Applied and Environmental Microbiology最新文献

{"title":"Selective human milk oligosaccharide utilization by members of the <i>Bifidobacterium pseudocatenulatum</i> taxon.","authors":"Rocio Sanchez-Gallardo, Francesca Bottacini, Ian J O'Neill, Maria Esteban-Torres, Rebecca Moore, Fionnuala M McAuliffe, Paul D Cotter, Douwe van Sinderen","doi":"10.1128/aem.00648-24","DOIUrl":"10.1128/aem.00648-24","url":null,"abstract":"<p><p>Human milk oligosaccharides (HMOs) are essentially unaffected by the digestive enzymes of the nursling and are known for their ability to enrich certain microbial species in the infant gut microbiota, in particular bifidobacteria. HMO metabolism has been studied in various bifidobacterial species such as <i>B. breve</i>, <i>B. bifidum,</i> and <i>B. longum</i> subsp. <i>infantis</i>. In the current study, we describe differential growth abilities elicited by twenty-three newly isolated <i>Bifidobacterium pseudocatenulatum</i> strains on particular HMOs, such as 2'-fucosyllactose (2'FL), 3-fucosyllactose (3FL), lacto-N-tetraose (LNT), and lacto-N-neotetraose (LNnT). Through gene-trait matching and comparative genome analysis, we identified genes involved in the degradation of fucosylated HMOs in this strain set, while we employed a transcriptomic approach to facilitate the identification and characterization of genes and associated enzymes involved in LNT metabolism by strain <i>B. pseudocatenulatum</i> MM0196. A total of 252 publicly available genomes of the <i>B. pseudocatenulatum</i> taxon were screened for homologs of the glycosyl hydrolases (GHs) identified here as being required for selected HMO metabolism. From this analysis, it is clear that all members of this species possess homologs of the genes involved in LNT degradation, while genes required for degradation of fucosylated HMOs are variably present.IMPORTANCEOur findings allow a better understanding of the complex interaction between <i>Bifidobacterium</i> and its host and provide a roadmap toward future applications of <i>B. pseudocatenulatum</i> as a probiotic with a focus on infant health. Furthermore, our investigations have generated information on the role of HMOs in shaping the infant gut microbiota, thus also facilitating applications of HMOs in infant nutrition, with potential extension into the mature or adult gut microbiota. Supplementation of HMOs is known to result in the modulation of bacterial communities toward a higher relative abundance of bifidobacteria, which in turn enforces their ability to modulate particular immune functions and strengthen the intestinal barrier. This work may therefore inspire future studies to improve the formulation of neonatal nutritional products, aimed at facilitating the development of a healthy digestive and immune system and reducing the differences in gut microbiota composition observed between breastfed and formula-fed babies or full-term and preterm infants.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0064824"},"PeriodicalIF":3.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11497806/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tools for genetic engineering and gene expression control in <i>Novosphingobium aromaticivorans</i> and <i>Rhodobacter sphaeroides</i>.","authors":"Ashley N Hall, Benjamin W Hall, Kyle J Kinney, Gabby G Olsen, Amy B Banta, Daniel R Noguera, Timothy J Donohue, Jason M Peters","doi":"10.1128/aem.00348-24","DOIUrl":"10.1128/aem.00348-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Alphaproteobacteria have a variety of cellular and metabolic features that provide important insights into biological systems and enable biotechnologies. For example, some species are capable of converting plant biomass into valuable biofuels and bioproducts that have the potential to contribute to the sustainable bioeconomy. Among the Alphaproteobacteria, &lt;i&gt;Novosphingobium aromaticivorans&lt;/i&gt;, &lt;i&gt;Rhodobacter sphaeroides&lt;/i&gt;, and &lt;i&gt;Zymomonas mobilis&lt;/i&gt; show promise as organisms that can be engineered to convert extracted plant lignin or sugars into bioproducts and biofuels. Genetic manipulation of these bacteria is needed to introduce engineered pathways and modulate expression of native genes with the goal of enhancing bioproduct output. Although recent work has expanded the genetic toolkit for &lt;i&gt;Z. mobilis&lt;/i&gt;, &lt;i&gt;N. aromaticivorans&lt;/i&gt; and &lt;i&gt;R. sphaeroides&lt;/i&gt; still need facile, reliable approaches to deliver genetic payloads to the genome and to control gene expression. Here, we expand the platform of genetic tools for &lt;i&gt;N. aromaticivorans&lt;/i&gt; and &lt;i&gt;R. sphaeroides&lt;/i&gt; to address these issues. We demonstrate that Tn&lt;i&gt;7&lt;/i&gt; transposition is an effective approach for introducing