Frontiers in Microbiology

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ISSN / EISSN : 1664-302X / 1664-302X
Published by: Frontiers Media SA (10.3389)
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Yang Liu, Qian Lin, Xuan Huang, Guitao Jiang, Chuang Li, Xu Zhang, Shengli Liu, Lingyun He, Yali Liu, , et al.
Published: 13 July 2021
Frontiers in Microbiology, Volume 12; doi:10.3389/fmicb.2021.698213

Abstract:
The present study investigated the effects of ferulic acid (FA) on the growth performance, serum cytokine profile, intestinal morphology, and intestinal microbiota in ducks at the growing stage. 300 female Linwu ducks at 28 days of age with similar body weights were randomly divided into five groups. Each group contained six replicates of 10 birds. The dietary treatments were corn-soybean-based diet supplemented with FA at the concentrations of 0 (control), 100, 200, 400, and 800 mg/kg diet. The results demonstrated that dietary FA at the levels of 200, 400, and 800 mg/kg increased the average daily gain (P = 0.01), 400 and 800 mg/kg FA increased the final body weight (P = 0.02), 100, 200, and 800 mg/kg FA increased the serum glutathione (P = 0.01), and 100, 400, and 800 mg/kg FA increased the glutathione peroxidase activities in birds (P < 0.01). Additionally, 200, 400, and 800 mg/kg dietary FA lowered the serum levels of interleukin-2 (P = 0.02) and interleukin-6 (P = 0.04). Moreover, the morphometric study of the intestines indicated that 400 mg/kg FA decreased the crypt depth in jejunum (P = 0.01) and caecum (P = 0.04), and increased the ratio of villus height to crypt depth in jejunum (P = 0.02). Significant linear and/or quadratic relationships were found between FA concentration and the measured parameters. 16S rRNA sequencing revealed that dietary FA increased the populations of genera Faecalibacterium, Paludicola, RF39, and Faecalicoccus in the cecum (P < 0.05), whereas decreased the populations of Anaerofilum and UCG-002 (P < 0.05). The Spearman correlation analysis indicated that phylum Proteobacteria were negatively, but order Oscillospirales, and family Ruminococcaceae were positively related to the parameters of the growth performance. Phylum Bacteroidetes, class Negativicutes and family Rikenellaceae were negatively associated with the parameters of the antioxidative capability. And phylum Cyanobacteria, Elusimicrobia, and Bacteroidetes, class Bacilli, family Rikenellaceae, and genus Prevotella were positively associated with the parameters of the immunological capability. Thus, it was concluded that the supplementations of 400 mg/kg FA in diet was able to improve the growth performance, antioxidative and immunological capabilities, intestinal morphology, and modulated the gut microbial construction of Linwu ducks at the growing stage.
, Tina C. Summerfield, Daniel C. Ducat, Xuefeng Lu, Alistair J. McCormick, Saul Purton
Published: 13 July 2021
Frontiers in Microbiology, Volume 12; doi:10.3389/fmicb.2021.725128

