DNA extraction bias is more pronounced for microbial eukaryotes than for prokaryotes
In this study, we compared the effect of two DNA preservation methods and six DNA extraction methods on the community profiles of both eukaryotes and prokaryotes in phototrophic biofilms on seagrass (Zostera marina) leaves from the Baltic Sea. We found that, whereas both DNA preservation and extraction method caused significant bias in perceived community composition for both eukaryotes and prokaryotes, extraction bias was more pronounced for eukaryotes than for prokaryotes. In particular, soft-bodied and hard-shelled eukaryotes like nematodes and diatoms, respectively, were differentially abundant depending on the extra...
Source: MicrobiologyOpen - September 30, 2022 Category: Microbiology Authors: Anne Brauer,
Mia M. Bengtsson Tags: COMMENTARY Source Type: research
Enriching captivity conditions with natural elements does not prevent the loss of wild ‐like gut microbiota but shapes its compositional variation in two small mammals
In this study, we assessed how the gut microbiota of two wild-caught small mammals, namelyCrocidura russula (Eulipotyphla, insectivore) andApodemus sylvaticus (Rodentia, omnivore), changed when bringing them into captivity. We analyzed fecal samples of 15 A. sylvaticus and 21 C. russula, immediately after bringing them into captivity and 5 weeks later, spread over two housing treatments: a “natural” setup enriched with elements freshly collected from nature and a “laboratory” setup with sterile artificial elements. Through sequencing of the V3–V4 region of the 16S recombinant RNA gene, we found that the initi...
Source: MicrobiologyOpen - September 28, 2022 Category: Microbiology Authors: Adam Koziol,
I ñaki Odriozola,
Lasse Nyholm,
Aoife Leonard,
Carlos San José,
Joana Pauperio,
Clara Ferreira,
Anders J. Hansen,
Ostaizka Aizpurua,
M. Thomas P. Gilbert,
Antton Alberdi Tags: ORIGINAL ARTICLE Source Type: research
Bacterial composition in Swedish raw drinking water reveals three major interacting ubiquitous metacommunities
ConclusionThe identification of ubiquitous persistent co-occurring bacterial metacommunities in freshwater habitats could potentially facilitate microbial source tracking analysis of contamination issues in freshwater sources. (Source: MicrobiologyOpen)
Source: MicrobiologyOpen - September 26, 2022 Category: Microbiology Authors: Bj örn Brindefalk,
Harald Brolin,
Melle Säve‐Söderbergh,
Edvin Karlsson,
David Sundell,
Per Wikström,
Karin Jacobsson,
Jonas Toljander,
Per Stenberg,
Andreas Sjödin,
Rikard Dryselius,
Mats Forsman,
Jon Ahlinder Tags: ORIGINAL ARTICLE Source Type: research
Defects in DNA double ‐strand break repair resensitize antibiotic‐resistant Escherichia coli to multiple bactericidal antibiotics
This study identified bacterial DNA double-strand break repair as a promising target for the development of resistance-breaking co-therapies. We observed that defects in the double-strand break repair pathway led to significant resensitization of antibiotic-resistantEscherichia coli toward five bactericidal antibiotics representing different functional classes. AbstractAntibiotic resistance is becoming increasingly prevalent amongst bacterial pathogens and there is an urgent need to develop new types of antibiotics with novel modes of action. One promising strategy is to develop resistance-breaker compounds, which inhibi...
Source: MicrobiologyOpen - September 23, 2022 Category: Microbiology Authors: Sarah A. Revitt ‐Mills,
Elizabeth K. Wright,
Madaline Vereker,
Callum O'Flaherty,
Fairley McPherson,
Catherine Dawson,
Antoine M. Oijen,
Andrew Robinson Tags: ORIGINAL ARTICLE Source Type: research
Geobacter sulfurreducens metabolism at different donor/acceptor ratios
The usual electron donor and carbon source of theGeobacter species is acetate, while fumarate is the usual electron acceptor. By choosing different acceptor/donor ratios, malate and succinate production byGeobacter sulfurreducens can be altered. The results provide optimization possibilities for chemical synthesis as well as for the application ofG. sulfurreducens in electrobiotechnology and remediation processes. AbstractGeobacter species have great application potential in remediation processes and electrobiotechnology. In all applications, understanding the metabolism will enable target-oriented optimization of the pro...
