterococcal isolates were also obtained, including two Streptococcus gallolyticus, one Vagococcus lutrae, one Lactococcus garvieae, and one Lactococcus formosensis isolate. Whole-genome sequencing analysis identified four novel OptrA variants, IDKKGPM, IDKKGP, KLDK, and EYDDI, in these isolates, whose flanking regions with a gene downstream were bounded by different insertion sequences. In conclusion, our optimized method displayed high sensitivity in the detection of -positive bacteria in fecal samples and revealed a high carriage rate in a healthy population. Although enterococci are dominant, multiple -carrying Gram-positive bacteria were also found. This study represented an optimized screening approach for the gene, which is an important mechanism of antimicrobial resistance to linezolid as a last resort for the treatment of infections caused by multiresistant Gram-positive bacteria. We revealed a high fecal carriage rate of the gene among adults by this method and reported the first identification of in Lactococcus formosensis as well as the identification of this gene in Vagococcus lutrae and of the gene in Ligilactobacillus salivarius of human origin, suggesting the wide spread of the gene in the Gram-positive bacterial community.
Topics: Adult; Humans; Oxazolidinones; Linezolid; Anti-Bacterial Agents; Enterococcus faecalis; Enterococcus faecium; Drug Resistance, Bacterial; Enterococcus; Gram-Positive Bacterial Infections; Microbial Sensitivity Tests
PubMed: 36377960
DOI: 10.1128/spectrum.02974-22 -
International Journal of Food Science 2024Indonesia has abundant traditional fermented food with various lactic acid bacteria (LAB), which can be developed into probiotics for pharmaceutical and functional food...
Indonesia has abundant traditional fermented food with various lactic acid bacteria (LAB), which can be developed into probiotics for pharmaceutical and functional food and feed products. This research is aimed at (1) obtaining and identifying LAB isolates and (2) studying the microbiome (bacterial diversity and abundance) of spontaneously-fermented traditional foods of Kalimantan Island, Cincalok, Tempoyak, and Mandai. To obtain LAB isolates, food samples were serially diluted and inoculated on MRS agar that contained 1% CaCO (MRSA). Isolates forming clear zones were purified and identified by DNA barcoding. The microbiome was studied using genomic-sequencing techniques and analysed for taxonomic composition. Seven pure isolates were obtained from Cincalok, two Tempoyak, and one Mandai. DNA barcoding revealed that the Cincalok seven isolates were (strain HSP-S16), (FSB201), , (SS1995), (S11-6), (C01), and (P3.1); two from Tempoyak, (E1D3BL1) and (UMCC-2996); and one from Mandai, (XAAS.x13; non-LAB). The , , , , and belong to LAB. The from Cincalok and non-LAB in these three fermented foods were the first documented report. The microbiome revealed the dominance of phyla in the fermented foods, with 93% in Cincalok, 89.94% in Tempoyak, and 60.32% in Mandai. On the genus level, Cincalok was dominated by 40.33%, 23.29%, 9.27%, and 6.84%. Meanwhile, Tempoyak was dominated only by 89.94%. Mandai were dominated by 31.97%, 17.14%, 16.85%, 15.15%, and 6.2%. However, Mandai's microbiome LAB was not culturable/isolated on MRSA. The plausibility is that those unculturable LAB require coculturing with other bacteria and additional media components to grow on MRSA. This study is the first report regarding the microbiome of Cincalok, Tempoyak, and Mandai, along with their culturable LAB isolates.
PubMed: 38715571
DOI: 10.1155/2024/6589766 -
Frontiers in Microbiology 2020The Atlantic horseshoe crab () is a common marine aquarium species and model organism for research. There is potential monetary and conservation value in developing a...
The Atlantic horseshoe crab () is a common marine aquarium species and model organism for research. There is potential monetary and conservation value in developing a stable captive population of horseshoe crabs, however, one major impediment to achieving captivity is a lack of knowledge regarding captive diseases. We utilized 16S rRNA gene amplicon sequencing to track changes in the microbiomes of four body locations in three wild-caught (tracked over 14 months in captivity) and three tank-acclimated (>2 years in captivity) adult in a touch tank at Shark Reef Aquarium at Mandalay Bay in Las Vegas, NV. The wild population hosted diverse and distinct microbiomes on the carapace (260 ± 96 amplicon sequence variants or ASVs), cloaca (345 ± 77 ASVs), gills (309 ± 36 ASVs), and oral cavity (359 ± 37 ASVs), which were dominated by classes , , and . A rapid decline in richness across all body locations was observed within 1 month of captivity, with tank-acclimated (>2 years) animals having <5% of the initial microbiome richness and a nearly completely restructured microbial community. Tank-acclimated horseshoe crabs possessed distinct microbiomes that were highly uneven and low in species richness on the carapace (31 ± 7 ASVs), cloaca (53 ± 19 ASVs), gills (17 ± 2 ASVs), and oral cavity (31 ± 13 ASVs). The carapace, oral cavity, and gills of the tank-acclimated animals hosted abundant populations of (>60%) and (>20%), both of which are known opportunistic pathogens of aquatic animals and can express chitinases, providing a plausible mechanism for the development of the carapace lesion pathology observed in this and other studies. The cloaca of the tank-acclimated animals was slightly more diverse than the other body locations with , , , and dominating the community. These results provide an important baseline on the microbiomes of both wild and tank-acclimated horseshoe crabs and underscore the need to continue to investigate how native microbial populations may protect animals from pathogens.
