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Frontiers in Microbiology 2022Bacterial communities in high-temperature Daqu and fermented grains are important for brewing Jiang-flavor Baijiu such as Danquan Baijiu. Daqu is a saccharifying and...
Bacterial communities in high-temperature Daqu and fermented grains are important for brewing Jiang-flavor Baijiu such as Danquan Baijiu. Daqu is a saccharifying and fermenting agent, which has a significant impact on the flavor of Baijiu. However, bacterial communities in three different types of samples from the Danquan distillery (dqjq_ck, dqjqcp, and dqjp3) were still unclear, which limited further development of Danquan Baijiu. "dqjq_ck" and "dqjqcp" indicate high-temperature Daqu at days 45 and 135, respectively. "dqjp3" indicates fermented grains. In this study, the bacterial communities of three samples were analyzed by Illumina Miseq high-throughput sequencing. The bacterial communities of three samples primarily composed of thermophilic bacteria and bacteria with stress resistance. The most abundant species in dqjq_ck, dqjqcp, and dqjp3 were , and , respectively. The main bacteria included , and in three samples (percentage was more than 1% in one of three samples). In our study, the succession of microbiota in three samples representing three important stages of Danquan Baijiu brewing was revealed. This article lays a good foundation for understanding the fermentation mechanism and screening some excellent indigenous bacteria to improve the quality of Danquan Baijiu in future.
PubMed: 35865918
DOI: 10.3389/fmicb.2022.883122 -
Scientific Reports Jul 2022The housefly (Musca domestica) is a wide-ranging insect, often associated with decaying matter from livestock and humans. The septic environments in which houseflies...
The housefly (Musca domestica) is a wide-ranging insect, often associated with decaying matter from livestock and humans. The septic environments in which houseflies live are believed to be a rich source for microbial acquisition. Although the housefly can harbor a wide range of microorganisms, it is not yet well known which microbes are always recurrent, which are dispensable and which environmentally dependent. In the present study, we aim at identifying which microbes are recurrently associated with the housefly gut throughout the species' life cycle and whether their acquisition relies on the fly's living environment. We surveyed three housefly strains-two of them kept under standard laboratory conditions for a long time and one wild-caught. To track any shifts happening throughout the lifecycle of the housefly and to test the consistency of the revealed microbial communities, we sampled houseflies at five developmental stages over the course of four consecutive generations. Both the bacterial and fungal microbiota of five developmental stages were studied for all samples, using amplicon sequencing for the 16S and ITS1 rRNA gene, respectively. Results revealed diverse microbial communities yet consistent for each of the two distinct sampling environments. The wild-caught population showed a more diverse and more distinct gut microbiota than the two laboratory strains, even though the strain was phylogenetically similar and shared geographic origin with one of them. Two bacterial genera, Myroides and Providencia, and two yeasts, Trichosporon and Candida tropicalis, were present in all sampled larvae and pupae, regardless of the strain. Analysis of the provided diet revealed that the flies acquired the yeasts through feeding. Our main findings show that houseflies might lose microbial diversity when reared in controlled environments, however they can maintain a consistent set of bacteria. We conclude that although the environment can facilitate certain microbial transmission routes for the housefly, and despite the fungal microbiota being largely acquired through diet, the larval bacterial gut microbiome remains relatively consistent within the same developmental stage.
Topics: Animals; Bacteria; Gastrointestinal Microbiome; Houseflies; Larva; Microbiota
PubMed: 35778448
DOI: 10.1038/s41598-022-15186-7 -
Frontiers in Microbiology 2022Red swamp crayfish () have become one of the favorite aquatic products in China. The modern farming mode which uses antibiotics to prevent diseases could impact the...
Red swamp crayfish () have become one of the favorite aquatic products in China. The modern farming mode which uses antibiotics to prevent diseases could impact the bacteria in crayfish intestines. Here, we determined the distribution and antimicrobial resistance phenotypes of the selected culturable bacteria in crayfish intestines and characterized an isolate with last-line antibiotic resistance determinant. Totally, 257 strains were isolated from 115 crayfish. These strains were highly diverse, with sp. ( = 94, 36.6%) and sp. ( = 88, 34.2%) being dominant. Other isolates belonged to genera , , , , , , , and . Most strains from crayfish were susceptible to all tested antibiotics. None of the isolates carried last-line antibiotic resistance genes except one isolate with was detected, which is the first report of -positive isolate from red swamp crayfish. Whole-genome sequencing suggested it belonged to ST48 and carried several resistance genes. was located within an Tn-like transposon linked to an external 5 bp sequence (ACTAT) on both sides on a IncHI1B/HI1A/FIA multi-replicon plasmid. This transposon was considered to be acquired by replicative transposition mediated by IS. The emergence of bacteria with last-line antibiotic resistance genes in crayfish poses serious threat to public health since crayfish could act as a reservoir for the transfer of resistance to humans.
