Pub Date : 2024-09-13DOI: 10.3390/microorganisms12091890
Coad Thomas Dow, Ellen S. Pierce, Leonardo A. Sechi
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that, over millions of years, became integrated into the human genome. While normally inactive, environmental stimuli such as infections have contributed to the transcriptional reactivation of HERV-promoting pathological conditions, including the development of autoimmunity, neurodegenerative disease and cancer. What infections trigger HERV activation? Mycobacterium avium subspecies paratuberculosis (MAP) is a pluripotent driver of human disease. Aside from granulomatous diseases, Crohn’s disease, sarcoidosis and Blau syndrome, MAP is associated with autoimmune disease: type one diabetes (T1D), multiple sclerosis (MS), rheumatoid arthritis (RA) and autoimmune thyroiditis. MAP is also associated with Alzheimer’s disease (AD) and Parkinson’s disease (PD). Autoimmune diabetes, MS and RA are the diseases with the strongest MAP/HERV association. There are several other diseases associated with HERV activation, including diseases whose epidemiology and/or pathology would prompt speculation for a causal role of MAP. These include non-solar uveal melanoma, colon cancer, glioblastoma and amyotrophic lateral sclerosis (ALS). This article further points to MAP infection as a contributor to autoimmunity, neurodegenerative disease and cancer via the un-silencing of HERV. We examine the link between the ever-increasing number of MAP-associated diseases and the MAP/HERV intersection with these diverse medical conditions, and propose treatment opportunities based upon this association.
{"title":"Mycobacterium paratuberculosis: A HERV Turn-On for Autoimmunity, Neurodegeneration, and Cancer?","authors":"Coad Thomas Dow, Ellen S. Pierce, Leonardo A. Sechi","doi":"10.3390/microorganisms12091890","DOIUrl":"https://doi.org/10.3390/microorganisms12091890","url":null,"abstract":"Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that, over millions of years, became integrated into the human genome. While normally inactive, environmental stimuli such as infections have contributed to the transcriptional reactivation of HERV-promoting pathological conditions, including the development of autoimmunity, neurodegenerative disease and cancer. What infections trigger HERV activation? Mycobacterium avium subspecies paratuberculosis (MAP) is a pluripotent driver of human disease. Aside from granulomatous diseases, Crohn’s disease, sarcoidosis and Blau syndrome, MAP is associated with autoimmune disease: type one diabetes (T1D), multiple sclerosis (MS), rheumatoid arthritis (RA) and autoimmune thyroiditis. MAP is also associated with Alzheimer’s disease (AD) and Parkinson’s disease (PD). Autoimmune diabetes, MS and RA are the diseases with the strongest MAP/HERV association. There are several other diseases associated with HERV activation, including diseases whose epidemiology and/or pathology would prompt speculation for a causal role of MAP. These include non-solar uveal melanoma, colon cancer, glioblastoma and amyotrophic lateral sclerosis (ALS). This article further points to MAP infection as a contributor to autoimmunity, neurodegenerative disease and cancer via the un-silencing of HERV. We examine the link between the ever-increasing number of MAP-associated diseases and the MAP/HERV intersection with these diverse medical conditions, and propose treatment opportunities based upon this association.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
(1) Background: The successful treatment of infective endocarditis (IE) relies on detecting causative pathogens to administer targeted antibiotic therapy. In addition to standard microbiological cultivation of pathogens from tissue obtained during heart valve surgery, the potential of molecular biological methods was evaluated. (2) Methods: A retrospective study was performed on heart valve tissue from 207 patients who underwent heart valve surgery for IE. FISHseq (fluorescence in situ hybridization combined with 16S rRNA gene PCR and sequencing) was performed in addition to conventional culture-based microbiological diagnostics. The diagnostic performance of FISHseq was compared with the conventional methods and evaluated in the clinical context. (3) Results: Overall, FISHseq provided a significantly higher rate of specific pathogen detection than conventional valve culture (68.1% vs. 33.3%, p < 0.001). By complementing the findings from blood culture and valve culture, FISHseq was able to provide a new microbiological diagnosis in 10% of cases, confirm the cultural findings in 24.2% of cases and provide greater diagnostic accuracy in 27.5% of cases. FISHseq could identify a pathogen in blood-culture-negative IE in 46.2% of cases, while valve culture provided only 13.5% positive results (p < 0.001). (4) Conclusions: This study demonstrates that using FISHseq as an additional molecular biological technique for diagnostics in IE adds substantial diagnostic value, with potential implications for the treatment of IE. It provides pathogen detection, especially in cases where conventional microbiological cultivation is negative or inconclusive.