Abstract:
Editorial on the Research Topic Exploring the Growing Role of Cyanobacteria in Industrial Biotechnology and Sustainability A major challenge of the 21st Century is the development of innovative, sustainable biotechnologies able to replace fossil fuel derived synthetic routes for production of bulk chemicals and high-value materials. Potentially, this challenge could be met in part through the use of cyanobacteria, the only prokaryotes capable of oxygenic photosynthesis, as microbial hosts for development of next generation industrial biotechnologies. The production of cyanobacterial biomass and synthesis of bioproducts does not require arable land, thereby avoiding competition with food production. Minimal nutrients are needed for cyanobacterial growth, and many species can be cultured in seawater, avoiding use of limited freshwater supplies. In addition, cyanobacteria can synthesize a range of high-value commercial compounds e.g., healthcare relevant pharmaceuticals, nutraceuticals, and industrial materials (Ducat et al., 2011), and their derived photo-production technology has been industrialized in several countries, including the USA, China, and Japan (Zahra et al., 2020). However, expanding the use of cyanobacteria for production of a wider range of compounds is still restricted by multiple factors. These include the naturally slow growth rate and low biomass accumulation of most cyanobacterial species, although the recent discovery of several species, such as Synechococcus sp. PCC 11901 (Wlodarczyk et al., 2020), with doubling times as short as 2 h, is a promising development. The challenges of low cost culturing in outdoor photobioreactors, development of strains capable of synthesizing commercial quantities of the desired compound, and a lack of low-cost and sustainable methods for compound extraction also impede commercialization of cyanobacterial biotechnology. Strain development is hampered by genetic tools that are less developed than those available for established heterotrophic platforms such as Escherichia coli and Saccharomyces cerevisiae. Finally, our understanding of many core physiological and biochemical processes in cyanobacteria, even in the most widely studied model cyanobacterium, Synechocystis sp. PCC 6803 (6803), is incomplete (Mills et al., 2020). The publications in this special issue address many of these considerations. In terms of strain selection for biotechnology applications, many factors need to be considered including growth and biomass accumulation, long term storage of strains at −80°C, growth in seawater and genetic tractability. Jeong et al. sequenced a new Synechocystis species, PCC 7338 (7338), which can be cultured in seawater, and compared it to multiple freshwater species, including 6803. Although the majority of genes were conserved in all the species examined, a number were unique to 7338 and likely involved in salt tolerance. Shaw et al. examined 26 photosynthetic co-cultures (consisting of a cyanobacterium and associated heterotrophic microbes) collected from a range of geographical locations and different ecosystems, focusing upon extreme environments such as hot springs and Antarctic ponds. Sequence analysis of these strains highlighted the diversity of species surviving within these extreme conditions, and provides potential opportunities for discovery of new proteins and biotechnologically-valuable compounds. A greater understanding of cyanobacterial biology will aid commercialization of cyanobacterial biotechnology. Karlsen et al. examined why protein levels are relatively constant in 6803 subjected to artificial day-night cycles, despite the transcriptional profile of many genes altering under these conditions. Their data demonstrates that slow protein turnover and not translational regulation is the main factor in controlling protein amounts. These results have ramifications for synthetic biology and that controlling the abundance of heterologous proteins not only has to take into account expression but also degradation of the target protein. Thirumurthy et al. investigated the role of type IV pili in extracellular electron transport in 6803. This process may play a role in photoprotection by exporting excess electrons but can also be exploited for electricity production using biophotovoltaic devices, a type of microbial fuel cell (McCormick et al., 2015). Using pili-deficient mutants, their data shows that deleting these appendages has no effect on electron export, suggesting that other compounds, likely soluble electron carriers, may perform this role. Development of new molecular tools, such as CyanoGate, a modular Golden Gate cloning kit (Vasudevan et al., 2019), aids research into understanding cyanobacterial biology and the engineering of strains for biotechnology applications. Gale et al. described the development of a CyanoGate-compatible dual reporter system to quantify and compare the efficiency of transcriptional terminators within and between species. A suite of 34 terminators were characterized and five were identified with high efficiencies in 6803, Synechococcus elongatus UTEX 2973 and E. coli. Zhang et al. utilized knock out/down and overexpression strategies to characterize twelve genes potentially involved in cell division and/or elongation in Synechococcus elongatus PCC 7942. Their work has advanced our understanding of these processes and identified several new targets for engineering cell morphology in cyanobacteria. The remaining publications focus on engineering cyanobacteria for development of efficient strains more suitable for biotechnology or for higher production of a range of compounds. Wang et al. detail in their comprehensive review the recent progress in manipulating cyanobacteria for production of a range of compounds, including fatty acids, alcohols, hydrocarbons, and fatty acid esters. Song et al. analyzed the effect of minimizing photorespiratory carbon losses by expression of the...
Juan Zhong, Xuewu Hu, Xingyu Liu, Xinglan Cui, Ying Lv, Chuiyun Tang, Mingjiang Zhang, Hongxia Li, Lang Qiu, Weimin Sun
Published: 13 July 2021
Frontiers in Microbiology, Volume 12; doi:10.3389/fmicb.2021.676391

