Frontiers in Microbiology

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ISSN / EISSN : 1664-302X / 1664-302X
Published by: Frontiers Media SA (10.3389)
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Sébastien Renoud, Jordan Vacheron, Danis Abrouk, Claire Prigent-Combaret, Laurent Legendre, Daniel Muller,
Published: 26 January 2022
Frontiers in Microbiology, Volume 12; https://doi.org/10.3389/fmicb.2021.760512

Abstract:
The beneficial effects of plant growth–promoting Rhizobacteria (PGPR) entail several interaction mechanisms with the plant or with other root-associated microorganisms. These microbial functions are carried out by multiple taxa within functional groups and contribute to rhizosphere functioning. It is likely that the inoculation of additional PGPR cells will modify the ecology of these functional groups. We also hypothesized that the inoculation effects on functional groups are site specific, similarly as the PGPR phytostimulation effects themselves. To test this, we assessed in the rhizosphere of field-grown maize the effect of seed inoculation with the phytostimulatory PGPR Azospirillum lipoferum CRT1 on the size and/or diversity of selected microbial functional groups important for plant growth, using quantitative polymerase chain reaction and/or Illumina MiSeq metabarcoding. The functional groups included bacteria able to fix nitrogen (a key nutrient for plant growth), producers of 1-aminocyclopropane-1-carboxylate (ACC) deaminase (which modulate ethylene metabolism in plant and stimulate root growth), and producers of 2,4-diacetylphloroglucinol (an auxinic signal enhancing root branching). To test the hypothesis that such ecological effects were site-specific, the functional groups were monitored at three different field sites, with four sampling times over two consecutive years. Despite poor inoculant survival, inoculation enhanced maize growth. It also increased the size of functional groups in the three field sites, at the maize six-leaf and flowering stages for diazotrophs and only at flowering stage for ACC deaminase and 2,4-diacetylphloroglucinol producers. Sequencing done in the second year revealed that inoculation modified the composition of diazotrophs (and of the total bacterial community) and to a lesser extent of ACC deaminase producers. This study revealed an ecological impact that was field specific (even though a few taxa were impacted in all fields) and of unexpected magnitude with the phytostimulatory Azospirillum inoculant, when considering microbial functional groups. Further methodological developments are needed to monitor additional functional groups important for soil functioning and plant growth under optimal or stress conditions.
Pavle Banović, Adrian A. Díaz-Sánchez, Verica Simin, Angélique Foucault-Simonin, Clemence Galon, Alejandra Wu-Chuang, Dragana Mijatović, Dasiel Obregón, ,
Published: 26 January 2022
Frontiers in Microbiology, Volume 12; https://doi.org/10.3389/fmicb.2021.797399

Abstract:
Ticks carry numerous pathogens that, if transmitted, can cause disease in susceptible humans and animals. The present study describes our approach on how to investigate clinical presentations following tick bites in humans. To this aim, the occurrence of major tick-borne pathogens (TBPs) in human blood samples (n = 85) and the ticks collected (n = 93) from the same individuals were tested using an unbiased high-throughput pathogen detection microfluidic system. The clinical symptoms were characterized in enrolled patients. In patients with suspected TBP infection, serological assays were conducted to test for the presence of antibodies against specific TBPs. A field study based on One Health tenets was further designed to identify components of a potential chain of infection resulting in Rickettsia felis infection in one of the patients. Ticks species infesting humans were identified as Ixodes ricinus, Rhipicephalus sanguineus sensu lato (s.l.), Dermacentor reticulatus, and Haemaphysalis punctata. Five patients developed local skin lesions at the site of the tick bite including erythema migrans, local non-specific reactions, and cutaneous hypersensitivity reaction. Although Borrelia burgdorferi s.l., Babesia microti, Anaplasma phagocytophilum, and Candidatus Cryptoplasma sp. DNAs were detected in tick samples, different Rickettsia species were the most common TBPs identified in the ticks. The presence of TBPs such as Rickettsia helvetica, Rickettsia monacensis, Borrelia lusitaniae, Borrelia burgdorferi, Borrelia afzelii, A. phagocytophilum, and B. microti in ticks was further confirmed by DNA sequencing. Two of the patients with local skin lesions had IgG reactive against spotted fever group rickettsiae, while IgM specific to B. afzelii, Borrelia garinii, and Borrelia spielmanii were detected in the patient with erythema migrans. Although R. felis infection was detected in one human blood sample, none of the components of the potential chain of infection considered in this study tested positive to this pathogen either using direct pathogen detection in domestic dogs or xenodiagnosis in ticks collected from domestic cats. The combination of high-throughput screening of TBPs and One Health approaches might help characterize chains of infection leading to human infection by TBPs, as well as prevalence of emerging rickettsial pathogens in the Balkan region.
Mohd Baasir Gaisawat, Silvia Lopez-Escalera, Chad W. MacPherson, Michèle M. Iskandar, Thomas A. Tompkins,
Published: 26 January 2022
Frontiers in Microbiology, Volume 12; https://doi.org/10.3389/fmicb.2021.698638