PubMed: 35747368
DOI: 10.3389/fmicb.2022.911777 -
Journal of the College of Physicians... Apr 2022The myroides bacteria species are multidrug-resistant gram-negative aerobic bacilli. The genus myroides comprises two species, i.e., M. odoratimimus and M. odoratus,...
The myroides bacteria species are multidrug-resistant gram-negative aerobic bacilli. The genus myroides comprises two species, i.e., M. odoratimimus and M. odoratus, and is usually associated with infections in immunocompromised patients; though infections in immunocompetent individuals have also been reported. They are a rare cause of infection worldwide. So far, only 53 cases have been reported in the literature. Here, we report a case of recurrent urinary tract infection by myroides species. This is the first documented case in Saudi Arabia to the best of our knowledge. Key Words: Myroides, Recurrent UTI, Renal transplant recipient, Immunosuppression.
Topics: Flavobacteriaceae; Flavobacteriaceae Infections; Humans; Immunocompromised Host; Kidney Transplantation; Urinary Tract Infections
PubMed: 35633005
DOI: 10.29271/jcpsp.2022.Supp1.S34 -
Indian Journal of Medical Microbiology 2022In this study, it was aimed to investigate the combined synergistic efficacy of colistin (CT), meropenem (MEM), and ciprofloxacin (CIP) antibiotics on planktonic and...
PURPOSE
In this study, it was aimed to investigate the combined synergistic efficacy of colistin (CT), meropenem (MEM), and ciprofloxacin (CIP) antibiotics on planktonic and biofilm forms in Myroidesodoratimimus strains isolated from various clinical specimens.
METHODS
Antibiotic susceptibility was determined by the Kirby-Bauer disk diffusion method. In addition, minimum inhibitory concentrations (MIC) of CIP, MEM, and CT were studied using the standardized broth microdilution method. In vitro synergistic activity of antibiotics against M. odoratimimus planktonic bacteria strains was studied by the Micro Broth Checkerboard method. The microtiter plate (MtP) method was used to determine the effectiveness of antibiotics on M. odoratimimus biofilm formation.
RESULTS
A zone of inhibition was not observed against other antibiotics used except amikacin and linezolid in all strains. While CT/MEM and CT/CIP combinations have a synergistic effect on all strains, the combination CIP/MEM has an additive effect. According to the biofilm inhibition results, all three antibiotics inhibited biofilm formation. However, the efficacy of MEM (60.3-76.5%) and CIP (60.2-77.8%) was approximately two times higher than that of CT (25.4-34.5%). In addition, the effectiveness of combinations of antibiotics on biofilm formation was examined and the percentage of inhibition was 30.8% when CT was used alone, while the biofilm inhibition rates of CT/MEM and CT/CIP were 92.4% and 91.7%, respectively. MEM/CIP combination was inhibited biofilm formation by 75.7%.
CONCLUSIONS
This study is the first report showing the efficacy of CT, MEM and CIP antibiotics, which are frequently used in clinical practice, in combination on M. odoratimimus planktonic and biofilm forms. The findings of our study are particularly guiding for combined antibiotic treatment options in immunosuppressed patients admitted to an intensive care unit (ICU). The CT/MEM combination is currently used frequently. In addition, these results are important in terms of supporting in vitro that CT/CIP and MEM/CIP combinations can also be used as a treatment option in M. odoratimimus related infections.
Topics: Anti-Bacterial Agents; Biofilms; Ciprofloxacin; Colistin; Flavobacteriaceae; Humans; Meropenem; Microbial Sensitivity Tests
PubMed: 35491280
DOI: 10.1016/j.ijmmb.2022.04.004 -
Journal of Medical Microbiology Apr 2022Colorectal cancer (CRC) is one of the most common cancers worldwide. Multiple risk factors are involved in CRC development, including age, genetics, lifestyle, diet and...