engineered DNA into the chromosome of &lt;i&gt;N. aromaticivorans&lt;/i&gt; and &lt;i&gt;R. sphaeroides&lt;/i&gt;. We screen a synthetic promoter library to identify isopropyl β-D-1-thiogalactopyranoside-inducible promoters with regulated activity in both organisms (up to ~15-fold induction in &lt;i&gt;N. aromaticivorans&lt;/i&gt; and ~5-fold induction in &lt;i&gt;R. sphaeroides&lt;/i&gt;). Combining Tn&lt;i&gt;7&lt;/i&gt; integration with promoters from our library, we establish CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) interference systems for &lt;i&gt;N. aromaticivorans&lt;/i&gt; and &lt;i&gt;R. sphaeroides&lt;/i&gt; (up to ~10-fold knockdown in &lt;i&gt;N. aromaticivorans&lt;/i&gt; and &lt;i&gt;R. sphaeroides&lt;/i&gt;) that can target essential genes and modulate engineered pathways. We anticipate that these systems will greatly facilitate both genetic engineering and gene function discovery efforts in these species and other Alphaproteobacteria.IMPORTANCEIt is important to increase our understanding of the microbial world to improve health, agriculture, the environment, and biotechnology. For example, building a sustainable bioeconomy depends on the efficient conversion of plant material to valuable biofuels and bioproducts by microbes. One limitation in this conversion process is that microbes with otherwise promising properties for conversion are challenging to genetically engineer. Here we report genetic tools for &lt;i&gt;Novosphingobium aromaticivorans&lt;/i&gt; and &lt;i&gt;Rhodobacter sphaeroides&lt;/i&gt; that add to the burgeoning set of tools available for genome engineering and gene expression in Alphaproteobacteria. Our approaches allow straightforward insertion of engineered pathways into the &lt;i&gt;N. aromaticivorans&lt;/i&gt; or &lt;i&gt;R. sphaeroides&lt;/i&gt; genome and control of gene expression by inducing genes with synthetic promoters or repressing genes u","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0034824"},"PeriodicalIF":3.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11497788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using patterns of shared taxa to infer bacterial dispersal in human living environment in urban and rural areas.","authors":"M Grönroos, A Jumpponen, M I Roslund, N Nurminen, S Oikarinen, A Parajuli, O H Laitinen, O Cinek, L Kramna, J Rajaniemi, H Hyöty, R Puhakka, A Sinkkonen","doi":"10.1128/aem.00903-24","DOIUrl":"10.1128/aem.00903-24","url":null,"abstract":"<p><p>Contact with environmental microbial communities primes the human immune system. Factors determining the distribution of microorganisms, such as dispersal, are thus important for human health. Here, we used the relative number of bacteria shared between environmental and human samples as a measure of bacterial dispersal and studied these associations with living environment and lifestyles. We analyzed amplicon sequence variants (ASVs) of the V4 region of 16S rDNA gene from 347 samples of doormat dust as well as samples of saliva, skin swabs, and feces from 53 elderly people in urban and rural areas in Finland at three timepoints. We first enumerated the ASVs shared between doormat and one of the human sample types (i.e., saliva, skin swab, or feces) of each individual subject and calculated the shared ASVs as a proportion of all ASVs in the given sample type of that individual. We observed that the patterns for the proportions of shared ASVs differed among seasons and human sample type. In skin samples, there was a negative association between the proportion of shared ASVs and the coverage of built environment (a proxy for degree of urbanization), whereas in saliva data, this association was positive. We discuss these findings in the context of differing species pools in urban and rural environments.</p><p><strong>Importance: </strong>Understanding how environmental microorganisms reach and interact with humans is a key question when aiming to increase human contacts with natural microbiota. Few methods are suitable for studying microbial dispersal at relatively large spatial scales. Thus, we tested an indirect method and studied patterns of bacterial taxa that are shared between humans and their living environment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0090324"},"PeriodicalIF":3.