{"title":"Diagnostic Benefit of Molecular Imaging in Patients Undergoing Heart Valve Surgery for Infective Endocarditis","authors":"Dustin Greve, Emma Sartori, Hector Rodriguez Cetina Biefer, Stefania-Teodora Sima, Dinah Von Schöning, Frieder Pfäfflin, Miriam Songa Stegemann, Volkmar Falk, Annette Moter, Judith Kikhney, Herko Grubitzsch","doi":"10.3390/microorganisms12091889","DOIUrl":"https://doi.org/10.3390/microorganisms12091889","url":null,"abstract":"(1) Background: The successful treatment of infective endocarditis (IE) relies on detecting causative pathogens to administer targeted antibiotic therapy. In addition to standard microbiological cultivation of pathogens from tissue obtained during heart valve surgery, the potential of molecular biological methods was evaluated. (2) Methods: A retrospective study was performed on heart valve tissue from 207 patients who underwent heart valve surgery for IE. FISHseq (fluorescence in situ hybridization combined with 16S rRNA gene PCR and sequencing) was performed in addition to conventional culture-based microbiological diagnostics. The diagnostic performance of FISHseq was compared with the conventional methods and evaluated in the clinical context. (3) Results: Overall, FISHseq provided a significantly higher rate of specific pathogen detection than conventional valve culture (68.1% vs. 33.3%, p < 0.001). By complementing the findings from blood culture and valve culture, FISHseq was able to provide a new microbiological diagnosis in 10% of cases, confirm the cultural findings in 24.2% of cases and provide greater diagnostic accuracy in 27.5% of cases. FISHseq could identify a pathogen in blood-culture-negative IE in 46.2% of cases, while valve culture provided only 13.5% positive results (p < 0.001). (4) Conclusions: This study demonstrates that using FISHseq as an additional molecular biological technique for diagnostics in IE adds substantial diagnostic value, with potential implications for the treatment of IE. It provides pathogen detection, especially in cases where conventional microbiological cultivation is negative or inconclusive.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.3390/microorganisms12091884
Paulina Amšiejūtė-Graziani, Vaclovas Jurgelevičius, Simona Pilevičienė, Žygimantas Janeliūnas, Jana Radzijevskaja, Algimantas Paulauskas, Česlova Butrimaitė-Ambrozevičienė, Ingrida Jacevičienė
Deformed wing virus (DWV) is known as one of the main viruses that affect honeybees’ health all around the world. The virus has two widespread genotypes, DWV-A and DWV-B (VDV-1), transmitted mainly by V. destructor mites. In this study, we collected honeycombs with covered broods from 73 apiaries in eight Lithuanian regions and initially investigated the prevalence of V. destructor mites. Mites were collected from May to the end of July in 2021 from 124 hives. The prevalence of V. destructor infestations in beehives reached 30% and 63% in investigated apiaries. The presence of DWV-A and DWV-B pathogens in mites and broods was examined by RT-qPCR targeting the CRPV-capsid region. The molecular characterization of the virus in mite samples was based on sequence analysis of the RNA-dependent RNA polymerase (RdRp) region. In addition, leader polypeptide (LP), structural protein (Vp3), Helicase, and RdRp genes were used for phylogenetic characterization of dual infection. The prevalences of DWV-B in mites and broods were 56.5% and 31.5%, respectively, while DWV-A was detected in 12.9% of mite samples and 24.7% of brood samples. Some of the examined mite samples harboured dual virus infections. Our findings showed that bee colonies from the same apiary were not always infected by the same viruses. Some bee colonies were virus-free, while others were highly infected. Phylogenetic analysis of 21 sequences demonstrated the presence of highly variable DWV-B and DWV-A genotypes in Lithuania and possible recombinant variants of the virus. This study represents the first molecular characterization of mite-borne pathogens hosted by honeybees (Apis mellifera) in Lithuania.
