Microorganisms, Volume 7, Issue 6 (June 2019) – 31 articles

Epstein–Barr virus (EBV) successfully persists in the vast majority of adults but causes lymphoid and epithelial malignancies in a small fraction of latently infected individuals. Innate immunity is the first-line antiviral defense, which EBV has to evade in favor of its own replication and infection. EBV uses multiple strategies to perturb innate immune signaling pathways activated by Toll-like, RIG-I-like, NOD-like, and AIM2-like receptors as well as cyclic GMP-AMP synthase. EBV also counteracts interferon production and signaling, including TBK1-IRF3 and JAK-STAT pathways. However, activation of innate immunity also triggers pro-inflammatory response and proteolytic cleavage of caspases, both of which exhibit proviral activity under some circumstances. Pathogenic inflammation also contributes to EBV oncogenesis. EBV activates NFκB signaling and induces pro-inflammatory cytokines. Through differential modulation of the proviral and antiviral roles of caspases and other host factors at different stages of infection, EBV usurps cellular programs for death and inflammation to its own benefits. The outcome of EBV infection is governed by a delicate interplay between innate immunity and EBV. A better understanding of this interplay will instruct prevention and intervention of EBV-associated cancers. Full article

Current scientific debate addresses whether species richness in animal communities may negatively moderate pathogen transmission and disease outcome (dilution effect), or to the contrary, if disease emergence benefits from more diverse community assemblages (amplification effect). The result may not depend exclusively on patterns of host species biodiversity but may depend on the specific composition of reservoir hosts and vectors, and their ecology. Host–pathogen interactions have shaped variations in parasite virulence, transmissibility and specificity. In the same way the importance of factors related to host exposure or to life history trade-offs are expected to vary. In this study, we demonstrate that ungulate host species richness correlates with increased community competence to maintain and transmit pathogens of the Mycobacterium tuberculosis complex (MTC) in game-managed areas in Mediterranean Spain. Therefore, we should consider natural and artificial variations in life histories of pathogens and host communities to characterize the impact of biodiversity on the health of diverse assemblages of human and animal communities. Since most approaches assessing epidemiology and transmission of shared pathogens only involve single- or pair-species, further research is needed to better understand the infection dynamics from complete community assemblages, at least in chronic diseases such as tuberculosis and in non-natural animal communities. Full article

Coinciding with the increase in sequenced bacteria, mining of bacterial genomes for biosynthetic gene clusters (BGCs) has become a critical component of natural product discovery. The order Myxococcales, a reputable source of biologically active secondary metabolites, spans three suborders which all include natural product producing representatives. Utilizing the BiG-SCAPE-CORASON platform to generate a sequence similarity network that contains 994 BGCs from 36 sequenced myxobacteria deposited in the antiSMASH database, a total of 843 BGCs with lower than 75% similarity scores to characterized clusters within the MIBiG database are presented. This survey provides the biosynthetic diversity of these BGCs and an assessment of the predicted chemical space yet to be discovered. Considering the mere snapshot of myxobacteria included in this analysis, these untapped BGCs exemplify the potential for natural product discovery from myxobacteria. Full article

The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address two broad classes of corollaries of antibiotics overuse and misuse. Firstly, we discuss the spread of antibiotic resistance from hotspots of resistance evolution to the environment, with special concerns given to potential vectors of resistance transmission. Secondly, we outline the effects of antibiotic pollution independent of resistance evolution on natural microbial populations, as well as invertebrates and vertebrates. We close with an overview of current regional policies tasked with curbing the effects of antibiotics pollution and outline areas in which such policies are still under development. Full article

Malaria is a severe disease caused by parasites of the genus Plasmodium, which is transmitted to humans by a bite of an infected female mosquito of the species Anopheles. Malaria remains the leading cause of mortality around the world, and early diagnosis and fast-acting treatment prevent unwanted outcomes. It is the most common disease in Africa and some countries of Asia, while in the developed world malaria occurs as imported from endemic areas. The sweet sagewort plant was used as early as the second century BC to treat malaria fever in China. Much later, quinine started being used as an antimalaria drug. A global battle against malaria started in 1955, and Croatia declared 1964 to be the year of eradication of malaria. The World Health Organization carries out a malaria control program on a global scale, focusing on local strengthening of primary health care, early diagnosis of the disease, timely treatment, and disease prevention. Globally, the burden of malaria is lower than ten years ago. However, in the last few years, there has been an increase in the number of malaria cases around the world. It is moving towards targets established by the WHO, but that progress has slowed down. Full article