Abstract:
The remediation of uranium (U) through phosphate-solubilizing bacteria (PSB) is an emerging technique as well as an interesting phenomenon for transforming mobile U into stable minerals in the environment. While studies are well needed for in-depth understanding of the mechanism of U(VI) immobilization by PSB. In this study, two PSB were isolated from a U-tailing repository site. These bacterial strains (ZJ-1 and ZJ-3) were identified as Bacillus spp. by the sequence analysis of 16S ribosomal RNA (rRNA) genes. Incubation of PSB in liquid medium showed that the isolate ZJ-3 could solubilize more than 230 mg L–1 P from glycerol-3-phosphate and simultaneously removed over 70% of 50 mg L–1 U(VI) within 1 h. During this process, the rapid appearance of yellow precipitates was observed. The microscopic and spectroscopic analysis demonstrated that the precipitates were associated with U-phosphate compound in the form of saleeite-like substances. Besides, scanning electron microscopy coupled with energy-dispersive X-ray (SEM-EDS) and Fourier transform infrared spectroscopy (FTIR) analysis of the precipitates confirmed that the extracellular polymeric substances (EPS) might also play a key role in U sequestration. Furthermore, SEM and FTIR analysis revealed that part of U(VI) was adsorbed on the bacterial surface through cellular phosphate, hydroxy, carboxyl, and amide groups. This study provides new insights into the synergistic strategies enhancing U immobilization rates by Bacillus spp. that uses glycerol-3-phosphate as the phosphorus source, the process of which contributes to harmful pollutant biodegradation.
, Erica A. Birkholz,
Published: 13 July 2021
Frontiers in Microbiology, Volume 12; doi:10.3389/fmicb.2021.641317

Abstract:
Bacteriophages and their bacterial hosts are ancient organisms that have been co-evolving for billions of years. Some jumbo phages, those with a genome size larger than 200 kilobases, have recently been discovered to establish complex subcellular organization during replication. Here, we review our current understanding of jumbo phages that form a nucleus-like structure, or “Phage Nucleus,” during replication. The phage nucleus is made of a proteinaceous shell that surrounds replicating phage DNA and imparts a unique subcellular organization that is temporally and spatially controlled within bacterial host cells by a phage-encoded tubulin (PhuZ)-based spindle. This subcellular architecture serves as a replication factory for jumbo Pseudomonas phages and provides a selective advantage when these replicate in some host strains. Throughout the lytic cycle, the phage nucleus compartmentalizes proteins according to function and protects the phage genome from host defense mechanisms. Early during infection, the PhuZ spindle positions the newly formed phage nucleus at midcell and, later in the infection cycle, the spindle rotates the nucleus while delivering capsids and distributing them uniformly on the nuclear surface, where they dock for DNA packaging. During the co-infection of two different nucleus-forming jumbo phages in a bacterial cell, the phage nucleus establishes Subcellular Genetic Isolation that limits the potential for viral genetic exchange by physically separating co-infection genomes, and the PhuZ spindle causes Virogenesis Incompatibility, whereby interacting components from two diverging phages negatively affect phage reproduction. Thus, the phage nucleus and PhuZ spindle are defining cell biological structures that serve roles in both the life cycle of nucleus-forming jumbo phages and phage speciation.
, Jessica L. Halpin, Carolina Lúquez
Published: 13 July 2021
Frontiers in Microbiology, Volume 12; doi:10.3389/fmicb.2021.688240