Source: MicrobiologyOpen - September 22, 2022 Category: Microbiology Authors: Hanna Marianne Fr ühauf‐Wyllie,
Dirk Holtmann Tags: ORIGINAL ARTICLE Source Type: research
Bacteriophages pass through candle ‐shaped porous ceramic filters: Application for the collection of viruses in soil water
This study proposes to use porous candles as a new tool for collecting soil water viruses. In the first step, the passage of model viruses through the ceramic part of the candles was investigated. Regarding the field application, the experiments carried out showed a successful recovery of viruses, demonstrating the relevance and efficiency of such a tool for the collection of viruses from soil water in the context of metagenomic studies of viral communities. AbstractDespite the ubiquity of viruses in soils, their diversity in soil water has not been explored, mainly due to the difficulty of collecting them. In hydrology, s...
Source: MicrobiologyOpen - September 21, 2022 Category: Microbiology Authors: Perrine Florent,
Henry ‐Michel Cauchie,
Malte Herold,
Leslie Ogorzaly Tags: ORIGINAL ARTICLE Source Type: research
Isolation of extended ‐spectrum β‐lactamase‐producing Escherichia coli from Japanese red fox (Vulpes vulpes japonica)
We report here that extended-spectrum beta-lactamase producers may have spilled over from humans and domestic animals. This suggests that handling dropped feces with care around areas of human activity is essential. AbstractAntimicrobial resistance is a global concern requiring a one-health approach. Given wild animals can harbor antimicrobial-resistant bacteria (ARB), we investigated their presence in 11 fecal samples from wild animals using deoxycholate hydrogen sulfide lactose agar with or without cefotaxime (CTX, 1 mg/L). Thus, we isolated CTX-resistantEscherichia coli from two Japanese red fox fecal samples. One st...
Source: MicrobiologyOpen - September 21, 2022 Category: Microbiology Authors: Tetsuo Asai,
Michiyo Sugiyama,
Tsutomu Omatsu,
Masato Yoshikawa,
Toshifumi Minamoto Tags: COMMENTARY Source Type: research
Comparative analysis of Listeria monocytogenes plasmid transcriptomes reveals common and plasmid ‐specific gene expression patterns and high expression of noncoding RNAs
This study performed gene expression analysis of threeListeria monocytogenes plasmids from three differentL. monocytogenes strains. These findings further our understanding of the dynamic expression ofL. monocytogenes plasmid-encoded genes in diverse environmental conditions and highlight the need to expand the study ofL. monocytogenes plasmid gene function AbstractRecent research demonstrated that someListeria monocytogenes plasmids contribute to stress survival. However, only a few studies have analyzed gene expression patterns ofL. monocytogenes plasmids. In this study, we identified four previously published stress-res...
Source: MicrobiologyOpen - September 19, 2022 Category: Microbiology Authors: Justin M. Anast,
Andrea J. Etter,
Stephan Schmitz ‐Esser Tags: ORIGINAL ARTICLE Source Type: research
De novo biosynthesis of α‐aminoadipate via multi‐strategy metabolic engineering in Escherichia coli
This study is the first to present the effective biosynthesis of α-aminoadipat e inE. coli using multi-strategy metabolic engineering. (Source: MicrobiologyOpen)
Source: MicrobiologyOpen - September 2, 2022 Category: Microbiology Authors: Yang Zhang,
Meng Liu,
Bingqi Cai,
Keqin He,
Meng Wang,
Biqiang Chen,
Tianwei Tan Tags: ORIGINAL ARTICLE Source Type: research
Issue Information
(Source: MicrobiologyOpen)
Source: MicrobiologyOpen - September 1, 2022 Category: Microbiology Tags: ISSUE INFORMATION Source Type: research
Discrimination of Escherichia coli, Shigella flexneri, and Shigella sonnei using lipid profiling by MALDI ‐TOF mass spectrometry paired with machine learning
This study aimed to address the challenge of rapid discrimination betweenEscherichia coli andShigella spp. using MALDI-TOF MS in the negative ion mode for lipid profiling coupled with machine learning. BothE. coli andShigella species are closely related; they share high sequence homology, reported for 16S rRNA gene sequence similarities betweenE. coli andShigella spp. exceeding 99%, and a similar protein expression pattern but are epidemiologically distinct. A bacterial collection of 45E. coli, 48Shigella flexneri, and 62Shigella sonnei clinical isolates were submitted to lipid profiling in negative ion mode using the MALD...