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11498140/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142124601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transient infection of <i>Euprymna scolopes</i> with an engineered D-alanine auxotroph of <i>Vibrio fischeri</i>.","authors":"Macey Coppinger, Liu Yang, David L Popham, Edward Ruby, Eric V Stabb","doi":"10.1128/aem.01298-24","DOIUrl":"10.1128/aem.01298-24","url":null,"abstract":"<p><p>The symbiosis between <i>Vibrio fischeri</i> and the Hawaiian bobtail squid, <i>Euprymna scolopes</i>, is a tractable and well-studied model of bacteria-animal mutualism. Here, we developed a method to transiently colonize <i>E. scolopes</i> using D-alanine (D-ala) auxotrophy of the symbiont, controlling the persistence of viable infection by supplying or withholding D-ala. We generated alanine racemase (<i>alr</i>) mutants of <i>V. fischeri</i> that lack avenues for mutational suppression of auxotrophy or reversion to prototrophy. Surprisingly, an ∆<i>alr</i> mutant did not require D-ala to grow in a minimal medium, a phenomenon requiring <i>metC</i>, which encodes cystathionine β-lyase. Likewise, overexpression of <i>metC</i> suppressed D-ala auxotrophy in a rich medium. To block potential mechanisms of suppression, we combined the ∆<i>alr</i> mutation with deletions of <i>metC</i> and/or <i>bsrF</i>, which encodes a broad-spectrum racemase and investigated the suppression rates of four D-ala auxotrophic strains. We then focused on ∆<i>alr</i> ∆<i>bsrF</i> mutant MC13, which has a suppression rate of <10^-9. When D-ala was removed from a growing culture of MC13, cells rounded and lysed within 40 minutes. Transient colonization of <i>E. scolopes</i> was achieved by inoculating squid in seawater containing MC13 and D-ala, and then transferring the squid into water lacking D-ala, which resulted in loss of viable symbionts within hours. Interestingly, the symbionts within crypt 3 persisted longer than those of crypt 1, suggesting a difference in bacterial growth rate in distinct crypt environments. Our study highlights a new approach for inducing transient colonization and provides insight into the biogeography of the <i>E. scolopes</i> light organ.IMPORTANCEThe importance of this study is multi-faceted, providing a valuable methodological tool and insight into the biology of the symbiosis between <i>Vibrio fischeri</i> and <i>Euprymna scolopes</i>. First, the study sheds light on the critical role of D-ala for bacterial growth, and the underpinnings of D-ala synthesis. Our observations that <i>metC</i> obviates the need for D-ala supplementation of an <i>alr</i> mutant in minimal medium and that MetC-dependent growth correlates with D-ala in peptidoglycan, corroborate and extend previous findings in <i>Escherichia coli</i> regarding a role of MetC in D-ala production. Second, our isolation of robust D-ala auxotrophs led us to a novel method for studying the squid-<i>Vibrio</i> symbiosis, allowing for transient colonization without the use of antibiotics, and revealed intriguing differences in symbiont growth parameters in distinct light organ crypts. This work and the methodology developed will contribute to our understanding of the persistence and dynamics of <i>V. fischeri</i> within its host.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0129824"},"PeriodicalIF":3.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11497789/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A gene regulating ergot alkaloid biosynthesis in <i>Metarhizium brunneum</i>.","authors":"Samantha J Fabian, Chey R Steen, F Heath Damron, Celeste A DeRiggi, Daniel G Panaccione","doi":"10.1128/aem.01051-24","DOIUrl":"10.1128/aem.01051-24","url":null,"abstract":"<p><p>Ergot alkaloid synthesis (<i>eas</i>) gene clusters found in several fungi encode biosynthesis of agriculturally and pharmaceutically important ergot alkaloids. Although the biosynthetic genes of the ergot alkaloid pathway have been well characterized, regulation of those genes is unknown. We characterized a gene with sequence similarity to a putative transcription factor and that was found adjacent to the <i>eas</i> cluster of <i>Metarhizium brunneum</i>, a plant symbiont and insect pathogen. Function of the novel gene, <i>easR,</i> was explored by CRISPR-Cas9-derived gene knockouts. To maximize potential for ergot alkaloid accumulation, strains of <i>M. brunneum</i> were injected into larvae of the insect <i>Galleria mellonella</i>. Larvae infected with the wild type contained abundant ergot alkaloids, but those infected with <i>easR</i> knockouts lacked detectable ergot alkaloids. The <i>easR</i> knockout strains had significantly reduced or no detectable mRNA from <i>eas</i> cluster genes in RNAseq and qualitative RT-PCR analyses, whereas the wild-type strain contained abundant mRNA from all <i>eas</i> genes. These data demonstrate that the product of <i>easR</i> is required for ergot alkaloid accumulation and provide evidence that it has a role in the expression of ergot alkaloid biosynthesis genes. Larvae infected with an <i>easR</i> knockout survived significantly longer than those infected with the wild type (<i>P</i> < 0.0001), indicating a role for EasR, and indirectly confirming a role for ergot alkaloids, in the virulence of <i>M. brunneum</i> to insects. Homologs of <i>easR</i> were found associated with <i>eas</i> clusters of at least 15 other ergot alkaloid-producing fungi, indicating that EasR homologs may contribute to regulation of ergot alkaloid synthesis in additional fungi.