Abstract:
Three cases of infant botulism were reported in a small Colorado town between 1981 and 1984. The first two cases occurred in 1981, 6 months apart, and the third case occurred in 1984. Clostridium botulinum type A was isolated from stool of all three case patients and from environmental samples of the patient’s homes. An epidemiological investigation and follow-up study were conducted from 1981 to 1986 and concluded the cases were likely related. In this study, we sought to determine whether the C. botulinum type A clinical isolates were related to each other and to isolates obtained from environmental samples. We performed whole genome sequencing (WGS) for 17 isolates associated with this potential cluster of infant botulism. Fifteen isolates were confirmed to be C. botulinum type A(B) and contained botulinum toxin gene subtypes A1 and B5 by WGS; these strains formed a monophyletic cluster in a phylogeny and were considered closely related to each other (0–18 high-quality single-nucleotide polymorphisms), but distinct from other C. botulinum type A(B) in Colorado and elsewhere in the United States. Results of our study suggest that the three infant botulism cases could have represented a cluster due to a C. botulinum type A(B) strain present in the environment.
, Johannes S. Vrouwenvelder, Pascal Saikaly
Published: 13 July 2021
Frontiers in Microbiology, Volume 12; doi:10.3389/fmicb.2021.668761

Abstract:
This work describes the chemical composition of extracellular polymeric substances (EPS) produced by three bacteria (RO1, RO2, and RO3) isolated from a biofouled reverse osmosis (RO) membrane. We isolated pure cultures of three bacterial strains from a 7-year-old biofouled RO module that was used in a full-scale seawater treatment plant. All the bacterial strains showed similar growth rates, biofilm formation, and produced similar quantities of proteins and polysaccharides. The gel permeation chromatography showed that the EPS produced by all the strains has a high molecular weight; however, the EPS produced by strains RO1 and RO3 showed the highest molecular weight. Fourier Transform Infrared Spectroscopy (FTIR), Proton Nuclear Magnetic Resonance (1H NMR), and Carbon NMR (13C NMR) were used for a detailed characterization of the EPS. These physicochemical analyses allowed us to identify features of EPS that are important for biofilm formation. FTIR analysis indicated the presence of α-1,4 glycosidic linkages (920 cm–1) and amide II (1,550 cm–1) in the EPS, the presence of which has been correlated with the fouling potential of bacteria. The presence of α-glycoside linkages was further confirmed by 13C NMR analysis. The 13C NMR analysis also showed that the EPS produced by these bacteria is chemically similar to foulants obtained from biofouled RO membranes in previous studies. Therefore, our results support the hypothesis that the majority of substances that cause fouling on RO membranes originate from bacteria. Investigation using 1H NMR showed that the EPS contained a high abundance of hydrophobic compounds, and these compounds can lead to flux decline in the membrane processes. Genome sequencing of the isolates showed that they represent novel species of bacteria belonging to the genus Bacillus. Examination of genomes showed that these bacteria carry carbohydrates-active enzymes that play a role in the production of polysaccharides. Further genomic studies allowed us to identify proteins involved in the biosynthesis of EPS and flagella involved in biofilm formation. These analyses provide a glimpse into the physicochemical properties of EPS found on the RO membrane. This knowledge can be useful in the rational design of biofilm control treatments for the RO membrane.
Qihui Gu, Moutong Chen, Jumei Zhang, Weipeng Guo, Huiqing Wu, Ming Sun, Lei Wei, Juan Wang, Xianhu Wei, Youxiong Zhang, et al.
Published: 13 July 2021
Frontiers in Microbiology, Volume 12; doi:10.3389/fmicb.2021.687511