Colorectal cancer (CRC) is one of the most common cancers worldwide. Multiple risk factors are involved in CRC development, including age, genetics, lifestyle, diet and environment. Of these, the role of the gut microbiota in cancer biology is increasingly recognized. Micro-organisms have been widely detected in stool samples, but few mucosal samples have been detected and sequenced in depth. Analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues with metagenomics sequencing. Twenty-eight paired tumour and non-tumour tissues from 14 patients undergoing surgery for CRC were analysed. We removed the influence of eukaryotic cells via culture. The composition of mucosal microbiota in intestinal mucosa were detected and analysed with metagenomic sequencing. Compared with non-cultured mucosal sample, 80 % bacteria species could be detected after culture. Moreover, after culture, additional 30 % bacteria could be detected, compared with non-cultured samples. Since after culture it was difficult to estimate the original abundance of microbiome, we focused on the identification of the CRC tissue-specific species. There were 298 bacterial species, which could only be cultured and detected in CRC tissues. and could be isolated from all the tumour samples of 14 CRC patients, suggesting that these species may be related to tumour occurrence and development. Further functional analysis indicated that bacteria from CRC tissues showed more active functions, including basic metabolism, signal transduction and survival activities. We used a new method based on culture to implement information on prokaryotic taxa, and related functions, which samples were from colorectal tissues. This method is suitable for removing eukaryotic contamination and detecting micro-organisms from other tissues.
Topics: Bacteria; Colorectal Neoplasms; Gastrointestinal Microbiome; Humans; Intestinal Mucosa; Metagenomics
PubMed: 35467501
DOI: 10.1099/jmm.0.001523 -
Microorganisms Mar 2022Plant-growth-promoting endophytes (PGPE) are a kind of beneficial microorganisms which could inhabit plant tissues to antagonize certain plant pathogens and promote the...
Plant-growth-promoting endophytes (PGPE) are a kind of beneficial microorganisms which could inhabit plant tissues to antagonize certain plant pathogens and promote the host plant's growth and development. At present, many studies have confirmed the mutualistic effect of endophytes with plants, but there are few systematic studies on beneficial roles between endophytes and , especially on the PGPE characteristics of the forage and environmental restoration plant. This study aimed to isolate PGPE from , evaluate their effects on plant growth, and ultimately acquire desirable microbial inoculants for agricultural use. First, endophytes were isolated from by plant re-inoculation experiment, and identified by morphological and molecular analyses. Fixation medium and methods were carried out to assess the nitrogen fixation ability of the strains. Then, the ability to dissolve phosphorus was determined by the Olsen and silicate medium methods; secretory IAA was measured by Salkowski colorimetric method; and the inhibitive effects on phytopathogen were observed by confrontation culture. Twenty-one strains were isolated from four varieties of , among which 14 strains with plant-growth-promoting characteristics were obtained by re-inoculation experiments, including seven endophytic bacteria and seven endophytic fungi. Further evaluation of three selected strains with the most significant PGP attributes were performed by using the pot re-inoculation experiment which revealed that TG2-B derived from was the most effective plant-growth-promoting agent due to its ability to produce high levels of IAA; the strain exhibited the most robust ability in dissolving inorganic phosphorus; and manifested a conspicuously antagonistic effect against a variety of plant pathogens. For the first time, this study reports the identification of endophytes that were able to promote plant growth and have a considerable antagonistic effects on plant pathogens, which could be considered as microbial inoculants for using in improving crop production and plant disease control.
PubMed: 35456782
DOI: 10.3390/microorganisms10040731 -
Food Research International (Ottawa,... May 2022Zoning is typically adopted by food manufacturers and classified into three different zones including Zone 1 (food contact surface), Zone 2 (proximity to food and food...
Zoning is typically adopted by food manufacturers and classified into three different zones including Zone 1 (food contact surface), Zone 2 (proximity to food and food contact surfaces) and Zone 3 (remote surfaces from processing). In this study, environmental surfaces belonging to these three zones were sampled during food processing in a fresh-cut vegetables (FVs) processing facility located in Beijing, China. Bacterial loads in terms of aerobic plate count and coliform count were evaluated by culture-dependent techniques. The profile and diversity of bacterial community in these three zones were investigated by high-throughput sequencing. Zone 1 showed similar microbiota and predominated by Pseudomonas and Acinetobacter, while the predominant genera on Zone 2 or 3 were quite varied among different processing steps. The SourceTracker analysis showed that most of the bacteria (above 80%) on surfaces were from unknown sources, while sorting and disinfection & cleaning steps contributed equally to the bacterial community of cutting areas. Microbial association network analysis revealed strong positive interactions of Comamonas and Janthinobacterium with Myroides and Serratia, respectively, whereas Pseudomonas showed no significant correlation with other genera. The function of microbial communities was predicted based on BugBase 16S rRNA database, and the results indicated that the proportions of potential biofilm-forming bacteria were above 70% in all samples, and species of Pseudomonas, Comamonas, Chryseobacterium and Janthinobacterium were opportunistic pathogens or spoilage bacteria. This study evaluated the bacteria risks including bacterial load, composition, as well as potential bacterial interaction, function and microbial transfer on food processing surfaces, which will facilitate our better understanding on the cross-contaminations and preventions of harmful microorganism in FVs processing industry.
