microbiology research articles 2022

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Research articles

Longitudinal multi-omics analyses of the gut–liver axis reveals metabolic dysregulation in hepatitis C infection and cirrhosis

Multi-omics analyses of gut microbiome, liver and blood samples from patients with hepatitis C infection before and after removal of the virus reveal metabolic dysregulation along the gut–liver axis.

• Rabab O. Ali
• Gabriella M. Quinn
• Theo Heller

Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

This Resource combines amplicon sequencing, shotgun metagenomic sequencing and untargeted metabolomics to provide a global view of microbial–metabolite associations across Earth’s environments.

• Justin P. Shaffer
• Louis-Félix Nothias

Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria

The dcw cluster has an ancient origin and has been inherited vertically by all Bacteria.

• Daniela Megrian
• Simonetta Gribaldo

Mycobiota and diet-derived fungal xenosiderophores promote Salmonella gastrointestinal colonization

Siderophores from diet-derived or intestinal fungi can be used by Salmonella for growth in the murine gut.

• William Santus
• Amisha P. Rana
• Judith Behnsen

A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings

Genomic analyses of Klebsiella isolates sampled from multiple human, animal and environmental sources in Northern Italy explore Klebsiella population diversity and show that transmission of multidrug-resistant clones between clinical and environmental settings is scarce.

• Harry A. Thorpe
• Ross Booton
• Edward J. Feil

PCRCR complex is essential for invasion of human erythrocytes by Plasmodium falciparum

A heteromeric disulfide-linked complex binds to the RCR complex and is required for invasion of human erythrocytes by Plasmodium falciparum .

• Stephen W. Scally
• Tony Triglia
• Alan F. Cowman

Safety and immunogenicity of a prefusion non-stabilized spike protein mRNA COVID-19 vaccine: a phase I trial

A phase 1 clinical trial evaluates the safety, tolerability and immunogenicity of the ChulaCov19 mRNA vaccine in healthy adults.

• Sivaporn Gatechompol
• Wonngarm Kittanamongkolchai
• Kiat Ruxrungtham

Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency

HIV-1 latency is enabled by SMC5/6-mediated epigenetic silencing of unintegrated viral genomes.

• Ishak D. Irwan
• Hal P. Bogerd
• Bryan R. Cullen

Immune correlates analysis of the ENSEMBLE single Ad26.COV2.S dose vaccine efficacy clinical trial

Gold-standard evidence for correlates of protection is provided by analysis of a randomized phase 3 trial of Ad26.COV2.S for protection against moderate to severe-critical COVID-19 disease.

• Adrian B. McDermott
• Ruben O. Donis

Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission

White-tailed deer are a potential reservoir of SARS-CoV-2 variants.

• Bradley Pickering
• Oliver Lung
• Jeff Bowman

Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations

Tecovirimat blocks replication of 2022 monkeypox virus isolate in vitro, supporting its use in ongoing human clinical trials.

• Gaëlle Frenois-Veyrat
• Franck Gallardo
• Jean-Nicolas Tournier

Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem

Aerobic methanotrophy is a rare trait, yet bacteria with this capacity are key players in the global methane cycle. Here the authors find a methanotrophic Mycobacterium in a cave, indicating that methane utilization is more widespread across bacteria than previously assumed.

• Rob J. M. van Spanning
• Qingtian Guan
• Wilbert Bitter

Single-cell measurements and modelling reveal substantial organic carbon acquisition by Prochlorococcus

Single-cell measurements and modelling show that the cyanobacterium Prochlorococcus obtain most of the carbon required for growth from mixotrophy, extending their ecological range and impact in the water column.

• Dikla Aharonovich
• Daniel Sher

Bacteriophage genome engineering with CRISPR–Cas13a

A phage genetic engineering platform will enable a better understanding of phage biology and engineering of phage therapies.

• Jingwen Guan
• Agnès Oromí-Bosch
• Joseph Bondy-Denomy

Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing

A CRISPR-Cas13 enzyme is shown to have potent anti-phage activity that is harnessed to produce a phage genome engineering method with broad utility.

• Benjamin A. Adler
• Tomas Hessler
• Jennifer A. Doudna

Structure and function of a bacterial type III-E CRISPR–Cas7-11 complex

Recently discovered type III-E CRISPR–Cas systems use the single Cas7-11 effector to cleave foreign RNA. Here the authors use cryo-electron microscopy and biochemical approaches to reveal the mechanisms underlying crRNA maturation, target RNA recognition and cleavage, and communication with the protease Csx29 by Cas7-11.

• Xiaoshen Wang

Enterotoxin tilimycin from gut-resident Klebsiella promotes mutational evolution and antibiotic resistance in mice

Production of the enterotoxin tilimycin by gut-resident Klebsiella species can alter gut microbiota composition, induce mutational evolution and drive the emergence of antibiotic resistance in mice.

• Sabine Kienesberger
• Ellen L. Zechner

Evasion of cGAS and TRIM5 defines pandemic HIV

Innate immune evasion is key to evolution of the pandemic lineage of HIV.

