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Microorganisms Oct 2021Lactic acid bacteria (LAB) are probiotic candidates that may restore the balance of microbiota populations in intestinal microbial ecosystems by controlling pathogens...
Lactic acid bacteria (LAB) are probiotic candidates that may restore the balance of microbiota populations in intestinal microbial ecosystems by controlling pathogens and thereby promoting host health. The goal of this study was to isolate potential probiotic LAB strains and characterize their antimicrobial abilities against pathogens in intestinal microbiota. Among 54 LAB strains isolated from fermented products, five LAB strains (NSMJ15, NSMJ16, NSMJ23, NSMJ42, and NFFJ04) were selected as potential probiotic candidates based on in vitro assays of acid and bile salt tolerance, cell surface hydrophobicity, adhesion to the intestinal epithelium, and antagonistic activity. Phylogenetic analysis based on 16S rRNA genes showed that they have high similarities of 99.58-100% to strains NSMJ15 and NFFJ04, NSMJ16, NSMJ23, and NSMJ42. To characterize their antimicrobial abilities against pathogens in intestinal microbiota, the impact of cell-free supernatant (CFS) treatment in 10% (/) fecal suspensions prepared using pooled cattle feces was investigated using in vitro batch cultures. Bacterial community analysis using rRNA amplicon sequencing for control and CFS-treated fecal samples at 8 and 16 h incubation showed the compositional change after CFS treatment for all five LAB strains. The changed compositions were similar among them, but there were few variable increases or decreases in some bacterial groups. Interestingly, as major genera that could exhibit pathogenicity and antibiotic resistance, the members of , , , , and were decreased at 16 h in all CFS-treated samples. Species-level classification suggested that the five LAB strains are antagonistic to gut pathogens. This study showed the probiotic potential of the five selected LAB strains; in particular, their antimicrobial properties against pathogens present in the intestinal microbiota. These strains would therefore seem to play an important role in modulating the intestinal microbiome of the host.
PubMed: 34683462
DOI: 10.3390/microorganisms9102141 -
Proceedings of the National Academy of... Jun 2021While it is well recognized that the environmental resistome is global, diverse, and augmented by human activities, it has been difficult to assess risk because of the...
While it is well recognized that the environmental resistome is global, diverse, and augmented by human activities, it has been difficult to assess risk because of the inability to culture many environmental organisms, and it is difficult to evaluate risk from current sequence-based environmental methods. The four most important criteria to determine risk are whether the antibiotic-resistance genes (ARGs) are a complete, potentially functional complement; if they are linked with other resistances; whether they are mobile; and the identity of their host. Long-read sequencing fills this important gap between culture and short sequence-based methods. To address these criteria, we collected feces from a ceftiofur-treated cow, enriched the samples in the presence of antibiotics to favor ARG functionality, and sequenced long reads using Nanopore and PacBio technologies. Multidrug-resistance genes comprised 58% of resistome abundance, but only 0.8% of them were plasmid associated; fluroquinolone-, aminoglycoside-, macrolide-lincosamide-streptogramin (MLS)-, and β-lactam-resistance genes accounted for 2.7 to 12.3% of resistome abundance but with 19 to 78% located on plasmids. A variety of plasmid types were assembled, some of which share low similarity to plasmids in current databases. Enterobacteriaceae were dominant hosts of antibiotic-resistant plasmids; physical linkage of extended-spectrum β-lactamase genes (, , , and ) was largely found with aminoglycoside-, MLS-, tetracycline-, trimethoprim-, phenicol-, sulfonamide-, and mercury-resistance genes. A draft circular chromosome of was assembled; it carries MLS-, tetracycline- (including and on an integrative conjugative element), and trimethoprim-resistance genes flanked by many transposase genes and insertion sequences, implying that they remain transferrable.