{"title":"Molecular Characterization and Phylogenetic Analysis of Honeybee (Apis mellifera) Mite-Borne Pathogen DWV-A and DWV-B Isolated from Lithuania","authors":"Paulina Amšiejūtė-Graziani, Vaclovas Jurgelevičius, Simona Pilevičienė, Žygimantas Janeliūnas, Jana Radzijevskaja, Algimantas Paulauskas, Česlova Butrimaitė-Ambrozevičienė, Ingrida Jacevičienė","doi":"10.3390/microorganisms12091884","DOIUrl":"https://doi.org/10.3390/microorganisms12091884","url":null,"abstract":"Deformed wing virus (DWV) is known as one of the main viruses that affect honeybees’ health all around the world. The virus has two widespread genotypes, DWV-A and DWV-B (VDV-1), transmitted mainly by V. destructor mites. In this study, we collected honeycombs with covered broods from 73 apiaries in eight Lithuanian regions and initially investigated the prevalence of V. destructor mites. Mites were collected from May to the end of July in 2021 from 124 hives. The prevalence of V. destructor infestations in beehives reached 30% and 63% in investigated apiaries. The presence of DWV-A and DWV-B pathogens in mites and broods was examined by RT-qPCR targeting the CRPV-capsid region. The molecular characterization of the virus in mite samples was based on sequence analysis of the RNA-dependent RNA polymerase (RdRp) region. In addition, leader polypeptide (LP), structural protein (Vp3), Helicase, and RdRp genes were used for phylogenetic characterization of dual infection. The prevalences of DWV-B in mites and broods were 56.5% and 31.5%, respectively, while DWV-A was detected in 12.9% of mite samples and 24.7% of brood samples. Some of the examined mite samples harboured dual virus infections. Our findings showed that bee colonies from the same apiary were not always infected by the same viruses. Some bee colonies were virus-free, while others were highly infected. Phylogenetic analysis of 21 sequences demonstrated the presence of highly variable DWV-B and DWV-A genotypes in Lithuania and possible recombinant variants of the virus. This study represents the first molecular characterization of mite-borne pathogens hosted by honeybees (Apis mellifera) in Lithuania.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.3390/microorganisms12091887
Armanda Rodrigues, Graça Alexandre-Pires, Ana Valério-Bolas, Telmo Nunes, Isabel Pereira da Fonseca, Gabriela Santos-Gomes
Human zoonotic visceral leishmaniasis (ZVL) and canine leishmaniasis (CanL) constitute a major public and veterinary health concern and are both caused by the infection with the protozoan parasite Leishmania infantum. One of the main target organs in CanL is the liver. This complex organ, composed of various highly specialized cell types, has garnered significant attention from the scientific community as a crucial player in innate immune functions. In the context of CanL, liver infection by parasites and the host immune response generated strongly influence the disease outcome. Thus, taking advantage of a co-culture system involving canine hepatocytes and L. infantum-infected autologous Kupffer cells (KCs), allowing cell-to-cell interaction, the current report aims to shed light on the hepatocyte-KCs immune interaction. The co-culture of infected KCs with hepatocytes revealed a vital role of these cells in the activation of a local immune response against L. infantum parasites. Although KCs alone can be immunologically silenced by L. infantum infection, the cell-to-cell interaction with hepatocytes in co-culture can lead to local immune activation. In co-culture it was observed gene expression increased the number of innate immune receptors, specifically cell membrane TLR2 and cytoplasmatic NOD1 along with high TNF-α generation. Altogether, these results suggest that the immune response generated in co-culture could induce the recruitment of other circulating cells to contain and contribute to the resolution of the infection in the liver. This work also enhances our understanding of the liver as a vital organ in innate immunity within the context of CanL.