</p><p><strong>Importance: </strong>Ergot alkaloids produced by several species of fungi are important as contaminants of food and feed in agriculture and also as the foundation of numerous pharmaceuticals prescribed for dementia, migraines, hyperprolactinemia, and several other disorders. Information on control of the ergot alkaloid pathway may contribute to strategies to limit their production in agricultural settings or increase their yield for pharmaceutical production. Our results demonstrate that a previously uncharacterized gene clustered with the ergot alkaloid synthesis genes is required for the sufficient transcription of the ergot alkaloid biosynthesis genes. This observation suggests the gene encodes a factor regulating transcription of those biosynthetic genes.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0105124"},"PeriodicalIF":3.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11497822/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The energy metabolism of <i>Cupriavidus necator</i> in different trophic conditions.","authors":"Michael Jahn, Nick Crang, Arvid H Gynnå, Deria Kabova, Stefan Frielingsdorf, Oliver Lenz, Emmanuelle Charpentier, Elton P Hudson","doi":"10.1128/aem.00748-24","DOIUrl":"10.1128/aem.00748-24","url":null,"abstract":"<p><p>The \"knallgas\" bacterium <i>Cupriavidus necator</i> is attracting interest due to its extremely versatile metabolism. <i>C. necator</i> can use hydrogen or formic acid as an energy source, fixes CO₂ <i>via</i> the Calvin-Benson-Bassham (CBB) cycle, and grows on organic acids and sugars. Its tripartite genome is notable for its size and duplications of key genes (CBB cycle, hydrogenases, and nitrate reductases). Little is known about which of these isoenzymes and their cofactors are actually utilized for growth on different substrates. Here, we investigated the energy metabolism of <i>C. necator</i> H16 by growing a barcoded transposon knockout library on succinate, fructose, hydrogen (H₂/CO₂), and formic acid. The fitness contribution of each gene was determined from enrichment or depletion of the corresponding mutants. Fitness analysis revealed that (i) some, but not all, molybdenum cofactor biosynthesis genes were essential for growth on formate and nitrate respiration. (ii) Soluble formate dehydrogenase (FDH) was the dominant enzyme for formate oxidation, not membrane-bound FDH. (iii) For hydrogenases, both soluble and membrane-bound enzymes were utilized for lithoautotrophic growth. (iv) Of the six terminal respiratory complexes in <i>C. necator</i> H16, only some are utilized, and utilization depends on the energy source. (v) Deletion of hydrogenase-related genes boosted heterotrophic growth, and we show that the relief from associated protein cost is responsible for this phenomenon. This study evaluates the contribution of each of <i>C. necator</i>'s genes to fitness in biotechnologically relevant growth regimes. Our results illustrate the genomic redundancy of this generalist bacterium and inspire future engineering strategies.IMPORTANCEThe soil bacterium <i>Cupriavidus necator</i> can grow on gas mixtures of CO₂, H₂, and O₂. It also consumes formic acid as carbon and energy source and various other substrates. This metabolic flexibility comes at a price, for example, a comparatively large genome (6.6 Mb) and a significant background expression of lowly utilized genes. In this study, we mutated every non-essential gene in <i>C. necator</i> using barcoded transposons in order to determine their effect on fitness. We grew the mutant library in various trophic conditions including hydrogen and formate as the sole energy source. Fitness analysis revealed which of the various energy-generating iso-enzymes are actually utilized in which condition. For example, only a few of the six terminal respiratory complexes are used, and utilization depends on the substrate. We also show that the protein cost for the various lowly utilized enzymes represents a significant growth disadvantage in specific conditions, offering a route to rational engineering of the genome. All fitness data are available in an interactive app at https://m-jahn.shinyapps.io/ShinyLib/.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0074824"},"PeriodicalIF":3.