Hydrocarbon extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial global efforts into mitigating this environmental disruption are underway. The global petroleum industry is moving more and more into exploiting unconventional oil reserves, such as oil sands and shale oil. The Albertan oil sands are one example of unconventional oil reserves; this mixture of sand and heavy bitumen lying under the boreal forest of Northern Alberta represent one of the world’s largest hydrocarbon reserves, but extraction also requires the disturbance of a delicate northern ecosystem. Considerable effort is being made by various stakeholders to mitigate environmental impact and reclaim anthropogenically disturbed environments associated with oil sand extraction. In this review, we discuss the eukaryotic microbial communities associated with the boreal ecosystem and how this is affected by hydrocarbon extraction, with a particular emphasis on the reclamation of tailings ponds, where oil sands extraction waste is stored. Microbial eukaryotes, or protists, are an essential part of every global ecosystem, but our understanding of how they affect reclamation is limited due to our fledgling understanding of these organisms in anthropogenically hydrocarbon-associated environments and the difficulties of studying them. We advocate for an environmental DNA sequencing-based approach to determine the microbial communities of oil sands associated environments, and the importance of studying the heterotrophic components of these environments to gain a full understanding of how these environments operate and thus how they can be integrated with the natural watersheds of the region. Full article

Pathogenic mycobacteria are known for their ability to maintain persistent infections in various mammals. The canonical pathogen in this genus is Mycobacterium tuberculosis and this bacterium is particularly successful at surviving and replicating within macrophages. Here, we will highlight the metabolic processes that M. tuberculosis employs during infection in macrophages and compare these findings with what is understood for other pathogens in the M. tuberculosis complex. Full article

Intestinal microbiota is closely associated with various metabolic diseases such as type 2 diabetes (T2D), and microbiota is definitely affected by diet. However, more work is required to gain detailed information about gut metagenome and their associated impact with diet in T2D patients. We used a streptozotocin-high-fat diet (HFD) to induce a T2D mouse model and investigated the effect of standard chow diet and HFD on the composition and function of gut microbiota. We found that a HFD could worsen the diabetes status compared with a standard diet. 16S rRNA gene sequencing revealed that a HFD caused a large disturbance to the microbial structure and was linked to an increased ratio of Firmicutes to Bacteroidetes. A HFD increased the bacteria of the Ruminococcaceae and Erysipelotrichaceae family and decreased the bacteria of S24-7 and Rikenellaceae. Meanwhile, a HFD decreased the abundance of Parabacteroides distasonis and Eubacterium dolichum, both of which have previously been reported to alleviate obesity and metabolic dysfunctions. Moreover, PICRUSt-predicted KEGG pathways related to membrane transport, lipid metabolism, and xenobiotics biodegradation and metabolism were significantly elevated in HFD-fed T2D mice. Our results provide insights into dietary and nutritional approaches for improving host metabolism and ameliorating T2D. Full article

Penicillium expansum is a major postharvest pathogen that infects different fruits, mainly through injuries inflicted during harvest or subsequent handling after harvest. Several effectors were suggested to mediate pathogenicity of P. expansum in fruit tissue. Among these effectors Nep1-like proteins (NLPs), produced by various microorganisms with different lifestyles, are known for their ability to induce necrosis in dicot plants and were shown to be involved in virulence of several plant-related pathogens. This study was aimed at the identification and functional characterization of two NLP genes found in the genome of P. expansum. The genes were designated Penlp1 and Penlp2 and were found to code type1 and type3 NLP respectively. Necrosis-inducing activity of the two proteins was demonstrated by transient expression in Nicotiana benthamiana leaves. While Penlp1 expression was induced during apple infection and in liquid culture, the highest level of Penlp2 expression was found in ungerminated spores. Deletion of Penlp1, but not Penlp2, resulted in reduced virulence on apples manifested by reduced rate of lesion development (disease severity). Full article