{"title":"Kupffer Cells and Hepatocytes: A Key Relation in the Context of Canine Leishmaniasis","authors":"Armanda Rodrigues, Graça Alexandre-Pires, Ana Valério-Bolas, Telmo Nunes, Isabel Pereira da Fonseca, Gabriela Santos-Gomes","doi":"10.3390/microorganisms12091887","DOIUrl":"https://doi.org/10.3390/microorganisms12091887","url":null,"abstract":"Human zoonotic visceral leishmaniasis (ZVL) and canine leishmaniasis (CanL) constitute a major public and veterinary health concern and are both caused by the infection with the protozoan parasite Leishmania infantum. One of the main target organs in CanL is the liver. This complex organ, composed of various highly specialized cell types, has garnered significant attention from the scientific community as a crucial player in innate immune functions. In the context of CanL, liver infection by parasites and the host immune response generated strongly influence the disease outcome. Thus, taking advantage of a co-culture system involving canine hepatocytes and L. infantum-infected autologous Kupffer cells (KCs), allowing cell-to-cell interaction, the current report aims to shed light on the hepatocyte-KCs immune interaction. The co-culture of infected KCs with hepatocytes revealed a vital role of these cells in the activation of a local immune response against L. infantum parasites. Although KCs alone can be immunologically silenced by L. infantum infection, the cell-to-cell interaction with hepatocytes in co-culture can lead to local immune activation. In co-culture it was observed gene expression increased the number of innate immune receptors, specifically cell membrane TLR2 and cytoplasmatic NOD1 along with high TNF-α generation. Altogether, these results suggest that the immune response generated in co-culture could induce the recruitment of other circulating cells to contain and contribute to the resolution of the infection in the liver. This work also enhances our understanding of the liver as a vital organ in innate immunity within the context of CanL.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.3390/microorganisms12091888
Hirona Ikeda, Sumio Maeda
Persister cells (PCs), a subpopulation occurring within normal cells, exhibit a transient tolerance to antibiotics because of their dormant state. PCs are categorized into two types: type I PCs, which emerge during the stationary phase, and type II PCs, which emerge during the logarithmic phase. Using the conventional colony-forming method, we previously demonstrated that type I PCs of Escherichia coli form more frequently in air–solid biofilm culture than in liquid culture. In the current study, we modified a cell filamentation method as a more efficient and rapid alternative for quantifying PCs. This modified method yielded results consistent with those of the conventional method with 103–104 times higher sensitivity and less detection time, within several hours, and further revealed the existence of multiple levels of type I PCs, including a substantial number of deeply dormant cells. This study also discovered a potential epigenetic memory mechanism, spanning several generations (four or six cell divisions), which influences type II PC formation based on prior biofilm experience in E. coli.
固着细胞（PCs）是正常细胞中的一个亚群，由于处于休眠状态，因此对抗生素具有短暂的耐受性。固着细胞分为两种类型：一种是在静止期出现的 I 型固着细胞，另一种是在对数期出现的 II 型固着细胞。我们曾使用传统的菌落形成法证明，大肠埃希菌的 I 型 PC 在气固生物膜培养中比在液体培养中更容易形成。在目前的研究中，我们改进了细胞丝状化方法，将其作为量化 PC 的一种更有效、更快速的替代方法。这种改良方法的结果与传统方法一致，灵敏度提高了 103-104 倍，检测时间缩短了数小时，并进一步揭示了多层次 I 型 PC 的存在，包括大量深度休眠细胞。这项研究还发现了一种潜在的表观遗传记忆机制，这种机制跨越数代（四或六次细胞分裂），根据大肠杆菌先前的生物膜经验影响 II 型 PC 的形成。
{"title":"Characterization of Escherichia coli Persisters from Biofilm Culture: Multiple Dormancy Levels and Multigenerational Memory in Formation","authors":"Hirona Ikeda, Sumio Maeda","doi":"10.3390/microorganisms12091888","DOIUrl":"https://doi.org/10.3390/microorganisms12091888","url":null,"abstract":"Persister cells (PCs), a subpopulation occurring within normal cells, exhibit a transient tolerance to antibiotics because of their dormant state. PCs are categorized into two types: type I PCs, which emerge during the stationary phase, and type II PCs, which emerge during the logarithmic phase. Using the conventional colony-forming method, we previously demonstrated that type I PCs of Escherichia coli form more frequently in air–solid biofilm culture than in liquid culture. In the current study, we modified a cell filamentation method as a more efficient and rapid alternative for quantifying PCs. This modified method yielded results consistent with those of the conventional method with 103–104 times higher sensitivity and less detection time, within several hours, and further revealed the existence of multiple levels of type I PCs, including a substantial number of deeply dormant cells. This study also discovered a potential epigenetic memory mechanism, spanning several generations (four or six cell divisions), which influences type II PC formation based on prior biofilm experience in E. coli.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.3390/microorganisms12091891
Samantha McCarlie, Charlotte Boucher-van Jaarsveld, Robert Bragg
During the COVID-19 pandemic, the surge in disinfectant use emphasised their pivotal role in infection control. While the majority of antimicrobial resistance research focuses on antibiotics, resistance to biocides, which are present in disinfectants and sanitisers, is escalating. Serratia sp. HRI is a highly resistant isolate, and through the study of this organism, the molecular mechanisms of resistance may be uncovered. Serratia sp. HRI was treated with the disinfectant benzalkonium chloride in preparation for RNA sequencing. Through mining of the RNA-Seq differential expression data, an uncharacterised Major Facilitator Superfamily (MFS) efflux pump gene was found to be up-regulated at least four-fold at four different time points of exposure. Real-time PCR revealed this uncharacterised MFS efflux gene was up-regulated after exposure to benzalkonium chloride and two additional disinfectants, didecyldimethylammonium chloride (DDAC) and VirukillTM. Additionally, expression of this gene was found to be higher at 20 min versus 90 min of exposure, indicating that the up-regulation of this gene is an initial response to biocide treatment that decreases over time. This suggests that MFS efflux pumps may be an initial survival mechanism for microorganisms, allowing time for longer-term resistance mechanisms. This work puts forward a novel biocide resistance gene that could have a major impact on biocide susceptibility and resistance.
