Journal of Microbiology

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Linking the gut microbiota to persistent symptoms in survivors of COVID-19 after discharge: Yaya Zhou† , Jianchu Zhang† , Dongmei Zhang , Wan-Li Ma , Xiaorong Wang; J. Microbiol. 2021;59(10):941-948. Published online August 12, 2021; DOI: https://doi.org/10.1007/s12275-021-1206-5

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Several follow-up studies have found that COVID-19 (coronavirus disease 2019) patients had persistent symptoms after discharge. Gut microbiota play an important role in human health and immune responses. Therefore, this study investigated the gut microbiota of recovered COVID-19 patients and the correlations between gut microbiota and persistent symptoms after discharge. Stool samples were collected from 15 recovered healthcare workers (HCWs) with COVID-19 at three months after discharge, in addition, stool samples were collected from 14 healthy controls (HCs) to perform 16S rRNA gene sequencing between May and July 2020. Compared with HCs, recovered HCWs had reduced bacterial diversity at three months after discharge, with a significantly higher relative abundance of opportunistic pathogens, and a significantly lower relative abundance of beneficial bacteria. In addition, Escherichia unclassified was positively correlated with persistent symptoms at three months after discharge, including fatigue (r = 0.567, p = 0.028), chest tightness after activity (r = 0.687, p = 0.005), and myalgia (r = 0.523, p = 0.045). Intestinibacter bartlettii was positively correlated with anorexia (r = 0.629, p = 0.012) and fatigue (r = 0.545, p = 0.036). However, Faecalibacterium prausnitzii was negatively correlated with chest tightness after activity (r = -0.591, p = 0.02), and Intestinimonas butyriciproducens was negatively correlated with cough (r = -0.635, p = 0.011). In conclusion, the gut microbiota of recovered HCWs with COVID-19 at three months after discharge was different from that of HCs, and altered gut microbiota was correlated with persistent symptoms after discharge, highlighting that gut microbiota may play an important role in the recovery of patients with COVID-19.

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Molecular characterization of the Saccharomycopsis fibuligera ATF genes, encoding alcohol acetyltransferase for volatile acetate ester formation: Hye Yun Moon , Hyeon Jin Kim , Ki Seung Kim , Su Jin Yoo , Dong Wook Lee , Hee Je Shin , Jeong Ah Seo , Hyun Ah Kang; J. Microbiol. 2021;59(6):598-608. Published online May 29, 2021; DOI: https://doi.org/10.1007/s12275-021-1159-8

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Abstract

Aroma ester components produced by fermenting yeast cells via alcohol acetyltransferase (AATase)-catalyzed intracellular reactions are responsible for the fruity character of fermented alcoholic beverages, such as beer and wine. Acetate esters are reportedly produced at relatively high concentrations by non-Saccharomyces species. Here, we identified 12 ATF orthologues (SfATFs) encoding putative AATases, in the diploid genome of Saccharomycopsis fibuligera KJJ81, an isolate from wheat-based Nuruk in Korea. The identified SfATF proteins (SfAtfp) display low sequence identities with S. cerevisiae Atf1p (between 13.3 and 27.0%). All SfAtfp identified, except SfAtf(A)4p and SfAtf(B)4p, contained the activation domain (HXXXD) conserved in other Atf proteins. Culture supernatant analysis using headspace gas chromatography mass spectrometry confirmed that the recombinant S. cerevisiae strains expressing SfAtf(A)2p, SfAtf(B)2p, and SfAtf(B)6p produced high levels of isoamyl and phenethyl acetates. The volatile aroma profiles generated by the SfAtf proteins were distinctive from that of S. cerevisiae Atf1p, implying difference in the substrate preference. Cellular localization analysis using GFP fusion revealed the localization of SfAtf proteins proximal to the lipid particles, consistent with the presence of amphipathic helices at their N- and C-termini. This is the first report that systematically characterizes the S. fibuligera ATF genes encoding functional AATases responsible for acetate ester formation using higher alcohols as substrate, demonstrating their biotechnological potential for volatile ester production.

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Characterization and phylogenetic analysis of the complete mitochondrial genome of Saccharomycopsis fibuligera (lindner) Klocker 1907 (saccharomycetales: saccharomycopsidaceae)
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Review

Microbial phenomics linking the phenotype to function: The potential of Raman spectroscopy: Jin-Kyung Hong , Soo Bin Kim , Eun Sun Lyou , Tae Kwon Lee; J. Microbiol. 2021;59(3):249-258. Published online January 26, 2021; DOI: https://doi.org/10.1007/s12275-021-0590-1

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Abstract

Raman spectroscopy is a promising tool for identifying microbial phenotypes based on single cell Raman spectra reflecting cellular biochemical biomolecules. Recent studies using Raman spectroscopy have mainly analyzed phenotypic changes caused by microbial interactions or stress responses (e.g., antibiotics) and evaluated the microbial activity or substrate specificity under a given experimental condition using stable isotopes. Lack of labelling and the nondestructive pretreatment and measurement process of Raman spectroscopy have also aided in the sorting of microbial cells with interesting phenotypes for subsequently conducting physiology experiments through cultivation or genome analysis. In this review, we provide an overview of the principles, advantages, and status of utilization of Raman spectroscopy for studies linking microbial phenotypes and functions. We expect Raman spectroscopy to become a next-generation phenotyping tool that will greatly contribute in enhancing our understanding of microbial functions in natural and engineered systems.