The present study explored the differences in gastric microbiome between three distinct populations of Southeast Asia. These include the isolated Orang Asli population and modern Malaysians, as well as patients from Myanmar, the least developed country in the region. All 79 subjects recruited in this study had Helicobacter pylori infection. Based on alpha diversity analysis, Orang Asli had the richest and most diverse gastric microbiome, followed by Myanmar and modern Malaysian groups. Beta diversity analysis revealed significant separation of samples between different populations. These observations are likely to be associated with the level of modernization of each population. Our data further suggested increased bacterial species richness and diversity of the gastric microbiome in individuals who were less modernized, particularly in the Orang Asli group, could suppress the growth of H. pylori. In addition, there were significant variations in the gastric microbiome between modern Malaysians with different types of gastric diseases. Notably, Cutibacterium acnes was present at significantly greater abundance level in patients with non-ulcerative dyspepsia than those with peptic-ulcer diagnosis. This suggests that C. acnes may also play a role in gastritis besides H. pylori, which merits further investigation. Full article

The human gut is inhabited by overcrowded prokaryotic communities, a major component of which is the virome, comprised of viruses, bacteriophages, archaea, eukaryotes and bacteria. The virome is required for luminal homeostasis and, by their lytic or synergic capacities, they can regulate the microbial community structure and activity. Dysbiosis is associated with numerous chronic human diseases. Since the virome can impact microbial genetics and behavior, understanding its biology, composition, cellular cycle, regulation, mode of action and potential beneficial or hostile activities can change the present paradigm of the cross-talks in the luminal gut compartment. Celiac disease is a frequent autoimmune disease in which viruses can play a role in disease development. Based on the current knowledge on the enteric virome, in relation to celiac disease pathophysiological evolvement, the current review summarizes the potential interphases between the two. Exploring and understanding the role of the enteric virome in gluten-dependent enteropathy might bring new therapeutic strategies to change the luminal eco-event for the patient’s benefit. Full article

Pectobacterium carotovorum is a gram-negative bacterium that, together with other soft rot Enterobacteriaceae causes soft rot disease in vegetables, fruits, and ornamental plants through the action of exoproteins including plant cell wall-degrading enzymes (PCWDEs). Although pathogenicity in these bacteria is complex, virulence levels are proportional to the levels of plant cell wall-degrading exoenzymes (PCWDEs) secreted. Two low enzyme-producing transposon Tn5 mutants were isolated, and compared to their parent KD100, the mutants were less virulent on celery petioles and carrot disks. The inactivated gene responsible for the reduced virulence phenotype in both mutants was identified as wcaG. The gene, wcaG (previously denoted fcl) encodes NAD-dependent epimerase/dehydratase, a homologue of GDP-fucose synthetase of Escherichia coli. In Escherichia coli, GDP-fucose synthetase is involved in the biosynthesis of the exopolysaccharide, colanic acid (CA). The wcaG mutants of P. carotovorum formed an enhanced level of biofilm in comparison to their parent. In the hydrophobicity test the mutants showed more hydrophobicity than the parent in hexane and hexadecane as solvents. Complementation of the mutants with extrachromosomal copies of the wild type gene restored these functions to parental levels. These data indicate that NAD-dependent epimerase/dehydratase plays a vital rule in cell surface properties, exoenzyme production, and virulence in P. carotovorum. Full article

Trans-splicing mechanisms have been documented in many lineages that are widely distributed phylogenetically, including dinoflagellates. The spliced leader (SL) sequence itself is conserved in dinoflagellates, although its gene sequences and arrangements have diversified within or across different species. In this study, we present 18 Fugacium kawagutii SL genes identified from stranded RNA-seq reads. These genes typically have a single SL but can contain several partial SLs with lengths ranging from 103 to 292 bp. Unexpectedly, we find the SL gene transcripts contain sequences upstream of the canonical SL, suggesting that generation of mature transcripts will require additional modifications following trans-splicing. We have also identified 13 SL-like genes whose expression levels and length are comparable to Dino-SL genes. Lastly, introns in these genes were identified and a new site for Sm-protein binding was proposed. Overall, this study provides a strategy for fast identification of SL genes and identifies new sequences of F. kawagutii SL genes to supplement our understanding of trans-splicing. Full article