• Lorena Zuliani-Alvarez
• Morten L. Govasli
• Greg J. Towers

Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial

This Article reports the emergence of SARS-CoV-2 escape mutations during bamlanivimab therapy in the setting of a phase II clinical trial.

• Manish C. Choudhary
• Kara W. Chew
• Akbar Shahkolahi

Coinfection by influenza A virus and respiratory syncytial virus produces hybrid virus particles

Chimeric particles are formed when influenza A virus and respiratory syncytial virus coinfect lung cells in vitro.

• Joanne Haney
• Swetha Vijayakrishnan
• Pablo R. Murcia

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Page 1 of 109

Characterization of genes related to the efflux pump and porin in multidrug-resistant Escherichia coli strains isolated from patients with COVID-19 after secondary infection

Escherichia coli ( E. coli ) is a multidrug resistant opportunistic pathogen that can cause secondary bacterial infections in patients with COVID-19. This study aimed to determine the antimicrobial resistance profi...

• View Full Text

Correction: Uncovering the complexity of childhood undernutrition through strain‑level analysis of the gut microbiome

The original article was published in BMC Microbiology 2024 24 :73

Optimization of fermentation conditions and medium components for chrysomycin a production by Streptomyces sp. 891-B6

Chrysomycin A (CA) is a promising antibiotic for treatment of Gram-positive bacterial infections and cancers. In order to enhance CA yield, optimization of fermentation conditions and medium components was car...

Integrative metagenomic analysis reveals distinct gut microbial signatures related to obesity

Obesity is a metabolic disorder closely associated with profound alterations in gut microbial composition. However, the dynamics of species composition and functional changes in the gut microbiome in obesity r...

Ultraviolet C inactivation of Coxiella burnetii for production of a structurally preserved whole cell vaccine antigen

Q fever, a worldwide-occurring zoonotic disease, can cause economic losses for public and veterinary health systems. Vaccines are not yet available worldwide and currently under development. In this regard, it...

Neutrophil extracellular traps formation: effect of Leishmania major promastigotes and salivary gland homogenates of Phlebotomus papatasi in human neutrophil culture

Leishmaniasis as a neglected tropical disease (NTD) is caused by the inoculation of Leishmania parasites via the bite of phlebotomine sand flies. After an infected bite, a series of innate and adaptive immune res...

Assessment of bacterial profile, antimicrobial susceptibility status, and associated factors of isolates among hospitalized patients at Dessie Comprehensive Specialized Hospital, Northeast Ethiopia

Antimicrobial resistant bacteria among hospitalized patients are becoming a major public health threat worldwide, mainly in developing countries. Infections by these multidrug resistant pathogens cause high ra...

A review of emerging health threats from zoonotic New World mammarenaviruses

Despite repeated spillover transmission and their potential to cause significant morbidity and mortality in human hosts, the New World mammarenaviruses remain largely understudied. These viruses are endemic to...

Impact of Limosilactobacillus fermentum probiotic treatment on gut microbiota composition in sahiwal calves with rotavirus diarrhea: A 16S metagenomic analysis study”

Diarrhea poses a major threat to bovine calves leading to mortality and economic losses. Among the causes of calf diarrhea, bovine rotavirus is a major etiological agent and may result in dysbiosis of gut micr...

Genetic characterizations of Cryptosporidium spp. from children with or without diarrhea in Wenzhou, China: high probability of zoonotic transmission

Cryptosporidium is a highly pathogenic parasite responsible for diarrhea in children worldwide. Here, the epidemiological status and genetic characteristics of Cryptosporidium in children with or without diarrhea...

Effect of stress urinary incontinence on vaginal microbial communities

Postpartum women often experience stress urinary incontinence (SUI) and vaginal microbial dysbiosis, which seriously affect women’s physical and mental health. Understanding the relationship between SUI and va...

Hospital distribution, seasonality, time trends and antifungal susceptibility profiles of all Aspergillus species isolated from clinical samples from 2015 to 2022 in a tertiary care hospital

Aspergillus species cause a variety of serious clinical conditions with increasing trend in antifungal resistance. The present study aimed at evaluating hospital epidemiology and antifungal susceptibility of all ...

Comparative analysis of proteomic adaptations in Enterococcus faecalis and Enterococcus faecium after long term bile acid exposure

All gastrointestinal pathogens, including Enterococcus faecalis and Enterococcus faecium , undergo adaptation processes during colonization and infection. In this study, we investigated by data-independent acquisi...

Influence of PhoPQ and PmrAB two component system alternations on colistin resistance from non- mcr colistin resistant clinical E. Coli strains

The current understanding of acquired chromosomal colistin resistance mechanisms in Enterobacterales primarily involves the disruption of the upstream PmrAB and PhoPQ two-component system (TCS) control caused by ...

Staphylococcus aureus foldase PrsA contributes to the folding and secretion of protein A

Staphylococcus aureus secretes a variety of proteins including virulence factors that cause diseases. PrsA, encoded by many Gram-positive bacteria, is a membrane-anchored lipoprotein that functions as a foldase t...