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immunostimulatory activity of lipoteichoic acid with three fatty acid residues derived from <i>Limosilactobacillus antri</i> JCM 15950^T.","authors":"Shino Yamasaki-Yashiki, Tsukasa Shiraishi, Mai Gyobu, Haruna Sasaki, Jun Kunisawa, Shin-Ichi Yokota, Yoshio Katakura","doi":"10.1128/aem.01197-24","DOIUrl":"10.1128/aem.01197-24","url":null,"abstract":"<p><p>Some strains of lactic acid bacteria can regulate the host's intestinal immune system. Bacterial cells and membrane vesicles (MVs) of <i>Limosilactobacillus antri</i> JCM 15950^T promote immunoglobulin A (IgA) production in murine Peyer's patch cells via toll-like receptor (TLR) 2. This study aimed to investigate the role of lipoteichoic acid (LTA), a ligand of TLR2, in the immunostimulatory activity of these bacterial cells and their MVs. LTA extracted from bacterial cells was purified through hydrophobic interaction chromatography and then divided into fractions LTA1 and LTA2 through anion-exchange chromatography. LTA1 induced greater interleukin (IL)-6 production from macrophage-like RAW264 cells than LTA2, and the induced IL-6 production was suppressed by TLR2 neutralization using an anti-TLR2 antibody. The LTAs in both fractions contained two hexose residues in the glycolipid anchor; however, LTA1 was particularly rich in triacyl LTA. The free hydroxy groups in the glycerol phosphate (GroP) repeating units were substituted by d-alanine (d-Ala) and α-glucose in LTA1, but only by α-glucose in LTA2. The dealanylation of LTA1 slightly suppressed IL-6 production in RAW264 cells, whereas deacylation almost completely suppressed IL-6 production. Furthermore, IL-6 production induced by dealanylated LTA1 was markedly higher than that induced by dealanylated LTA2. These results indicated that the critical moieties for the immunostimulatory activity of <i>L. antri</i>-derived LTA were the three fatty acid residues rather than the substitution with d-Ala in GroP. LTA was also detected in MVs, suggesting that the triacyl LTA, but not the diacyl LTA, translocated to the MVs and conferred immunostimulatory activity.</p><p><strong>Importance: </strong>Some lactic acid bacteria activate the host intestinal immune system via toll-like receptor (TLR) 2. Lipoteichoic acid (LTA) is a TLR2 ligand; however, the moieties of LTA that determine its immunostimulatory activity remain unclear because of the wide diversity of LTA partial structures. We found that <i>Limosilactobacillus antri</i> JCM 15950^T has three types of LTAs (triacyl, diacyl, and monoacyl LTAs). Specifically, structural analysis of the LTAs revealed that triacyl LTA plays a crucial role in immunostimulation and that the fatty acid residues are essential for the activity. The three acyl residues are characteristic of LTAs from many lactic acid bacteria, and our findings can explain the immunostimulatory mechanisms widely exhibited by lactic acid bacteria. Furthermore, the immunostimulatory activity of membrane vesicles released by <i>L. antri</i> JCM 15950^T is due to the transferred LTA, demonstrating a novel mechanism of membrane vesicle-mediated immunostimulation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0119724"},"PeriodicalIF":3.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11497808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders in <i>Acinetobacter pittii</i>.","authors":"Elise M Van Fossen, Jared O Kroll, Lindsey N Anderson, Andrew D McNaughton, Daisy Herrera, Yasuhiro Oda, Andrew J Wilson, William C Nelson, Neeraj Kumar, Andrew R Frank, Joshua R Elmore, Pubudu Handakumbura, Vivian S Lin, Robert G Egbert","doi":"10.1128/aem.01026-24","DOIUrl":"10.1128/aem.01026-24","url":null,"abstract":"<p><p>Interactions between plants and soil microbial communities that benefit plant growth and enhance nutrient acquisition are driven by the selective release of metabolites from plant roots, or root exudation. To investigate these plant-microbe interactions, we developed a photoaffinity probe based on sorgoleone (<u>so</u>rgoleone <u>d</u>iazirine <u>a</u>lkyne for <u>p</u>hoto<u>a</u>ffinity <u>l</u>abeling, SoDA-PAL), a hydrophobic secondary metabolite and allelochemical produced in <i>Sorghum bicolor</i> root exudates. We applied SoDA-PAL to the identification of sorgoleone-binding proteins in <i>Acinetobacter pittii</i> SO1, a potential plant growth-promoting microbe isolated from sorghum rhizosphere soil. Competitive photoaffinity labeling of <i>A. pittii</i> whole cell lysates with SoDA-PAL identified 137 statistically enriched proteins, including putative transporters, transcriptional regulators, and a subset of proteins with predicted enzymatic functions. We performed computational protein modeling and docking with sorgoleone to prioritize candidates for experimental validation and then confirmed binding of sorgoleone to four of these proteins <i>in vitro</i>: the α/β fold hydrolase SrgB (OH685_09420), a fumarylacetoacetase (OH685_02300), a lysophospholipase (OH685_14215), and an unannotated hypothetical protein (OH685_18625). Our application of this specialized sorgoleone-based