Abstract:
Phenol is a toxic organic molecule that is widely detected in the natural environment, even in drinking water sources. Biological methods were considered to be a good tool for phenol removal, especially microbial immobilized technology. However, research on the “seed” bacteria along with microbial community analysis in oligotrophic environment such as drinking water system has not been addressed. In this study, Acinetobacter sp. DW-1 with high phenol degradation ability had been isolated from a drinking water biofilter was used as seeded bacteria to treat phenol micro-polluted drinking water source. Meanwhile, the whole genome of strain DW-1 was sequenced using nanopore technology. The genomic analysis suggests that Acinetobacter sp. DW-1 could utilize phenol via the β-ketoadipate pathway, including the catechol and protocatechuate branches. Subsequently, a bio-enhanced polyhedral hollow polypropylene sphere (BEPHPS) filter was constructed to investigate the stability of the seeded bacteria during the water treatment process. The denatured gradient gel electrophoresis (DGGE) profile and the quantification of phenol hydroxylase gene results indicate that when the BEPHPS filter was operated for 56 days, Acinetobacter sp. was still a persistent and competitive bacterium in the treatment group. In addition, 16S rRNA gene amplicon sequencing results indicate that Acinetobacter sp., as well as Pseudomonas sp., Nitrospira sp., Rubrivivax sp. were the predominant bacteria in the treatment group, which were different from that in the CK group. This study provides a better understanding of the mechanisms of phenol degradation by Acinetobacter sp. DW-1 at the gene level, and provides new insights into the stability of seeded bacteria and its effects on microbial ecology during drinking water treatment.
, Sampa Mukherjee, Chih-Hao Hsu, Shenia Young, Errol Strain, Qijing Zhang, Glenn E. Tillman, Cesar Morales, Jovita Haro, Shaohua Zhao
Published: 13 July 2021
Frontiers in Microbiology, Volume 12; doi:10.3389/fmicb.2021.703890

Abstract:
Campylobacter species are among the leading foodborne bacterial agents of human diarrheal illness. The majority of campylobacteriosis has been attributed to Campylobacter jejuni (85% or more), followed by Campylobacter coli (5–10%). The distribution of C. jejuni and C. coli varies by host organism, indicating that the contribution to human infection may differ between isolation sources. To address the relative contribution of each source to C. coli infections in humans, core genome multilocus sequence type with a 200-allele difference scheme (cgMLST200) was used to determine cgMLST type for 3,432 C. coli isolated from food animals (n = 2,613), retail poultry meats (n = 389), human clinical settings (n = 285), and environmental sources (n = 145). Source attribution was determined by analyzing the core genome with a minimal multilocus distance methodology (MMD). Using MMD, a higher proportion of the clinical C. coli population was attributed to poultry (49.6%) and environmental (20.9%) sources than from cattle (9.8%) and swine (3.2%). Within the population of C. coli clinical isolates, 70% of the isolates that were attributed to non-cecal retail poultry, dairy cattle, beef cattle and environmental waters came from two cgMLST200 groups from each source. The most common antibiotic resistance genes among all C. coli were tetO (65.6%), bla OXA – 193 (54.2%), aph(3′)-IIIa (23.5%), and aadE-Cc (20.1%). Of the antibiotic resistance determinants, only one gene was isolated from a single source: bla OXA – 61 was only isolated from retail poultry. Within cgMLST200 groups, 17/17 cgMLST200-435 and 89/92 cgMLST200-707 isolates encoded for aph(3’)-VIIa and 16/16 cgMLST200-319 harbored aph(2’)-If genes. Distribution of bla OXA alleles showed 49/50 cgMLST200-5 isolates contained bla OXA – 498 while bla OXA – 460 was present in 37/38 cgMLST200-650 isolates. The cgMLST200-514 group revealed both ant(6)-Ia and sat4 resistance genes in 23/23 and 22/23 isolates, respectively. Also, cgMLST200-266 and cgMLST200-84 had GyrAT86I mutation with 16/16 (100%) and 14/15 (93.3%), respectively. These findings illustrate how cgMLST and MMD methods can be used to evaluate the relative contribution of known sources of C. coli to the human burden of campylobacteriosis and how cgMLST typing can be used as an indicator of antimicrobial resistance in C. coli.
Qiaozhen Li, Jing Chen, Jianyu Liu, Hailong Yu, Lujun Zhang, Chunyan Song, Yu Li, Ning Jiang, Qi Tan, , et al.
Published: 13 July 2021
Frontiers in Microbiology, Volume 12; doi:10.3389/fmicb.2021.627099