Abstract:
Clostridioides difficile infection (CDI) is frequently associated with intestinal injury and mucosal barrier dysfunction, leading to an inflammatory response involving neutrophil localization and upregulation of pro-inflammatory cytokines. The severity of clinical manifestations is associated with the extent of the immune response, which requires mitigation for better clinical management. Probiotics could play a protective role in this disorder due to their immunomodulatory ability in gastrointestinal disorders. We assessed five single-strain and three multi-strain probiotics for their ability to modulate CDI fecal water (FW)-induced effects on T84 cells. The CDI-FW significantly (p < 0.05) decreased T84 cell viability. The CDI-FW-exposed cells also exhibited increased pro-inflammatory cytokine production as characterized by interleukin (IL)-8, C-X-C motif chemokine 5, macrophage inhibitory factor (MIF), IL-32, and tumor necrosis factor (TNF) ligand superfamily member 8. Probiotics were associated with strain-specific attenuation of the CDI-FW mediated effects, whereby Saccharomyces boulardii CNCM I-1079 and Lacticaseibacillus rhamnosus R0011 were most effective in reducing pro-inflammatory cytokine production and in increasing T84 cell viability. ProtecFlor™, Lactobacillus helveticus R0052, and Bifidobacterium longum R0175 showed moderate effectiveness, and L. rhamnosus GG R0343 along with the two other multi-strain combinations were the least effective. Overall, the findings showed that probiotic strains possess the capability to modulate the CDI-mediated inflammatory response in the gut lumen.
Masaomi Kurokawa, Issei Nishimura, Bei-Wen Ying
Published: 26 January 2022
Frontiers in Microbiology, Volume 13; https://doi.org/10.3389/fmicb.2022.826894

Abstract:
Whether and how adaptive evolution adjusts the breadth of adaptation in coordination with the genome are essential issues for connecting evolution with ecology. To address these questions, experimental evolution in five Escherichia coli strains carrying either the wild-type genome or a reduced genome was performed in a defined minimal medium (C0). The ancestral and evolved populations were subsequently subjected to fitness and chemical niche analyses across an environmental gradient with 29 combinations of eight chemical components of the minimal medium. The results showed that adaptation was achieved not only specific to the evolutionary condition (C0), but also generally, to the environmental gradient; that is, the breadth of adaptation to the eight chemical niches was expanded. The magnitudes of the adaptive improvement and the breadth increase were both correlated with genome reduction and were highly significant in two out of eight niches (i.e., glucose and sulfate). The direct adaptation-induced correlated adaptation to the environmental gradient was determined by only a few genome mutations. An additive increase in fitness associated with the stepwise fixation of mutations was consistently observed in the reduced genomes. In summary, this preliminary survey demonstrated that evolution finely tuned the breadth of adaptation correlated with genome reduction.
Bárbara M. Schultz, Orlando A. Acevedo, Alexis M. Kalergis,
Published: 26 January 2022
Frontiers in Microbiology, Volume 13; https://doi.org/10.3389/fmicb.2022.798853