Topics: Animals; Anti-Bacterial Agents; Base Sequence; Cattle; Drug Resistance, Microbial; Environmental Microbiology; Feces; Gene Regulatory Networks; Genes, Bacterial; Genetic Linkage; Genetic Variation; Host Specificity; Microbiota; Phylogeny; Plasmids; Sequence Analysis, DNA
PubMed: 34161269
DOI: 10.1073/pnas.2024464118 -
International Journal of Medical... 2019: Accumulating evidence has shown that neuropsychiatric disorders are associated with gut microbiota through the gut-brain axis. However, the effects of antidepressant...
: Accumulating evidence has shown that neuropsychiatric disorders are associated with gut microbiota through the gut-brain axis. However, the effects of antidepressant treatment on gut microbiota are rarely studied. Here, we investigated whether stress led to gut microbiota changes and whether fluoxetine plays a role in microbiota alteration. : We investigated changes in gut microbiota in a depression model induced by chronic unpredicted mild stress (CUMS) and a restoration model by applying the classic antidepressant drug fluoxetine. : We found that stress led to low bacterial diversity, simpler bacterial network, and increased abundance of pathogens, such as , and conditional pathogens, such as , , and However, these changes were attenuated by fluoxetine directly and indirectly. Furthermore, the correlation analysis indicated strong correlations between gut microbiota and anxiety- and depression-like behaviors. : This study revealed that fluoxetine led to restoration of dysbiosis induced by stress stimulation, which may imply a possible pathway through which one CNS target drug plays its role in reshaping the gut microbiota.
Topics: Animals; Antidepressive Agents, Second-Generation; Anxiety; Depressive Disorder; Disease Models, Animal; Dysbiosis; Fluoxetine; Gastrointestinal Microbiome; Male; Mice, Inbred C57BL; Stress, Psychological
PubMed: 31588192
DOI: 10.7150/ijms.37322 -
Microorganisms Nov 2023Microbial communities can undergo significant successional changes during decay and decomposition, potentially providing valuable insights for determining the postmortem...
Microbial communities can undergo significant successional changes during decay and decomposition, potentially providing valuable insights for determining the postmortem interval (PMI). The microbiota produce various gases that cause cadaver bloating, and rupture releases nutrient-rich bodily fluids into the environment, altering the soil microbiota around the carcasses. In this study, we aimed to investigate the underlying principles governing the succession of microbial communities during the decomposition of pig carcasses and the soil beneath the carcasses. At early decay, the phylum and were the most abundant in both the winter and summer pig rectum. However, became the most abundant in the winter pig rectum in late decay. Using genus as a biomarker to estimate the PMI could get the MAE from 1.375 days to 2.478 days based on the RF model. The abundance of bacterial communities showed a decreasing trend with prolonged decomposition time. There were statistically significant differences in microbial diversity in the two periods (pre-rupture and post-rupture) of the four groups (WPG 0-8Dvs. WPG 16-40D, < 0.0001; WPS 0-16Dvs. WPS 24-40D, = 0.003; SPG 0D vs. SPG 8-40D, = 0.0005; and SPS 0D vs. SPS 8-40D, = 0.0208). Most of the biomarkers in the pre-rupture period belong to obligate anaerobes. In contrast, the biomarkers in the post-rupture period belong to aerobic bacteria. Furthermore, the genus shows a similar increase trend, whether in winter or summer. Together, these results suggest that microbial succession was predictable and can be developed into a forensic tool for estimating the PMI.
PubMed: 38004822
DOI: 10.3390/microorganisms11112811 -
Frontiers in Microbiology 2020The gut microbiota plays a key role in host health, and disruptions to gut bacterial homeostasis can cause disease. However, the effect of disease on gut microbiota...