Abstract:
Polysaccharides separated from Lentinula edodes are well known for their medicinal properties. However, the precise molecular mechanisms of polysaccharide biosynthesis in L. edodes remain unclear. In this study, the fruiting bodies of L. edodes in four developmental stages with significant differences in polysaccharide yield were collected, and the characteristics of polysaccharides were studied. De novo sequencing and comparative transcriptomic analysis were performed by using high-throughput Illumina RNA-sequencing. KS1P30, KS2P30, KS3P30, and KS4P30 were obtained from the four developmental stages, respectively, by hot water extraction and 30% ethanol precipitation. These four polysaccharides had good immune activity in vitro; all of them were β-glucopyranose with a high molecular weight. Glucose was the main monosaccharide component of these polysaccharides. High-quality clean reads (57.88, 53.17, 53.28, and 47.56 million for different growth stages) and mapping ratios ranging from 84.75 to 90.11% were obtained. In total, 11,493 (96.56%) unigenes and 18,924 (97.46%) transcripts were successfully annotated in five public databases. The biosynthetic pathway and related genes of LEFP30 were mined. The molecular mechanism of LEFP30 yield change in the different developmental stages was predicted. The results provide some insights into the possible mechanisms involved in the biosynthetic pathway of this kind of polysaccharide in L. edodes fruiting bodies. They also indicate that candidate genes can be used as important resources for biotechnology and molecular breeding to regulate L. edodes fruiting body polysaccharide biosynthesis.
Katherine Chacón-Vargas, Colin O. McCarthy, Dasol Choi, Long Wang, Jae-Hyuk Yu,
Published: 13 July 2021
Frontiers in Microbiology, Volume 12; doi:10.3389/fmicb.2021.691296

Abstract:
Microbes (bacteria, yeasts, molds), in addition to plants and animals, were domesticated for their roles in food preservation, nutrition and flavor. Aspergillus oryzae is a domesticated filamentous fungal species traditionally used during fermentation of Asian foods and beverage, such as sake, soy sauce, and miso. To date, little is known about the extent of genome and phenotypic variation of A. oryzae isolates from different clades. Here, we used long-read Oxford Nanopore and short-read Illumina sequencing to produce a highly accurate and contiguous genome assemble of A. oryzae 14160, an industrial strain from China. To understand the relationship of this isolate, we performed phylogenetic analysis with 90 A. oryzae isolates and 1 isolate of the A. oryzae progenitor, Aspergillus flavus. This analysis showed that A. oryzae 14160 is a member of clade A, in comparison to the RIB 40 type strain, which is a member of clade F. To explore genome variation between isolates from distinct A. oryzae clades, we compared the A. oryzae 14160 genome with the complete RIB 40 genome. Our results provide evidence of independent evolution of the alpha-amylase gene duplication, which is one of the major adaptive mutations resulting from domestication. Synteny analysis revealed that both genomes have three copies of the alpha-amylase gene, but only one copy on chromosome 2 was conserved. While the RIB 40 genome had additional copies of the alpha-amylase gene on chromosomes III, and V, 14160 had a second copy on chromosome II and an third copy on chromosome VI. Additionally, we identified hundreds of lineage specific genes, and putative high impact mutations in genes involved in secondary metabolism, including several of the core biosynthetic genes. Finally, to examine the functional effects of genome variation between strains, we measured amylase activity, proteolytic activity, and growth rate on several different substrates. RIB 40 produced significantly higher levels of amylase compared to 14160 when grown on rice and starch. Accordingly, RIB 40 grew faster on rice, while 14160 grew faster on soy. Taken together, our analyses reveal substantial genome and phenotypic variation within A. oryzae.
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