Source: MicrobiologyOpen - August 28, 2022 Category: Microbiology Authors: Jade Pizzato,
Wenhao Tang,
Sandrine Bernabeu,
R émy A. Bonnin,
Emmanuelle Bille,
Eric Farfour,
Thomas Guillard,
Olivier Barraud,
Vincent Cattoir,
Chloe Plouzeau,
Stéphane Corvec,
Vahid Shahrezaei,
Laurent Dortet,
Gerald Larrouy‐Maumus Tags: COMMENTARY Source Type: research
Distinguishing functional from structural roles of conserved pore residues during formate translocation by the FocA anion channel
This study categorizes seven other conserved residues that line each channel pore; two residues are relevant for formate translocation and five for pore integrity. Two asparagine residues proved to be important for structural stability of the pore, while K156 and N172 were identified to be crucial for bidirectional formate translocation. AbstractThe formate-specific anion channel FocA ofEscherichia coli belongs to the superfamily of homopentameric formate-nitrite transporters (FNT). Minimally nine amino acid residues are conserved in the formate translocation pore of each protomer of the pentamer, including a histidine (H2...
Source: MicrobiologyOpen - August 16, 2022 Category: Microbiology Authors: Michelle Kammel,
R. Gary Sawers Tags: ORIGINAL ARTICLE Source Type: research
Eating eggplants as a cucurbit feeder: Dietary shifts affect the gut microbiome of the melon fly Zeugodacus cucurbitae (Diptera, Tephritidae)
This study shows how local processes and host plants can strongly affect the composition of the insect microbiome and the importance of using adequately sampled populations. AbstractWhile contemporary changes in feeding preferences have been documented in phytophagous insects, the mechanisms behind these processes remain to be fully clarified. In this context, the insect gut microbiome plays a central role in adaptation to novel host plants. The cucurbit frugivorous fruit flyZeugodacus cucurbitae (Diptera, Tephritidae) has occasionally been reported on “unconventional” host plants from different families, including Sol...
Source: MicrobiologyOpen - August 16, 2022 Category: Microbiology Authors: Wouter Hendrycks,
H élène Delatte,
Laura Moquet,
Kostas Bourtzis,
Nele Mullens,
Marc De Meyer,
Thierry Backeljau,
Massimiliano Virgilio Tags: ORIGINAL ARTICLE Source Type: research
Early biofilm and streamer formation is mediated by wall shear stress and surface wettability: A multifactorial microfluidic study
We used a microfluidic platform to investigate biofilm development by applying four different wall shear stresses simultaneously and tested three different surfaces with varying hydrophobicity. Our key results showed that surface wettability played a role in biofilm formation forCobetia marina andPseudomonas aeruginosa at low shear stress. However, this was minimized as the shear stress increased. Biofilm streamers were observed at the highest shear stress. AbstractBiofilms are intricate communities of microorganisms encapsulated within a self-produced matrix of extra-polymeric substances (EPS), creating complex three-dime...
Source: MicrobiologyOpen - August 16, 2022 Category: Microbiology Authors: Alexander L. M. Chun,
Ali Mosayyebi,
Arthur Butt,
Dario Carugo,
Maria Salta Tags: ORIGINAL ARTICLE Source Type: research
The evolution of alkaliphilic biofilm communities in response to extreme alkaline pH values
Flocculants were used to seed biofilms in alkaline conditions (pH 11.0 –13.0). Biofilms had pH and redox values lower than that of the external environment. Extracellular polymeric materials comprising the biofilm may play a role in these changes. AbstractExtremes of pH present a challenge to microbial life and our understanding of survival strategies for microbial consortia, particularly at high pH, remains limited. The utilization of extracellular polymeric substances within complex biofilms allows micro-organisms to obtain a greater level of control over their immediate environment. This manipulation of the immediat...
Source: MicrobiologyOpen - August 16, 2022 Category: Microbiology Authors: Christopher J. Charles,
Simon P. Rout,
Brian R. Jackson,
Sally A. Boxall,
Sirwan Akbar,
Paul N. Humphreys Tags: ORIGINAL ARTICLE Source Type: research