The gut microbiota plays a key role in host health, and disruptions to gut bacterial homeostasis can cause disease. However, the effect of disease on gut microbiota assembly remains unclear and gut microbiota-based predictions of health status is a promising yet poorly established field. Using Illumina high-throughput sequencing technology, we compared the gut microbiota between healthy (HA and HB) and diarrhoeic (DS) groups and analyzed the functional profiles through a phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis. In addition, we estimated the correlation between gut microbiota structures and predicted the functional compositions. The results showed significant differences in the phylogenetic diversity (Pd), Shannon, and observed richness (Sobs) indices between the DS and HB groups, with significant differences observed in the gut microbiota composition between the DS group and the HA and HB groups. Linear discriminant analysis (LDA) effect size (LEfSe) results revealed that Proteobacteria were significantly enriched in the DS group; Bacteroidetes were significantly enriched in the HA and HB groups; and , , , , , , , , and were significantly enriched in the DS group. Venn diagrams revealed that there were many more unique genera in the DS group than the HA and HB groups. Among 102 sensitive species selected using the indicator method, 33 indicated a healthy status and 69 (e.g., , , , , , , , and ) indicated a diseased status. There was a significant and positive association between the composition and functional composition of the gut microbiota, thus indicating low functional redundancy of the frog gut bacterial community. disease was associated with changes in the gut microbiota, which subsequently disrupted bacterial-mediated functions. The results of this study can aid in revealing the effect of the gut microbiota on host health and provide a basis for elucidating the mechanism of the occurrence of disease.
PubMed: 32983063
DOI: 10.3389/fmicb.2020.02096 -
Insects Mar 2024The blowfly, (Diptera: Calliphoridae), is a well-known forensically important insect. Basic data related to have been well documented; but despite the pivotal role of...
The blowfly, (Diptera: Calliphoridae), is a well-known forensically important insect. Basic data related to have been well documented; but despite the pivotal role of gut microbes in various facets of insect biology, little is known about its gut microbiome. To investigate the gut bacterial community of and explore its stability, diet and developmental stage were selected as the two variables. Larvae were reared on bovine liver, swine manure, and chicken manure, and high-throughput sequencing of the 1st, 2nd, and 3rd instar larvae and the newly emerged adults was performed. According to our results, the alpha diversity of the gut bacterial community did not significantly vary among different diets and developmental stages. Principal coordinate analysis revealed that the gut microbiome of clustered together among different diets and developmental stages. The main phyla in the gut microbial community of were Firmicutes and Proteobacteria, and the dominant genera were , , , and . These findings characterized the gut microbiome of and demonstrated that the gut bacterial community is fairly stable. The dominant genera , , , and have the potential to serve as core microbiomes within the gut microbial community of .
PubMed: 38535376
DOI: 10.3390/insects15030181 -
Fish and Shellfish Immunology Reports Dec 2023Multi-modular enzyme complexes known as non-ribosomal peptide synthetases (NRPSs) and polyketide synthetases (PKSs) have been widely reported in bacteria that produce...
Multi-modular enzyme complexes known as non-ribosomal peptide synthetases (NRPSs) and polyketide synthetases (PKSs) have been widely reported in bacteria that produce secondary bioactive metabolites such as non-ribosomal peptides (NRPs) and polyketides (PKs), respectively. These NRPS/PKS pathways contribute to synthesizing several antibiotics, such as vancomycin, rifamycin, and bleomycin, which are vital in human medicine. The present study aimed to isolate gut-associated bacteria from mud crab , and detect NRPS and PKS gene clusters associated with it. This study included 36 bacterial isolates from five mud crab gut samples. Biosynthetic gene clusters (NRPS and PKS), were detected by PCR using degenerative primers specific to these genes. Three isolates (FKP2-4, FKP4-1, and FKP2-16) were positive for NRPS and two for PKS (FKP2-4 and FKP4-1) genes. The isolates were subjected to 16S rRNA gene amplification and sequenced. In silico analysis of the sequences using the Basic Local Alignment Search Tool (BLAST) identified the isolates FKP2-4, FKP4-1, and FKP2-16 as and , respectively, after comparing with the existing sequences available in the National Center for Biotechnology Information (NCBI) database. Compared to the control, it was observed that these isolates exhibited intriguing antagonistic activities against and . However, these isolates failed to show significant activity against . Exopolysaccharide production by the isolated organisms was tested using Zobell marine agar (ZMA) with 5% sucrose, but none of the colonies were mucoid or slimy.