A novel Gram staining positive, aerobic bacterium NEAU-HV1^T that exhibits antifungal activity against Exserohilum turcicum was isolated from a soil collected from Gama, Hadjer lamis, Chad. It was grown at 10–45 °C (optimum 30 °C), pH 5–10 (optimum pH 8), and 0–4% (w/v) NaCl (optimum 1%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NEAU-HV1^T was closely related to Sinomonas susongensis A31^T (99.24% sequence similarity), Sinomonas humi MUSC 117^T (98.76%), and Sinomonas albida LC13^T (98.68%). The average nucleotide identity values between NEAU-HV1^T and its most closely related species were 79.34−85.49%. The digital DNA–DNA hybridization values between NEAU-HV1^T and S. susongensis A31^T, S. albida LC13^T, and S. humi MUSC 117^T were 23.20, 23.50, and 22.80%, respectively, again indicating that they belonged to different taxa. The genomic DNA G+C content was 67.64 mol%. The whole cell sugars contained galactose, mannose, and rhamnose. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and four glycolipids. The respiratory quinone system comprised MK-9(H₂), MK-10(H₂), and MK-8(H₂). The major cellular fatty acids (>5%) were anteiso-C_15:0, anteiso-C_17:0, C_16:0, and iso-C_15:0. Based on the polyphasic analysis, it is suggested that the strain NEAU-HV1^T represents a novel species of the genus Sinomonas, for which the name Sinomonas gamaensis sp. nov. is proposed. The type strain is NEAU-HV1^T (= DSM 104514^T = CCTCC M 2017246^T). Full article

Pine mushroom (Tricholoma matsutake) is one of the most valued ectomycorrhizal fungi in Asia because of its unique pine-like aroma; however, due to exceptionally slow growth of its mycelia in artificial conditions, its cultivation has been largely deemed as not possible. Previous studies have shown that some bacteria and a few Trichoderma species associated with pine mushroom promoted the growth of T. matsutake isolate, but this effect is relatively unexplored. In this study, we investigated the diversity of microfungi in the fairy ring of T. matsutake and their effect on the growth of T. matsutake isolate. From 184 fungal isolates, 28 species were identified based on suitable molecular markers. Penicillium was most frequently observed (16 species), followed by Trichoderma (4 species). Five Zygomycota species showed a high promoting effect on the growth of T. matsutake while the effects of ascomycetes were mixed. The microfungi that promote the growth of T. matsutake can be useful for forest nursery and artificial cultivation of T. matsutake. Full article

Emerging threats of antimicrobial resistance necessitate the exploration of effective alternatives for healthy livestock growth strategies. ‘Immunosynbiotics’, a combination of immunoregulatory probiotics and prebiotics with synergistic effects when used together in feed, would be one of the most promising candidates. Lactobacilli are normal residents of the gastrointestinal tract of pigs, and many of them are able to exert beneficial immunoregulatory properties. On the other hand, wakame (Undaria pinnafida), an edible seaweed, has the potential to be used as an immunoregulatory prebiotic when added to livestock feed. Therefore, in order to develop a novel immunosynbiotic, we isolated and characterized immunoregulatory lactobacilli with the ability to utilize wakame. Following a month-long in vivo wakame feeding trial in 8-week-old Landrace pigs (n = 6), sections of intestinal mucous membrane were processed for bacteriological culture and followed by identification of pure colonies by 16S rRNA sequence. Each isolate was characterized in vitro in terms of their ability to assimilate to the wakame and to differentially modulate the expression of interleukin-6 (IL-6) and interferon beta (IFN-β) in the porcine intestinal epithelial (PIE) cells triggered by Toll-like receptor (TLR)-4 and TLR-3 activation, respectively. We demonstrated that feeding wakame to pigs significantly increased the lactobacilli population in the small intestine. We established a wakame-component adjusted culture media that allowed the isolation and characterization of a total of 128 Lactobacilli salivarius colonies from the gut of wakame-fed pigs. Interestingly, several L. salivarius isolates showed both high wakame assimilation ability and immunomodulatory capacities. Among the wakame assimilating isolates, L. salivarius FFIG71 showed a significantly higher capacity to upregulate the IL-6 expression, and L. salivarius FFIG131 showed significantly higher capacity to upregulate the IFN-β expression; these could be used as immunobiotic strains in combination with wakame for the development of novel immunologically active feeds for pigs. Full article