{"title":"Differential Expression Analysis Reveals Possible New Quaternary Ammonium Compound Resistance Gene in Highly Resistant Serratia sp. HRI","authors":"Samantha McCarlie, Charlotte Boucher-van Jaarsveld, Robert Bragg","doi":"10.3390/microorganisms12091891","DOIUrl":"https://doi.org/10.3390/microorganisms12091891","url":null,"abstract":"During the COVID-19 pandemic, the surge in disinfectant use emphasised their pivotal role in infection control. While the majority of antimicrobial resistance research focuses on antibiotics, resistance to biocides, which are present in disinfectants and sanitisers, is escalating. Serratia sp. HRI is a highly resistant isolate, and through the study of this organism, the molecular mechanisms of resistance may be uncovered. Serratia sp. HRI was treated with the disinfectant benzalkonium chloride in preparation for RNA sequencing. Through mining of the RNA-Seq differential expression data, an uncharacterised Major Facilitator Superfamily (MFS) efflux pump gene was found to be up-regulated at least four-fold at four different time points of exposure. Real-time PCR revealed this uncharacterised MFS efflux gene was up-regulated after exposure to benzalkonium chloride and two additional disinfectants, didecyldimethylammonium chloride (DDAC) and VirukillTM. Additionally, expression of this gene was found to be higher at 20 min versus 90 min of exposure, indicating that the up-regulation of this gene is an initial response to biocide treatment that decreases over time. This suggests that MFS efflux pumps may be an initial survival mechanism for microorganisms, allowing time for longer-term resistance mechanisms. This work puts forward a novel biocide resistance gene that could have a major impact on biocide susceptibility and resistance.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Burkholderia (sensu lato) is a diverse group of β-Proteobacteria that exists worldwide in various environments. The SBE clade of this group was thought to be mutualistic with stinkbugs. Riptortus–Burkholderia was suggested as an ideal model system for studying insect–microbe symbiosis. To explore the strain-level diversity of Burkholderia at the individual and population levels of Riptortus stinkbugs (Hemiptera: Alydidae), and to uncover the factors affecting the Burkholderia community, large-scale sampling of two Riptortus species and deep sequencing data (16S amplicon) were used in the present study. Our results showed that: (1) the proportions of facultative symbiotic bacteria Burkholderia were very high, with an average proportion of 87.1% in the samples; (2) only six out of 1373 Burkholderia amplicon sequence variants (ASVs) did not belong to the SBE clade, accounting for only 0.03% of Burkholderia; (3) a relatively small number of Burkholderia ASVs had a large number of sequences, with 22, 54, and 107 ASVs accounting for more than 1.0%, 0.1%, and 0.01% of the total Burkholderia sequences, respectively; (4) multiple Burkholderia ASVs were present in most Riptortus individuals, but there was one dominant or two codominant ASVs, and codominance was more likely to occur when the genetic distance between the two codominant ASVs was small; and (5) the beta diversity of Burkholderia was significantly different between the two host species (PerMANOVA: both Jaccard and Bray–Curtis, p < 0.001) and among localities (PerMANOVA: both Jaccard and Bray–Curtis, p < 0.001). Two-way PerMANOVA also indicated that both the host (Bray–Curtis, p = 0.020; Jaccard, p = 0.001) and geographical location (Bray–Curtis, p = 0.041; Jaccard, p = 0.045) influence Burkholderia communities; furthermore, Mantel tests showed that the Burkholderia communities were significantly correlated with the geographical distance of sample locations (R = 0.056, p = 0.001). Together, our findings demonstrate the fine-scale diversity of Burkholderia symbionts and suggest a region- and host-dependent pattern of Burkholderia in Riptortus stinkbugs.