PubMed: 32765431
DOI: 10.3389/fmicb.2020.01398 -
Frontiers in Microbiology 2020This study aimed to analyze the intestinal flora of male versus female swamp eels, which have the unique characteristic of sex reversal. Same-aged swamp eels from the...
This study aimed to analyze the intestinal flora of male versus female swamp eels, which have the unique characteristic of sex reversal. Same-aged swamp eels from the same parents, kept under the same conditions in terms of environment, diet, etc., were used as the study materials. After breeding for 1 year, 18 healthy swamp eels (nine males and nine females), weighing 39.4 ± 2.3 g, were selected. The intestinal contents of three swamp eels of the same sex were combined and labeled as follows: FM1-FM3 ( = 3) for females and MM1-MM3 ( = 3) for males. High-throughput sequencing was used to research the v3-v4 region of 16S rDNA in the intestinal flora. The results suggested significant differences in the structure, composition, and diversity of the intestinal flora of male versus female swamp eels. The relative abundances of Actinobacteria and Spirochaetes in female swamp eels were significantly higher ( < 0.05) than in male swamp eels at the phylum level. The relative abundances of , , and in female swamp eels were considerably higher ( < 0.05) than in male swamp eels at the genus level. The Alpha diversity of females was higher than that of males, and the Shannon index of females was also significantly higher ( < 0.05, Tukey's HSD) than that in males. Investigations of Beta diversity, including NMDS ordination, UPGMA cluster analysis, and PLS-DA analysis, showed that female and male swamp eels could be clearly distinguished based on significant differences in intestinal flora between the FM group and the MM group. LEfSe analysis showed that the dominant bacteria were in male swamp eels and , , , and in female swamp eels. The results showed dramatic differences in the intestinal flora between the sexes, which indicates the need for a more in-depth study on sex reversal in the future.
PubMed: 32425902
DOI: 10.3389/fmicb.2020.00699 -
Food Research International (Ottawa,... Jul 2022Umami peptides formed by microbial metabolism play an important role in the umami taste of Chouguiyu. In this study, 138 umami peptides and 6 kinds of proteases in two...
Umami peptides formed by microbial metabolism play an important role in the umami taste of Chouguiyu. In this study, 138 umami peptides and 6 kinds of proteases in two categories from 35 microbial genera were identified from Chouguiyu during the fermentation process by peptidomics and metagenomics analysis, respectively. The interaction network maps between the umami peptides and protease-producing microbial genera in each protease classification were constructed based on Pearson's correlation coefficient after a two-way orthogonal partial least squares (O2PLS) evaluation. The proteases classified in 34 clusters of orthologous groups (COG) from Vagococcus, Peptostreptococcus, Acinetobacter, Psychrobacter, and Enterococcus played a major role in the formation of umami peptides. The core umami peptides with the highest abundance and correlation were mainly derived from troponin and myosin in mandarin fish. The lactic acid bacteria contributed most to the hydrolysis preparation of these umami peptides. This study is beneficial to screen the proteases and related microbial strains to improve the umami taste of Chouguiyu.
Topics: Animals; China; Fermentation; Fishes; Peptide Hydrolases; Peptides; Taste
PubMed: 35761533
DOI: 10.1016/j.foodres.2022.111211 -
Scientific Reports Jan 2021Once the body dies, the indigenous microbes of the host begin to break down the body from the inside and play a key role thereafter. This study aimed to investigate the...
Once the body dies, the indigenous microbes of the host begin to break down the body from the inside and play a key role thereafter. This study aimed to investigate the probable shift in the composition of the rectal microbiota at different time intervals up to 15 days after death and to explore bacterial taxa important for estimating the time since death. At the phylum level, Proteobacteria and Firmicutes showed major shifts when checked at 11 different intervals and emerged at most of the postmortem intervals. At the species level, Enterococcus faecalis and Proteus mirabilis showed a downward and upward trend, respectively, after day 5 postmortem. The phylum-, family-, genus-, and species-taxon richness decreased initially and then increased considerably. The turning point occurred on day 9, when the genus, rather than the phylum, family, or species, provided the most information for estimating the time since death. We constructed a prediction model using genus-level data from high-throughput sequencing, and seven bacterial taxa, namely, Enterococcus, Proteus, Lactobacillus, unidentified Clostridiales, Vagococcus, unidentified Corynebacteriaceae, and unidentified Enterobacteriaceae, were included in this model. The abovementioned bacteria showed potential for estimating the shortest time since death.
Topics: Animals; Bacteria; DNA, Bacterial; Gastrointestinal Microbiome; Postmortem Changes; Rats; Rats, Sprague-Dawley
PubMed: 33420339
DOI: 10.1038/s41598-020-80633-2