As Streptomyces have shown an outstanding capacity for drug production, different campaigns in geographically distant locations currently aim to isolate new antibiotic producers. However, many of these newly isolated Streptomyces strains are classified as identical to already described species. Nevertheless, as discrepancies in terms of secondary metabolites and morphology are possible, we compared two Streptomyces strains with identical 16S rRNA gene sequences but geographically distant origins. Chosen were an Easter Island Streptomyces isolate (Streptomyces sp. SN25_8.1) and the next related type strain, which is Streptomyces griseus subsp. griseus DSM 40236^T isolated from Russian garden soil. Compared traits included phylogenetic relatedness based on 16S rRNA gene sequences, macro and microscopic morphology, antibiotic activity and secondary metabolite profiles. Both Streptomyces strains shared several common features, such as morphology and core secondary metabolite production. They revealed differences in pigmentation and in the production of accessory secondary metabolites which appear to be strain-specific. In conclusion, despite identical 16S rRNA classification Streptomyces strains can present different secondary metabolite profiles and may well be valuable for consideration in processes for drug discovery. Full article

The objective of this study was to develop predictive models for describing the inoculated Salmonella reductions on chicken during the scalding process in China. Salmonella reductions on chicken breasts at a 100 s treatment were 1.12 ± 0.07, 1.38 ± 0.01, and 2.17 ± 0.11 log CFU/g at scalding temperatures of 50, 60 and 70 °C, respectively. For chicken wingettes, 0.87 ± 0.02, 0.99 ± 0.14 and 1.11 ± 0.17 log CFU/g reductions were obtained at 50, 60 and 70 °C after the 100 s treatment, respectively. Greater bacterial reductions were observed on chicken breasts than on chicken wingettes (p < 0.05). A logistic (−1.12, 0.06) distribution could describe the bacterial reductions on chicken breasts at 50–60 °C. Weibull, exponential and log-linear models were compared for describing the bacterial reduction on chicken breasts at 70 °C and the Weibull model showed the best fit as indicated by the pseudo-R², root mean square error (RMSE) and standard error of prediction (SEP) values. For chicken wingettes, a logistic (−0.95, 0.07) distribution could be used to describe the bacterial reduction at 50–70 °C. The developed predictive models could provide parts of the input data for microbial risk assessment of the poultry supply chain in China. Full article

The goal of this study is to assess to what extent non-Saccharomyces yeasts can introduce aromatic changes of industrial interest in fermentative, varietal and aged aromas of wine. Aroma precursors from Riesling and Garnacha grapes were extracted and used in two independent sequential experiments. Synthetic musts were inoculated, either with Saccharomyces cerevisiae (Sc) or with Pichia kluyveri (Pk), Torulaspora delbrueckii (Td) or Lachancea thermotolerans (Lt), followed by Sc. The fermented samples were subjected to anoxic aging at 50 °C for 0, 1, 2 or 5 weeks before an aroma analysis. The fermentative aroma profiles were consistently changed by non-Saccharomyces: all strains induced smaller levels of isoamyl alcohol; Pk produced huge levels of aromatic acetates and can induce high levels of fatty acids (FA) and their ethyl esters (EE); Td produced large levels of branched acids and of their EE after aging, and induced smaller levels of FA and their EE; Lt produced reduced levels of FA and their EE. The varietal aroma was also deeply affected: TDN (1,1,6-trimethyl-1,2- dihydronaphthalene) levels in aged wines were reduced by Pk and enhanced by Lt in Garnacha; the levels of vinylphenols can be much reduced, particularly by Lt and Pk. TD and Lt can increase linalool and geraniol in young, but not in aged wines. Full article

Moraxella is an ocular bacterial pathogen isolated in cases of keratitis, conjunctivitis, and endophthalmitis. Gram-negative brick-shaped diplobacilli from ocular specimens, and slow growth in culture, are early indications of Moraxella ocular infection; however, identifying Moraxella to species can be complex and inconsistent. In this study, bacteria consistent with Moraxella were identified to species using: (1) DNA sequencing coupled with vancomycin susceptibility, (2) MALDI-TOF mass spectrometry, and (3) the Biolog ID system. Study samples consisted of nine ATCC Moraxella controls, 82 isolates from keratitis, 21 isolates from conjunctivitis, and 4 isolates from endophthalmitis. The ATCC controls were correctly identified. For keratitis, 66 (80.5%) were identified as M. nonliquefaciens, 7 (9.0%) as M. lacunata, 5 (6%) as M. osloensis, 2 (2.5%) as Acinetobacter lwoffii, 1 (1.0%) as M. bovis/nonliquefaciens, and 1 (1.0%) as M. osloensis/nonliquefaciens. For conjunctivitis, 9 (43.0%) were identified as M. osloensis, 6 (29.0%) as M. nonliquefaciens, 3 (14.3%) as Roseomonas, 2 (9.5%) as Acinetobacter (parvus, junii), and 1 (4.5%) as M. catarrhalis/nonliquefaciens. From endophthalmitis, 3 of 4 of the isolates were M. nonliquefaciens. Overall, M. nonliquefaciens and M. osloensis were identified in 70% (75 of 107) and 13% (14 of 107) of cases, respectively, totaling 83% (89 of 107). M. nonliquefaciens and M. osloensis are important bacterial pathogens of the eye as determined by DNA sequencing, MALDI-TOF MS, and Biolog. Although Moraxella catarrhalis is a clinical pathogen, other species of Moraxella appear to have a prominent role in eye infections. Full article