{"title":"Large-Scale Sampling Reveals the Strain-Level Diversity of Burkholderia Symbionts in Riptortus pedestris and R. linearis (Hemiptera: Alydidae)","authors":"Xin-Rui Hou, Si-Ying Fu, Yuan Wang, Jia-Yue Zhou, Tian-Yi Qi, Yan-Fei Li, Wen-Jun Bu, Huai-Jun Xue","doi":"10.3390/microorganisms12091885","DOIUrl":"https://doi.org/10.3390/microorganisms12091885","url":null,"abstract":"Burkholderia (sensu lato) is a diverse group of β-Proteobacteria that exists worldwide in various environments. The SBE clade of this group was thought to be mutualistic with stinkbugs. Riptortus–Burkholderia was suggested as an ideal model system for studying insect–microbe symbiosis. To explore the strain-level diversity of Burkholderia at the individual and population levels of Riptortus stinkbugs (Hemiptera: Alydidae), and to uncover the factors affecting the Burkholderia community, large-scale sampling of two Riptortus species and deep sequencing data (16S amplicon) were used in the present study. Our results showed that: (1) the proportions of facultative symbiotic bacteria Burkholderia were very high, with an average proportion of 87.1% in the samples; (2) only six out of 1373 Burkholderia amplicon sequence variants (ASVs) did not belong to the SBE clade, accounting for only 0.03% of Burkholderia; (3) a relatively small number of Burkholderia ASVs had a large number of sequences, with 22, 54, and 107 ASVs accounting for more than 1.0%, 0.1%, and 0.01% of the total Burkholderia sequences, respectively; (4) multiple Burkholderia ASVs were present in most Riptortus individuals, but there was one dominant or two codominant ASVs, and codominance was more likely to occur when the genetic distance between the two codominant ASVs was small; and (5) the beta diversity of Burkholderia was significantly different between the two host species (PerMANOVA: both Jaccard and Bray–Curtis, p < 0.001) and among localities (PerMANOVA: both Jaccard and Bray–Curtis, p < 0.001). Two-way PerMANOVA also indicated that both the host (Bray–Curtis, p = 0.020; Jaccard, p = 0.001) and geographical location (Bray–Curtis, p = 0.041; Jaccard, p = 0.045) influence Burkholderia communities; furthermore, Mantel tests showed that the Burkholderia communities were significantly correlated with the geographical distance of sample locations (R = 0.056, p = 0.001). Together, our findings demonstrate the fine-scale diversity of Burkholderia symbionts and suggest a region- and host-dependent pattern of Burkholderia in Riptortus stinkbugs.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mycotoxins, toxic compounds produced by fungi, pose significant risks to food safety and human health. This study investigates the bio-detoxification potential of 238 strains of lactic acid bacteria (LAB) and Bacillus spp., previously isolated from cereals (including mycotoxin-contaminated grains), against the emerging mycotoxin, enniatin B (ENB), and the prevalent mycotoxin, deoxynivalenol (DON). Out of the tested strains, 26 demonstrated notable mycotoxin reduction capabilities, including 2 Bacillus pumilus and 24 Bacillus licheniformis strains. B. licheniformis strains MA572, MA695, MA696, TR174a, TR284, TR363, and TR466a degraded ENB to levels below the detection limit, and six strains reduced DON by 30–35%; B. licheniformis TR251b and TR374 showed the highest DON reduction with 35.7%. The most promising strains for bio-detoxification were B. licheniformis TR284, which achieved a 100% reduction in ENB and a 28.6% reduction in DON and B. licheniformis TR388 with a 97.5% reduction in ENB and a 31.9% reduction in DON. None of the tested LAB strains significantly reduced either mycotoxin. These findings highlight the promising potential of B. licheniformis strains in bio-detoxifying mycotoxin-contaminated cereal products. Further research into the underlying detoxification mechanisms and safety aspects is essential to develop effective bio-detoxification strategies for enhancing food safety.