Abstract:
Neutrophils are innate immune cells that play an essential role during the clearance of pathogens that can release chromatin structures coated by several cytoplasmatic and granular antibacterial proteins, called neutrophil extracellular traps (NETs). These supra-molecular structures are produced to kill or immobilize several types of microorganisms, including bacteria and viruses. The contribution of the NET release process (or NETosis) to acute inflammation or the prevention of pathogen spreading depends on the specific microorganism involved in triggering this response. Furthermore, studies highlight the role of innate cells different from neutrophils in triggering the release of extracellular traps during bacterial infection. This review summarizes the contribution of NETs during bacterial and viral infections, explaining the molecular mechanisms involved in their formation and the relationship with different components of such pathogens.
Wenqiang Xu, Yu Fang, Mingyang Ding, Yajing Ren, Xiangfeng Meng, Guanjun Chen, , Weifeng Liu
Published: 26 January 2022
Frontiers in Microbiology, Volume 13; https://doi.org/10.3389/fmicb.2022.810066

Abstract:
The filamentous fungus Trichoderma reesei secretes large quantities of cellulases and hemicellulases that have found wide applications in industry. Compared with extensive studies on the mechanism controlling cellulase gene expression, less is known about the regulatory mechanism behind xylanase gene expression. Herein, several putative sugar transporter encoding genes that showed significant upregulation on xylan were identified in T. reesei. Deletion of one such gene, gat1, resulted in increased xylanase production but hardly affected cellulase induction. Further analyses demonstrated that deletion of gat1 markedly increased XYNI production at the transcriptional level and only exerted a minor effect on XYNII synthesis. In contrast, overexpressing gat1 caused a continuous decrease in xyn1 expression. Deletion of gat1 also affected the expression of xyn1 and pectinase genes when T. reesei was cultivated with galacturonic acid as the sole carbon source. Transcriptome analyses of Δgat1 and its parental strain identified 255 differentially expressed genes that are enriched in categories of glycoside hydrolases, lipid metabolism, transporters, and transcriptional factors. The results thus implicate a repressive role of the sugar transporter GAT1 in xyn1 expression and reveal that distinct regulatory mechanisms may exist in controlling the expression of different xylanase genes in T. reesei.
Published: 26 January 2022
Frontiers in Microbiology, Volume 13; https://doi.org/10.3389/fmicb.2022.847176