Background: Candida albicans’ ability to evade host immune responses represents a serious threat for vulnerable patients. Objectives: To investigate if (1) feces from healthy subjects exert anti-Candida activity; (2) fecal anti-Candida activity is modified by probiotic administration and (3) different probiotic differently modulate anti-Candida activity. Patients and methods: Feces from healthy donors were analyzed before and after seven days of dietary supplementation with two different probiotic formulations (VSL#3^®; Vivomixx^®). Candida albicans was cultured with decreasing concentrations of diluted feces, obtained before and after the treatment period. The relationship between anti-Candida activity of feces, interferon-α, anti-interferon-α antibodies and the expression of MxA, ISG15 and IFNAR1 was also evaluated. Results: Feces obtained prior to probiotic intake and feces collected after supplementation with VSL#3^® did not affect Candida albicans growth. On the contrary, a 3log₁₀ inhibition of Candida development was observed after Vivomixx^® intake. Interferon-α played a role in the inhibition of Candida growth. Conclusion: Fecal anti-Candida activity was not observed prior to probiotic supplementation. Seven days of administration of Vivomixx^® increased fecal anti-Candida activity, the same effect was not observed after intake of VSL#3^®. The probiotic-induced anti-Candida activity seems to be related to an increased local production and release of interferon-α. Clinical trials are needed to determine if a short pretreatment with specific probiotic formulations may increase anti-Candida defenses in patients at risk. Full article

Microbial diversity has always presented taxonomic challenges. With the popularity of next-generation sequencing technology, more unculturable bacteria have been sequenced, facilitating the discovery of additional new species and complicated current microbial classification. The major challenge is to assign appropriate taxonomic names. Hence, assessing the consistency between taxonomy and genomic relatedness is critical. We proposed and applied a genome comparison approach to a large-scale survey to investigate the distribution of genomic differences among microorganisms. The approach applies a genome-wide criterion, homologous coverage ratio (HCR), for describing the homology between species. The survey included 7861 microbial genomes that excluded plasmids, and 1220 pairs of genera exhibited ambiguous classification. In this study, we also compared the performance of HCR and average nucleotide identity (ANI). The results indicated that HCR and ANI analyses yield comparable results, but a few examples suggested that HCR has a superior clustering effect. In addition, we used the Genome Taxonomy Database (GTDB), the gold standard for taxonomy, to validate our analysis. The GTDB offers 120 ubiquitous single-copy proteins as marker genes for species classification. We determined that the analysis of the GTDB still results in classification boundary blur between some genera and that the marker gene-based approach has limitations. Although the choice of marker genes has been quite rigorous, the bias of marker gene selection remains unavoidable. Therefore, methods based on genomic alignment should be considered for use for species classification in order to avoid the bias of marker gene selection. On the basis of our observations of microbial diversity, microbial classification should be re-examined using genome-wide comparisons. Full article