Topics: Bacteria; Food Microbiology; Microbiota; Pseudomonas; RNA, Ribosomal, 16S; Vegetables
PubMed: 35400453
DOI: 10.1016/j.foodres.2022.111075 -
Acta Microbiologica Et Immunologica... Mar 2022Myroides spp. are opportunistic environmental Gram-negative bacteria. These affect mostly immunocompromised hosts and generally lead to soft tissue, and urinary tract...
Myroides spp. are opportunistic environmental Gram-negative bacteria. These affect mostly immunocompromised hosts and generally lead to soft tissue, and urinary tract infections. Bacteremia most commonly develop secondary to soft tissue or catheter related infections and may lead rarely to mortality. Myroides spp. are generally suscetible to fluoroquinolones, piperacillin/tazobactam, trimethoprim/sulfamethoxazole, carbapenems or tetracyclines however, pan-resistant isolates and multiple resistance genes have been reported in clinical isolates of Myroides spp. We report a pan-resistant Myroides odoratimimus bacteremia in a patient with severe COVID-19 ending with fatality and in this context a review of reported Myroides bacteremias are also described. In this study, a 64-year old male patient with history of coronary artery bypass was admitted to ICU with severe COVID-19 pneumonia accompanied by pneumomediastinum and pneumopericardium. Continous renal replacement therapy and extracorporeal membraneous-oxygenation were initiated due to acute renal failure and persistent hypercarbia/hypoxia, respectively. Within four weeks of hospitalization various episodes of bacteremia developed and multiple antibiotics were used. On the 5th week of follow-up, acute phase reactants increased and empirical broad spectrum antibiotics were initiated. Blood culture revealed Gram-negative rods. The patient became hypotensive and despite maximum medical care he was lost due to cardiac arrest. M. odoratimimus was identified by MALDI-TOF and the bacterium was pan-resistant. According to Center for Genomic Epidemiology results the strain was identified as M. odoratimimus PR63039 and the genome analysis revealed antibiotic resistance genes associated with resistance to beta-lactams (bla OXA-347, bla MUS-1, bla EBR-1), tetracyclines (tetX), sulfonamides (sul2), macrolides (ereD), (ermF).
PubMed: 35312630
DOI: 10.1556/030.2022.01702 -
Journal of Thoracic Disease Feb 2022The current COVID-19 pandemic is posing a major challenge to public health on a global scale. While it is generally believed that severe COVID-19 results from...
BACKGROUND
The current COVID-19 pandemic is posing a major challenge to public health on a global scale. While it is generally believed that severe COVID-19 results from over-expression of inflammatory mediators (i.e., a "cytokine storm"), it is still unclear whether and how co-infecting pathogens contribute to disease pathogenesis. To address this, we followed the entire course of the disease in cases with severe or critical COVID-19 to determine the presence and abundance of all potential pathogens present-the total "infectome"-and how they interact with the host immune system in the context of severe COVID-19.
METHODS
We examined one severe and three critical cases of COVID-19, as well as a set of healthy controls, with longitudinal samples (throat swab, whole blood, and serum) collected from each case. Total RNA sequencing (meta-transcriptomics) was performed to simultaneously investigate pathogen diversity and abundance, as well as host immune responses, in each sample. A Bio-Plex method was used to measure serum cytokine and chemokine levels.
RESULTS
Eight pathogens, SARS-CoV-2, (), (), (), (), , herpes simplex virus (HSV) and human cytomegalovirus (CMV), identified in patients with COVID-19 appeared at different stages of the disease. The dynamics of inflammatory mediators in serum and the respiratory tract were more strongly associated with the dynamics of the infectome compared with SARS-CoV-2 alone. Correlation analysis revealed that pulmonary injury was directly associated with cytokine levels, which in turn were associated with the proliferation of SARS-CoV-2 and co-infecting pathogens.
CONCLUSIONS
For each patient, the cytokine storm that resulted in acute lung injury and death involved a dynamic and highly complex infectome, of which SARS-CoV-2 was a component. These results indicate the need for a precision medicine approach to investigate both the infection and host response as a standard means of infectious disease characterization.
PubMed: 35280492
DOI: 10.21037/jtd-21-1284