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Journal Article

Distinct gut microbiotas between southern elephant seals and Weddell seals of Antarctica: Mincheol Kim , Hyunjun Cho , Won Young Lee; J. Microbiol. 2020;58(12):1018-1026. Published online December 2, 2020; DOI: https://doi.org/10.1007/s12275-020-0524-3

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Abstract

The gut microbiome provides ecological information about host animals, but we still have limited knowledge of the gut microbiome, particularly for animals inhabiting remote locations, such as Antarctica. Here, we compared fecal microbiota between southern elephant seals (Mirounga leonina) and Weddell seals (Leptonychotes weddelli), that are top predatory marine mammals in the Antarctic ecosystem, using 16S rRNA amplicon sequencing and assessed the relationships of the gut microbial communities to functional profiles using gut metabolite analysis. The bacterial community did not differ significantly by host species or sex at the phylum level, but the distinction at the family level was obvious. The family Ruminococcaceae (Firmicutes) was more abundant in southern elephant seals than in Weddell seals, and the families Acidaminococcaceae (Firmicutes) and Pasteurellaceae (Gammaproteobacteria) were uniquely present in Weddell seals. The fecal bacterial community structure was distinctively clustered by host species, with only 6.7% of amplicon sequence variants (ASVs) shared between host species. This result implies that host phylogeny rather than other factors, such as diet or age, could be the major driver of fecal microbiotic diversification. Interestingly, there was no apparent sex effect on bacterial community structure in Weddell seals, but the effect of sex was pronounced in adult southern elephant seals mainly due to the prevalence of Edwardsiella sp., suggesting that extreme sexual dimorphism may modulate the gut microbiota of southern elephant seals. Unlike the clear distinction in the taxonomic composition of fecal bacterial communities, there were no discernible differences in the profiles of potential microbial functions and gut metabolites between host species or sexes, indicating that functional redundancy dominates the gut microbiota of seals surveyed in this study.

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Review

[MINIREVIEW] The nature of meiotic chromosome dynamics and recombination in budding yeast: Soogil Hong , Jeong Hwan Joo , Hyeseon Yun , Keunpil Kim; J. Microbiol. 2019;57(4):221-231. Published online January 22, 2019; DOI: https://doi.org/10.1007/s12275-019-8541-9

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Abstract

During meiosis, crossing over allows for the exchange of genes between homologous chromosomes, enabling their segregation and leading to genetic variation in the resulting gametes. Spo11, a topoisomerase-like protein expressed in eukaryotes, and diverse accessory factors induce programmed doublestrand breaks (DSBs) to initiate meiotic recombination during the early phase of meiosis after DNA replication. DSBs are further repaired via meiosis-specific homologous recombination. Studies on budding yeast have provided insights into meiosis and genetic recombination and have improved our understanding of higher eukaryotic systems. Cohesin, a chromosome-associated multiprotein complex, mediates sister chromatid cohesion (SCC), and is conserved from yeast to humans. Diverse cohesin subunits in budding yeast have been identified in DNA metabolic pathways, such as DNA replication, chromosome segregation, recombination, DNA repair, and gene regulation. During cell cycle, SCC is established by multiple cohesin subunits, which physically bind sister chromatids together and modulate proteins that involve in the capturing and separation of sister chromatids. Cohesin components include at least four core subunits that establish and maintain SCC: two structural maintenance chromosome subunits (Smc1 and Smc3), an α-kleisin subunit (Mcd1/Scc1 during mitosis and Rec8 during meiosis), and Scc3/Irr1 (SA1 and SA2). In addition, the cohesin-associated factors Pds5 and Rad61 regulate structural modifications and cell cyclespecific dynamics of chromatin to ensure accurate chromosome segregation. In this review, we discuss SCC and the recombination pathway, as well as the relationship between the two processes in budding yeast, and we suggest a possible conserved mechanism for meiotic chromosome dynamics from yeast to humans.

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Novel strategy for isolating suppressors of meiosis-deficient mutants and its application for isolating the bcy1 suppressor: Shin, Deug Yong , Yun, Jean Ho , Yoo, Hyang Sook; J. Microbiol. 1997;35(1):61-65.

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Abstract: A novel strategy was developed for isolating suppressors from sporulation-deficient mutants. The mutation in the BCY1 gene, which codes for the regulatory subunit of cAMP-dependent protein kinase, when homozygous, results in diploids being meiosis and sporulation deficient. Two plasmids, YCp-MATα and YEp-SPOT7-lacZ, were introduced into MATα BCY1^+ or MATα bcy1 haploid cells. The transformant of the BCY1^+ haploid cell produced β-galactosidase under nutrient starvation, but the bcy1 transformant did not. Using this system, the mutagenesis experiment performed on the bcy1 transformant strain resulted in a number of sporulation mutants that produced β-galactosidase under nutrient starvation. One complementation group, sob1, was identified from the isolated suppressor mutants and characterized as a single recessive mutation by tetrad analysis. Genetic analysis revealed that the sob1 mutation suppressed the sporulation deficiency, the failure to arrest at the G1 phase of the cell cycle, and the sensitivity to heat or nitrogen starvation caused by the bcy1 mutation. However, the sob1 mutation did not suppress the sporulation deficiency of ime1 and of ime2 diploids. These results suggest that the sob1 mutation affects a gene which functions as a downstream regulator in both meiosis and cell cycle regulation.

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