Cryoconite holes are oases of microbial diversity on ice surfaces. In contrast to the Arctic, where during the summer most cryoconite holes are ‘open’, in Continental Antarctica they are most often ‘lidded’ or completely frozen year-round. Thus, they represent ideal systems for the study of microbial community assemblies as well as carbon accumulation, since individual cryoconite holes can be isolated from external inputs for years. Here, we use high-throughput sequencing of the 16S and 18S rRNA genes to describe the bacterial and eukaryotic community compositions in cryoconite holes and surrounding lake, snow, soil and rock samples in Queen Maud Land. We cross correlate our findings with a broad range of geochemical data including for the first time ¹³C and ¹⁴C analyses of Antarctic cryoconites. We show that the geographic location has a larger effect on the distribution of the bacterial community compared to the eukaryotic community. Cryoconite holes are distinct from the local soils in both ¹³C and ¹⁴C and their isotopic composition is different from similar samples from the Arctic. Carbon contents were generally low (≤0.2%) and older (6–10 ky) than the surrounding soils, suggesting that the cryoconite holes are much more isolated from the atmosphere than the soils. Full article

Treatment options for multidrug resistant Acinetobacter baumannii strains (MDR-AB) are limited. Minocycline has been used alone or in combination in the treatment of infections associated with AB. A systematic review of the clinical use of minocycline in nosocomial infections associated with MDR-AB was performed according to the PRISMA-P guidelines. PubMed-Medline, Scopus and Web of Science ^TM databases were searched from their inception until March 2019. Additional Google Scholar free searches were performed. Out of 2990 articles, 10 clinical studies (9 retrospective case series and 1 prospective single center trial) met the eligibility criteria. In total, 223 out of 268 (83.2%) evaluated patients received a minocycline-based regimen; and 200 out of 218 (91.7%) patients with available data received minocycline as part of a combination antimicrobial regimen (most frequently colistin or carbapenems). Pneumonia was the most common infection type in the 268 cases (80.6% with 50.4% ventilator-associated pneumonia). The clinical and microbiological success rates following minocycline treatment were 72.6% and 60.2%, respectively. Mortality was 20.9% among 167 patients with relevant data. In this systematic review, minocycline demonstrated promising activity against MDR-AB isolates. This review sets the ground for further studies exploring the role of minocycline in the treatment of MDR-AB associated infections. Full article

The koji mold Aspergillus oryzae is widely adopted for producing rice wine, wherein koji mold saccharifies rice starch and sake yeast ferments glucose to ethanol. During rice wine brewing, the accumulating ethanol becomes a major source of stress for A. oryzae, and there is a decline in hydrolysis efficiency. However, the protective mechanisms of A. oryzae against ethanol stress are poorly understood. In the present study, we demonstrate that ethanol adversity caused a significant inhibition of mycelium growth and conidia formation in A. oryzae, and this suppressive effect increased with ethanol concentration. Transmission electron microscopy analysis revealed that ethanol uptake triggered internal cellular perturbations, such as irregular nuclei and the aggregation of scattered vacuoles in A. oryzae cells. Metabolic analysis uncovered an increase in fatty acid unsaturation under high ethanol conditions, in which a large proportion of stearic acid was converted into linoleic acid, and the expression of related fatty acid desaturases was activated. Our results therefore improve the understanding of ethanol adaptation mechanisms in A. oryzae and offer target genes for ethanol tolerance enhancement via genetic engineering. Full article

Although spice extracts are well known to exhibit antibacterial properties, there is lack of a comprehensive evaluation of the antibacterial effect of spices against antibiotic-resistant bacteria. In the present study, ethanolic extracts from a total of 67 spices were comprehensively investigated for their in vitro antibacterial activities by agar well diffusion against two common food-borne bacteria, Staphylococcus aureus and Salmonella enteritidis, with multi-drug resistance. Results showed that S. aureus was generally more sensitive to spice extracts than S. enteritidis. Of the 67 spice extracts, 38 exhibited antibacterial activity against drug-resistant S. aureus, while only four samples were effective on drug-resistant S. enteritidis. In addition, 11 spice extracts with inhibition zones greater than 15 mm were further verified for their broad-spectrum antibacterial properties using another 10 drug-resistant S. aureus strains. It was found that five spice extracts, including galangal, fructus galangae, cinnamon, yellow mustard seed, and rosemary, exhibited the highest antibacterial capacity. Further cytotoxicity of these 11 spices was determined and LC₅₀ values were found to be more than 100 μg/mL except for galangal, rosemary, and sage, whose LC₅₀ values were 9.32 ± 0.83, 19.77 ± 2.17, and 50.54 ± 2.57, respectively. Moreover, the antioxidant activities (ferric-reducing antioxidant power (FRAP) and trolox equivalent antioxidant capacity (TEAC) values) and total phenolic content (TPC) of spice extracts were determined to establish possible correlations with the antibacterial activity. Although the antibacterial effect was positively correlated with the antioxidant activities and TPC, the correlation was weak (r < 0.5), indicating that the antibacterial activity could also be attributed to other components besides antioxidant polyphenols in the tested spice extracts. In conclusion, dietary spices are good natural sources of antibacterial agents to fight against antibiotic-resistant bacteria, with potential applications as natural food preservatives and natural alternatives to antibiotics in animal feeding. Full article