PubMed: 38162954
DOI: 10.1016/j.fsirep.2023.100104 -
Food Science and Biotechnology Mar 2021The effects of vacuum package combined with 0.1% ε-polylysine and 0.2% rosemary extract (V + RP) on the quality attributes and microbial communities of large yellow...
The effects of vacuum package combined with 0.1% ε-polylysine and 0.2% rosemary extract (V + RP) on the quality attributes and microbial communities of large yellow croaker () during ice storage were investigated. The quality was evaluated by chemical characteristics (total volatile basic nitrogen (TVB-N), K-value and biogenic amines (BAs)), microbiological indexes (Total viable counts (TVC), bacteria counts, bacteria counts, Psychrophilic bacteria counts (PBC)), changes in microbial composition were analyzed using high-throughput sequencing. Results showed that the increase of TVB-N, K-value, microorganisms and BAs could be inhibited by V + RP. and were detected in all samples. increases rapidly in the middle of storage. and were related to the decomposition of ATP, the formation of BAs, and TVB-N, respectively. In conclusion, V + RP presented the optimal effects, which could extend the shelf life of large yellow croaker for another 9 days compared with the control.
PubMed: 33868757
DOI: 10.1007/s10068-021-00880-5 -
Folia Microbiologica Apr 2022This work aimed to identify the key members of the bacterial community growing on common carp (Cyprinus carpio) fillets during chilled storage with next-generation...
This work aimed to identify the key members of the bacterial community growing on common carp (Cyprinus carpio) fillets during chilled storage with next-generation sequencing (NGS) and cultivation-dependent methods. Carp fillets were stored for 96 h at 2 °C and 6 °C with and without a vacuum package, and an additional frozen-thawed storage experiment was set for 120 days. Community profiles of the initial and stored fish samples were determined by amplicon sequencing. Conventional microbial methods were used parallelly for the enumeration and cultivation of the dominant members of the microbial community. Cultivated bacteria were identified with 16S rRNA sequencing and the MALDI-TOF MS method. Based on our results, the vacuum package greatly affected the diversity and composition of the forming microbial community, while temperature influenced the cell counts and consequently the microbiological criteria for shelf-life of the examined raw fish product. Next-generation sequencing revealed novel members of the chilled flesh microbiota such as Vagococcus vulneris or Rouxiella chamberiensis in the vacuum-packed samples. With traditional cultivation, 161 bacterial strains were isolated and identified at the species level, but the identified bacteria overlapped with only 45% of the dominant operational taxonomic units (OTUs) revealed by NGS. Next-generation sequencing is a promising and highly reliable tool recommended to reach a higher resolution of the forming microbial community of stored fish products. Knowledge of the initial microbial community of the flesh enables further optimization and development of processing and storage technology.
Topics: Animals; Bacteria; Carps; Food Microbiology; Food Storage; Microbiota; RNA, Ribosomal, 16S; Seafood
PubMed: 34877630
DOI: 10.1007/s12223-021-00935-4 -
Microorganisms Jul 2023A large variety of cheeses can be produced using different manufacturing processes and various starter or adjunct cultures. In this study, we have described the...
A large variety of cheeses can be produced using different manufacturing processes and various starter or adjunct cultures. In this study, we have described the succession of the microbial population during the commercial production and subsequent ripening of smear-ripened cheese using 16S rRNA gene sequencing. The composition of the microbiota during the first 6 days of production was constant and consisted mainly of LAB (lactic acid bacteria) originating from the starter culture. From day 7, the proportion of LAB decreased as other bacteria from the production environment appeared. From the 14th day of production, the relative proportion of LAB decreased further, and at the end of ripening, bacteria from the environment wholly dominated. These adventitious microbiota included , /, , and (Proteobacteria phylum), as well as and (Firmicutes phylum), (Fusobacteria phylum), and (Campylobacterota phylum), all of which appeared to be characteristic taxa associated with the cheese rind. Subsequent analysis showed that the production and ripening of smear-ripened cheese could be divided into three stages, and that the microbiota compositions of samples from the first week of production, the second week of production, and supermarket shelf life all differed.
PubMed: 37512907
DOI: 10.3390/microorganisms11071735