{"title":"Potential for the Bio-Detoxification of the Mycotoxins Enniatin B and Deoxynivalenol by Lactic Acid Bacteria and Bacillus spp","authors":"Sandra Mischler, Amandine André, Irene Chetschik, Susanne Miescher Schwenninger","doi":"10.3390/microorganisms12091892","DOIUrl":"https://doi.org/10.3390/microorganisms12091892","url":null,"abstract":"Mycotoxins, toxic compounds produced by fungi, pose significant risks to food safety and human health. This study investigates the bio-detoxification potential of 238 strains of lactic acid bacteria (LAB) and Bacillus spp., previously isolated from cereals (including mycotoxin-contaminated grains), against the emerging mycotoxin, enniatin B (ENB), and the prevalent mycotoxin, deoxynivalenol (DON). Out of the tested strains, 26 demonstrated notable mycotoxin reduction capabilities, including 2 Bacillus pumilus and 24 Bacillus licheniformis strains. B. licheniformis strains MA572, MA695, MA696, TR174a, TR284, TR363, and TR466a degraded ENB to levels below the detection limit, and six strains reduced DON by 30–35%; B. licheniformis TR251b and TR374 showed the highest DON reduction with 35.7%. The most promising strains for bio-detoxification were B. licheniformis TR284, which achieved a 100% reduction in ENB and a 28.6% reduction in DON and B. licheniformis TR388 with a 97.5% reduction in ENB and a 31.9% reduction in DON. None of the tested LAB strains significantly reduced either mycotoxin. These findings highlight the promising potential of B. licheniformis strains in bio-detoxifying mycotoxin-contaminated cereal products. Further research into the underlying detoxification mechanisms and safety aspects is essential to develop effective bio-detoxification strategies for enhancing food safety.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The preparation of artificial soil is a potential cooperative resource utilization scheme for red mud and phosphogypsum on a large scale, with a low cost and simple operation. The characteristics of the bacterial community structure and function in three artificial soils were systematically studied for the first time. Relatively rich bacterial communities were formed in the artificial soils, with relatively high abundances of bacterial phyla (e.g., Cyanobacteria, Proteobacteria, Actinobacteriota, and Chloroflexi) and bacterial genera (e.g., Microcoleus_PCC-7113, Rheinheimera, and Egicoccus), which can play key roles in various nutrient transformations, resistance to saline–alkali stress and pollutant toxicity, the enhancement of various soil enzyme activities, and the ecosystem construction of artificial soil. There were diverse bacterial functions (e.g., photoautotrophy, chemoheterotrophy, aromatic compound degradation, fermentation, nitrate reduction, cellulolysis, nitrogen fixation, etc.), indicating the possibility of various bacteria-dominated biochemical reactions in the artificial soil, which can significantly enrich the nutrient cycling and energy flow and enhance the fertility of the artificial soil and the activity of the soil life. The bacterial communities in the different artificial soils were generally correlated with major physicochemical factors (e.g., pH, OM, TN, AN, and AP), as well as enzyme activity factors (e.g., S-UE, S-SC, S-AKP, S-CAT, and S-AP), which comprehensively illustrates the complexity of the interaction between bacterial communities and environmental factors in artificial soils, and which may affect the succession direction of bacterial communities, the quality of the artificial soil environment, and the speed and direction of the development and maturity of the artificial soil. This study provides an important scientific basis for the synergistic soilization of two typical industrial solid wastes, red mud and phosphogypsum, specifically for the microbial mechanism, for the further evolution and development of artificial soil prepared using red mud and phosphogypsum.
{"title":"Characteristics of Bacterial Community Structure and Function in Artificial Soil Prepared Using Red Mud and Phosphogypsum","authors":"Yong Liu, Zhi Yang, Lishuai Zhang, Hefeng Wan, Fang Deng, Zhiqiang Zhao, Jingfu Wang","doi":"10.3390/microorganisms12091886","DOIUrl":"https://doi.org/10.3390/microorganisms12091886","url":null,"abstract":"The preparation of artificial soil is a potential cooperative resource utilization scheme for red mud and phosphogypsum on a large scale, with a low cost and simple operation. The characteristics of the bacterial community structure and function in three artificial soils were systematically studied for the first time. Relatively rich bacterial communities were formed in the artificial soils, with relatively high abundances of bacterial phyla (e.g., Cyanobacteria, Proteobacteria, Actinobacteriota, and Chloroflexi) and bacterial genera (e.g., Microcoleus_PCC-7113, Rheinheimera, and Egicoccus), which can play key roles in various nutrient transformations, resistance to saline–alkali stress and pollutant toxicity, the enhancement of various soil enzyme activities, and the ecosystem construction of artificial soil. There were diverse bacterial functions (e.g., photoautotrophy, chemoheterotrophy, aromatic compound degradation, fermentation, nitrate reduction, cellulolysis, nitrogen fixation, etc.), indicating