Reassortment events among influenza viruses occur naturally and may lead to the development of new and different subtypes which often ignite the possibility of an influenza outbreak. Between 2008 and 2010, highly pathogenic avian influenza (HPAI) H5 of the N1 subtype from the A/goose/Guangdong/1/96-like (Gs/GD) lineage generated novel reassortants by introducing other neuraminidase (NA) subtypes reported to cause most outbreaks in poultry. With the extensive divergence of the H5 hemagglutinin (HA) sequences of documented viruses, the WHO/FAO/OIE H5 Evolutionary Working Group clustered these viruses into a systematic and unified nomenclature of clade 2.3.4.4 currently known as “H5Nx” viruses. The rapid emergence and circulation of these viruses, namely, H5N2, H5N3, H5N5, H5N6, H5N8, and the regenerated H5N1, are of great concern based on their pandemic potential. Knowing the evolution and emergence of these novel reassortants helps to better understand their complex nature. The eruption of reports of each H5Nx reassortant through time demonstrates that it could persist beyond its usual seasonal activity, intensifying the possibility of these emerging viruses’ pandemic potential. This review paper provides an overview of the emergence of each novel HPAI H5Nx virus as well as its current epidemiological distribution. Full article

Based on a total of 6,295,650 sequences from the V3 and V4 regions (16S ribosomal RNA), the composition of the microorganism communities in the water of three Litopenaeus vannamei (Decapoda, Whiteleg shrimp; Soc Trang, Vietnam) ponds were identified. Pseudomonas (10–20.29%), Methylophilus (13.26–24.28%), and Flavobacterium (2.6–19.29%) were the most abundant genera. The total ammonia (TAN) concentration (p = 0.025) and temperature (p = 0.015) were significantly correlated with the relative abundance of Pseudomonas in two bacterial communities (ST1, ST4), whereas the predictive functions of microorganism communities based on 16S rRNA gene data was estimated using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUST), which showed that nitrogen metabolism was significantly negatively correlated (p = 0.049) with TAN concentration. The abundance of Pseudomonas and nitrogen metabolism increased with a decrease in TAN concentration. The correlation between TAN concentration and the abundance of Pseudomonas was followed by the isolation, and heterotrophic nitrifying performance analysis was used to confirm our findings. Six Pseudomonas strains capable of heterotrophic nitrification were isolated from the three water samples and showed a complete reduction of 100 mg/L NH₄Cl during a 96-h cultivation. These results indicate the potential of applying Pseudomonas in shrimp ponds for water treatment. Full article

The inactivation of Escherichia coli O157:H7 (E. coli) in physiological saline and lotus roots by high hydrostatic pressure (HHP) in combination with CO₂ or N₂ was studied. Changes in the morphology, cellular structure, and membrane permeability of the cells in physiological saline after treatments were investigated using scanning electron microscopy, transmission electron microscopy, and flow cytometry, respectively. It was shown that after HHP treatments at 150–550 MPa, CO₂-packed E. coli cells had higher inactivation than the N₂-packed and vacuum-packed cells, and no significant difference was observed in the latter two groups. Further, both the morphology and intracellular structure of CO₂-packed E.coli cells were strongly destroyed by high hydrostatic pressure. However, serious damage to the intracellular structures occurred in only the N₂-packed E. coli cells. During HHP treatments, the presence of CO₂ caused more disruptions in the membrane of E. coli cells than in the N₂-packed and vacuum-packed cells. These results indicate that the combined treatment of HHP and CO₂ had a strong synergistic bactericidal effect, whereas N₂ did not have synergistic effects with HHP. Although these two combined treatments had different effects on the inactivation of E. coli cells, the inactivation mechanisms might be similar. During both treatments, E. coli cells were inactivated by cell damage induced to the cellular structure through the membrane components and the extracellular morphology, unlike the independent HHP treatment. Full article