probe coupled with structural bioinformatics streamlines the identification of microbial proteins involved in metabolite recognition, metabolism, and toxicity, widening our understanding of the range of cellular pathways that can be affected by a plant secondary metabolite.IMPORTANCEHere, we demonstrate that a photoaffinity-based chemical probe modeled after sorgoleone, an important secondary metabolite released by sorghum roots, can be used to identify microbial proteins that directly interact with sorgoleone. We applied this probe to the sorghum-associated bacterium <i>Acinetobacter pittii</i> and showed that probe labeling is dose-dependent and sensitive to competition with purified sorgoleone. Coupling the probe with proteomics and computational analysis facilitated the identification of putative sorgoleone binders, including a protein implicated in a conserved pathway essential for sorgoleone catabolism. We anticipate that discoveries seeded by this workflow will expand our understanding of the molecular mechanisms by which specific metabolites in root exudates shape the sorghum rhizosphere microbiome.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0102624"},"PeriodicalIF":3.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11497774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142153014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigations of microbial adaptation to singular, binary, and fully formulated quaternary ammonium compounds.","authors":"Thomas Willmott, Paul P Kelly, Layali Jadaan, Danna R Gifford, Steven D Mercer, Gavin J Humphreys, Christopher G Knight, Jian R Lu, Andrew J McBain","doi":"10.1128/aem.00666-24","DOIUrl":"10.1128/aem.00666-24","url":null,"abstract":"<p><p>The study was conducted to inform risk assessments concerning microbial exposure to quaternary ammonium biocides (QUATs) by investigating their effects on 10 microbial strains of hygiene relevance. Biocides were divided into three categories: simple aqueous solutions, biocide mixtures, and formulated biocides. Organisms were grown in the presence of biocides for 10 generations and then subsequently for another 10 generations in biocide-free media. Control organisms were passaged 20 times in biocide-free media. Strains were then assessed for biocide and antibiotic susceptibility, changes in growth dynamics, and single nucleotide polymorphisms (SNPs). Biocide mixtures demonstrated greater antimicrobial potency than singular and formulated biocides. Susceptibility changes of under twofold were observed for all biocides tested. Susceptibility decreased significantly for organisms passaged with singular biocides (1.29- to 4.35-fold) and biocide mixtures (1.4- to 1.5-fold), but not for formulated biocides (1.3- to 1.84-fold) compared to controls. Antibiotic susceptibility both increased and decreased in passaged organisms, with heightened susceptibility occurring more frequently in the singular biocide group. Changes in susceptibility and growth dynamics were similar in the passaged and unexposed controls for fitness measures of adapted bacteria; there were no significant differences between biocide groups, but significantly lower generation and doubling times in organisms exposed to singular biocides. Similar frequencies in SNPs occurred for the three biocide groups and unexposed controls. While some adaptations occurred, particularly with singular biocides, the impact on antibiotic resistance and genomic mutations was limited. These findings suggest that the use of formulated QUATs may pose a comparatively lower risk for antimicrobial resistance.IMPORTANCEBiocides are used globally to control microbial growth and effective assessment of the risks and benefits of their use is therefore a high priority. Much of the data used to assess risk has been based on sub-lethal exposure of bacteria to singular biocides in simple aqueous solutions. This work builds on limited prior realism-based studies to demonstrate enhanced potency in biocidal mixtures; the mitigation of resistance selection by formulations and inconsistent cross-resistance effects with both increases and decreases in susceptibility for a wide range of antibiotics. These data can be used to better inform risk assessments of biocide deployment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0066624"},"PeriodicalIF":3.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11497780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Articles of Significant Interest in This Issue.","authors":"","doi":"10.1128/aem.02001-24","DOIUrl":"https://doi.org/10.1128/aem.02001-24","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":"90 10","pages":"e0200124"},"PeriodicalIF":3.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142493391","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}