Abstract:
Editorial on the Research TopicBacteriophages Isolation From the Environment and Their Antimicrobial Therapeutic Potential, Volume 2 The emergence and spread of antibiotic-resistant bacteria was one of the leading global concerns of the last century (Zaman et al., 2017; Chokshi et al., 2019). Today, at the beginning of the twenty-first century, bacteria still hold accountability for preponderant infectious pathogenesis. In the war against them, nature has equipped us with bacterial viruses (named bacteriophages or phages) that dwell on bacteria and can readily kill them (Chibani-Chennoufi et al., 2004). With the advancements in science and medicine, humankind is thriving toward using, manipulating, and repurposing the bacteriophages as effective antibacterials (Burrowes et al., 2011; Chan et al., 2013). However, the idea to use bacteriophages to combat bacterial infections is not entirely new (Wittebole et al., 2014). The first successful trials involving bacterial viruses against human and animal bacterial pathogens were done just after their initial discovery at the beginning of the twentieth century (Campbell, 2010). Unfortunately, these trials and treatments were virtually stopped when penicillin was successfully commercialized as the first antimicrobial (Gaynes, 2017). The twenty-first century seems to be the opening of the second golden age of bacteriophages with the increasing number of new scientific publications on the topic as well as the expanding societal understanding and approval for the use of (alive) bacterial viruses to fight bacterial infections in medicine, veterinary, food microbiology and agriculture applications. This global rediscovery of bacteriophages is also reflected in this Research Topic. One of the keystones to taking advantage of bacteriophages is identifying and thoroughly investigating them. The current thematic issue encloses several reports of isolation and characterization of lytic bacterial viruses to be used in medicine and veterinary. Khan et al. isolated an Escherichia coli C (phi x174 host) lytic phage named MSK and have exhaustively studied the genome of this novel phage. Authors have precisely distinguished 73 open reading frames (ORFs) having diverse functionalities, in which 46 of them showed marked similarity with the ORFs previously reported in Rtp group of bacteriophages. Belonging to the family of Drexlerviridae, MSK has exhibited potent lytic action against multidrug-resistant (MDR) E. coli and other pathogenic E. coli, Pseudomonas syringae, and Salmonella anatum strains. On similar lines, Xu et al. isolated another lytic bacteriophage from Shigella flexneri, named vB_ShiP-A7. This new member of Podoviridae rendered cogent antimicrobial effect against MDR strains of Shigella flexneri and E. coli, as evidenced from the in vivo murine based studies. A new virulent bacteriophage of the Myoviridae family vB_EcoM_swi3 (swi3) from swine feces has been isolated and characterized by Sui et al. This bacteriophage is effective against infections caused by Salmonella enteritidis and pathogenic E. coli, as evidenced from both in vitro and in vivo studies. Gorodnichev et al. isolated and characterized three virulent phages: Dep622, vB_KpnM_Seu621, and KpS8, possessing narrow specificity toward MDR Klebsiella pneumoniae with K23 capsule type. From the analyzed phages, Dep622 specifically demonstrated polysaccharide depolymerase activity and successfully protected Galleria mellonella larvae infected with MDR K. pneumoniae strain. Overuse and misuse of antibiotics may frequently lead to drug resistance in bacterial strains, and the common antibiotics are at the edge of failing. In such a scenario, bacteriophages may provide an attractive non-antibiotic approach to control pathogenic bacteria. Kortright et al. delineated the possibility of acquired cross-resistance in E. coli using two potential antibacterial agents- phage T6, phage U115 and an antibiotic albicidin. The study established that independent, selective resistance to any of these three antibacterial agents provided resistance to the other two. Whole-genome and targeted sequencing analysis of 29 samples showed that they all possess Tsx porin as a common point of interaction. In expounding the antimicrobial activity of bacteriophages, Yang et al. affirmed the efficiency of the KPP10 phage in treating Pseudomonas aeruginosa strain D4-induced pneumonia mouse models when administered intranasally. The model showed a significantly lower level of immunological indicators [TNFα, IL-1β, and IFN-γ] of infection without any lysis induced endotoxic shock. Apart from humans, livestock and aquaculture are highly susceptible to bacterial infections and may act as symptomatic or asymptomatic carriers compromising human health. Most of these bacteria have become MDR due to extensive misuse of antibiotics in the feedstocks (Martin et al., 2015). It is believed that, at least to some extent and in some applications, antibiotics may be replaced by environmental-friendly alternatives: bacteriophages. Pelyuntha et al. has reported isolation and application of phage cocktail showing potential antimicrobial activity against Salmonella spp., sampled from broiler farms in Thailand. The cocktail derived from the three phages displaying the highest lytic ability was documented to markedly reduce the growth of Salmonella sp. collected from different sources over the country without any specific drug resistance pattern. Xie et al. sampled Salmonella sp. from beef hide and soil to analyze the antibacterial efficiency of four previously reported genetically diverse groups of bacteriophages against the tested bacterial strains. The individual phages showed comparable activity to the cocktail titer in liquid...
Xu Liu, Yu Shi, Teng Yang, Gui-Feng Gao, Liyan Zhang, Ruoyu Xu, Chenxin Li, Ruiyang Liu, Junjie Liu, Haiyan Chu
Published: 26 January 2022
Frontiers in Microbiology, Volume 13; https://doi.org/10.3389/fmicb.2022.809074