the possibility of various bacteria-dominated biochemical reactions in the artificial soil, which can significantly enrich the nutrient cycling and energy flow and enhance the fertility of the artificial soil and the activity of the soil life. The bacterial communities in the different artificial soils were generally correlated with major physicochemical factors (e.g., pH, OM, TN, AN, and AP), as well as enzyme activity factors (e.g., S-UE, S-SC, S-AKP, S-CAT, and S-AP), which comprehensively illustrates the complexity of the interaction between bacterial communities and environmental factors in artificial soils, and which may affect the succession direction of bacterial communities, the quality of the artificial soil environment, and the speed and direction of the development and maturity of the artificial soil. This study provides an important scientific basis for the synergistic soilization of two typical industrial solid wastes, red mud and phosphogypsum, specifically for the microbial mechanism, for the further evolution and development of artificial soil prepared using red mud and phosphogypsum.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bacterial drug resistance is becoming an increasingly serious problem, and the development of antibacterial synergists is urgently needed. Combining existing antibiotics with promising nonantibiotic agents is one strategy that has been shown to be effective at overcoming the widespread emergence of antibiotic-resistant pathogens. In this study, we investigated the antibacterial activities and mechanism of naringenin (NG) combined with amikacin (AMK) against multidrug-resistant Escherichia coli (E. coli). We first measured the fractional inhibitory concentration (FIC) of NG combined with antibiotics via the checkerboard method. The results indicated that the combination of NG and AMK had a synergistic effect on E. coli ATCC 25922 and E. coli C7F3. In addition, this synergistic effect was verified by time-kill assays. Moreover, scanning electron microscopy (SEM) was used to observe cell morphology. The results showed that the cell wall of E. coli was destroyed. Furthermore, we assessed the leakage of alkaline phosphatase (AKP), K+, and protein. The extracellular AKP activity increased after the combinational group of 1/2MIC NG and 1/2MIC AMK, suggesting an impairment in cell wall permeability. An increase in the leakage of intracellular K+ and protein indicated an increase in cell inner membrane permeability. These results revealed that NG and AMK inhibited E. coli by damaging cell walls and membranes. In addition, PI uptake rapidly increased after treatment with NG and AMK. Confocal laser scanning microscopy (CLSM) revealed that NG caused cell wall and cell membrane damage in E. coli. In summary, our results provide a new strategy for responding to the development of E. coli drug resistance.
{"title":"In Vitro Antimicrobial Synergistic Activity and the Mechanism of the Combination of Naringenin and Amikacin Against Antibiotic-Resistant Escherichia coli","authors":"Lankun Yi, Mingze Cao, Xu Chen, Yubin Bai, Weiwei Wang, Xiaojuan Wei, Yuxiang Shi, Yongying Zhang, Tenghe Ma, Zhen Zhu, Jiyu Zhang","doi":"10.3390/microorganisms12091871","DOIUrl":"https://doi.org/10.3390/microorganisms12091871","url":null,"abstract":"Bacterial drug resistance is becoming an increasingly serious problem, and the development of antibacterial synergists is urgently needed. Combining existing antibiotics with promising nonantibiotic agents is one strategy that has been shown to be effective at overcoming the widespread emergence of antibiotic-resistant pathogens. In this study, we investigated the antibacterial activities and mechanism of naringenin (NG) combined with amikacin (AMK) against multidrug-resistant Escherichia coli (E. coli). We first measured the fractional inhibitory concentration (FIC) of NG combined with antibiotics via the checkerboard method. The results indicated that the combination of NG and AMK had a synergistic effect on E. coli ATCC 25922 and E. coli C7F3. In addition, this synergistic effect was verified by time-kill assays. Moreover, scanning electron microscopy (SEM) was used to observe cell morphology. The results showed that the cell wall of E. coli was destroyed. Furthermore, we assessed the leakage of alkaline phosphatase (AKP), K+, and protein. The extracellular AKP activity increased after the combinational group of 1/2MIC NG and 1/2MIC AMK, suggesting an impairment in cell wall permeability. An increase in the leakage of intracellular K+ and protein indicated an increase in cell inner membrane permeability. These results revealed that NG and AMK inhibited E. coli by damaging cell walls and membranes. In addition, PI uptake rapidly increased after treatment with NG and AMK. Confocal laser scanning microscopy (CLSM) revealed that NG caused cell wall and cell membrane damage in E. coli. In summary, our results provide a new strategy for responding to the development of E. coli drug resistance.","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":null,"pages":null},"PeriodicalIF":4.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142203404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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