Abstract:
Studies of methane-oxidizing bacteria are updating our views of their composition and function in paddy and natural wetlands. However, few studies have characterized differences in the methane-oxidizing bacterial communities between paddy and natural wetlands. Here, we conducted a 13C stable isotope-probing experiment and high-throughput sequencing to determine the structure profiling, co-occurrence relationships, and assembly processes of methanotrophic communities in four wetlands of Northeast China. There was a clear difference in community structure between paddy and natural wetlands. LEfSe analyses revealed that Methylobacter, FWs, and Methylosinus were enriched in natural wetlands, while Methylosarcina were prevailing in paddy, all identified as indicative methanotrophs. We observed distinct co-occurrence relationships between paddy and natural wetlands: more robust and complex connections in natural wetlands than paddy wetlands. Furthermore, the relative importance of stochastic processes was greater than that of deterministic processes, as stochastic processes explained >50% of the variation in communities. These results demonstrated that the co-occurrence relationships and assembly processes of active methanotrophic communities in paddy and natural wetlands were distinct. Overall, the results of this study enhance our understanding of the communities of methane-oxidizing bacteria in paddy and natural wetlands of Northeast China.
Lan Liu, Ai-Ping Lv, Manik Prabhu Narsing Rao, Yu-Zhen Ming, Nimaichand Salam, Meng-Meng Li, Ze-Tao Liu, Xiao-Tong Zhang, Jing-Yi Zhang, Wen-Dong Xian, et al.
Published: 25 January 2022
Frontiers in Microbiology, Volume 12; https://doi.org/10.3389/fmicb.2021.739234

Abstract:
Anaerobic ammonium oxidation (anammox) is an important process of the nitrogen cycle, and the anammox bacteria have been studied in a wide variety of environments. However, the distribution, diversity, and abundance of anammox bacteria in hot springs remain enigmatic. In this study, the anammox process was firstly investigated in hot springs of Conghua, China. Anammox-like bacterial sequences that closely affiliated to “Candidatus Brocadia,” “Candidatus Kuenenia,” “Candidatus Scalindua,” “Candidatus Anammoxoglobus,” and “Candidatus Jettenia” were detected. Several operational taxonomic units (OTUs) from this study shared low sequence identities to the 16S rRNA gene of the known anammox bacteria, suggesting that they might be representing putative novel anammox bacteria. A quantitative PCR analysis of anammox-specific 16S rRNA gene confirmed that the abundance of anammox bacteria ranged from 1.60 × 104 to 1.20 × 107 copies L–1. Nitrate was a key environmental factor defining the geographical distribution of the anammox bacterial community in the hot spring ecosystem. Dissolved inorganic carbon had a significant influence on anammox bacterial biodiversity. Our findings for the first time revealed that the diverse anammox bacteria, including putative novel anammox bacterial candidates, were present in Conghua hot spring, which extended the existence of anammox bacteria to the hot springs in China and expands our knowledge of the biogeography of anammox bacteria. This work filled up the research lacuna of anammox bacteria in Chinese hot spring habitat and would guide for enrichment strategies of anammox bacteria of Conghua hot springs.
Samira Soltani, Séverine Zirah, Sylvie Rebuffat, Frédéric Couture, Yvan Boutin, Eric Biron, Muriel Subirade,
Published: 25 January 2022
Frontiers in Microbiology, Volume 12; https://doi.org/10.3389/fmicb.2021.780355

Abstract:
Bacteriocins are receiving increased attention as potent candidates in food preservation and medicine. Although the inhibitory activity of bacteriocins has been studied widely, little is known about their gastrointestinal stability and toxicity toward normal human cell lines. The aim of this study was to evaluate the gastrointestinal stability and activity of microcin J25, pediocin PA-1, bactofencin A and nisin using in vitro models. In addition cytotoxicity and hemolytic activity of these bacteriocins were investigated on human epithelial colorectal adenocarcinoma cells (Caco-2) and rat erythrocytes, respectively. Pediocin PA-1, bactofencin A, and nisin were observed to lose their stability while passing through the gastrointestinal tract, while microcin J25 is only partially degraded. Besides, selected bacteriocins were not toxic to Caco-2 cells, and integrity of cell membrane was observed to remain unaffected in presence of these bacteriocins at concentrations up to 400 μg/mL. In hemolysis study, pediocin PA-1, bactofencin A, and nisin were observed to lyse rat erythrocytes at concentrations higher than 50 μg/mL, while microcin J25 showed no effect on these cells. According to data indicating gastrointestinal degradation and the absence of toxicity of pediocin PA-1, bactofencin A, and microcin J25 they could potentially be used in food or clinical applications.
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