Transcriptional dynamics during Rhodococcus erythropolis infection with phage WC1

Belonging to the Actinobacteria phylum, members of the Rhodococcus genus thrive in soil, water, and even intracellularly. While most species are non-pathogenic, several cause respiratory disease in animals and, m...

A hypervirulent Acinetobacter baumannii strain has robust anti-phagocytosis ability

Acinetobacter baumannii ( A. baumannii ) is associated with both hospital-acquired infections (HAP) and community-acquired pneumonia (CAP). In this study, we present a novel CAP-associated A. baumannii (CAP-AB) str...

Restoration of gut dysbiosis through Clostridium butyricum and magnesium possibly balance blood glucose levels: an experimental study

Diabetes mellitus (DM) is a chronic metabolic disorder characterized by an elevated level of blood glucose due to the absence of insulin secretion, ineffectiveness, or lack of uptake of secreted insulin in the...

Bacillus subtilis SOM8 isolated from sesame oil meal for potential probiotic application in inhibiting human enteropathogens

While particular strains within the Bacillus species, such as Bacillus subtilis , have been commercially utilised as probiotics, it is critical to implement screening assays and evaluate the safety to identify pot...

Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy

Vancomycin-resistant enterococci (VRE) are major opportunistic pathogens and the causative agents of serious diseases, such as urinary tract infections and endocarditis. VRE strains mainly include species of Ente...

Comparison of integron mediated antimicrobial resistance in clinical isolates of Escherichia coli from urinary and bacteremic sources

Antimicrobial resistance (AMR) is a global threat driven mainly by horizontal gene transfer (HGT) mechanisms through mobile genetic elements (MGEs) including integrons. The variable region (VR) of an integron ...

Structure predictions and functional insights into Amidase_3 domain containing N -acetylmuramyl-L-alanine amidases from Deinococcus indicus DR1

N -acetylmuramyl-L-alanine amidases are cell wall modifying enzymes that cleave the amide bond between the sugar residues and stem peptide in peptidoglycan. Amidases play a vital role in septal cell wall cleavag.....

Profile of non-tuberculous mycobacteria amongst tuberculosis presumptive people in Cameroon

Cameroon is a tuberculosis (TB) burden country with a 12% positivity among TB presumptive cases. Of the presumptive cases with a negative TB test, some are infected with Non-tuberculous Mycobacteria (NTM). How...

In vitro investigation of relationship between quorum-sensing system genes, biofilm forming ability, and drug resistance in clinical isolates of Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogen in the health-care systems and one of the primary causative agents with high mortality in hospitalized patients, particularly immunocompromised. The limitation ...

Relationship between heart failure and intestinal inflammation in infants with congenital heart disease

The association between heart failure (HF) and intestinal inflammation caused by a disturbed intestinal microbiota in infants with congenital heart disease (CHD) was investigated.

Clostridium butyricum inhibits the inflammation in children with primary nephrotic syndrome by regulating Th17/Tregs balance via gut-kidney axis

Primary nephrotic syndrome (PNS) is a common glomerular disease in children. Clostridium butyricum ( C. butyricum), a probiotic producing butyric acid, exerts effective in regulating inflammation. This study was d...

Human-derived bacterial strains mitigate colitis via modulating gut microbiota and repairing intestinal barrier function in mice

Unbalanced gut microbiota is considered as a pivotal etiological factor in colitis. Nevertheless, the precise influence of the endogenous gut microbiota composition on the therapeutic efficacy of probiotics in...

In vitro and in silico studies of enterobactin-inspired Ciprofloxacin and Fosfomycin first generation conjugates on the antibiotic resistant E. coli OQ866153

The emergence of antimicrobial resistance in bacterial pathogens is a growing concern worldwide due to its impact on the treatment of bacterial infections. The "Trojan Horse" strategy has been proposed as a po...

HPV-associated cervicovaginal microbiome and host metabolome characteristics

Cervicovaginal microbiome plays an important role in the persistence of HPV infection and subsequent disease development. However, cervicovaginal microbiota varied cross populations with different habits and r...

Transcriptomic and physiological analyses of Trichoderma citrinoviride HT-1 assisted phytoremediation of Cd contaminated water by Phragmites australis

Plant growth promoting microbe assisted phytoremediation is considered a more effective approach to rehabilitation than the single use of plants, but underlying mechanism is still unclear. In this study, we co...

Long-term push–pull cropping system shifts soil and maize-root microbiome diversity paving way to resilient farming system

The soil biota consists of a complex assembly of microbial communities and other organisms that vary significantly across farming systems, impacting soil health and plant productivity. Despite its importance, ...

Pretreatment with an antibiotics cocktail enhances the protective effect of probiotics by regulating SCFA metabolism and Th1/Th2/Th17 cell immune responses

Probiotics are a potentially effective therapy for inflammatory bowel disease (IBD); IBD is linked to impaired gut microbiota and intestinal immunity. However, the utilization of an antibiotic cocktail (Abx) p...

High-throughput sequencing reveals differences in microbial community structure and diversity in the conjunctival tissue of healthy and type 2 diabetic mice

To investigate the differences in bacterial and fungal community structure and diversity in conjunctival tissue of healthy and diabetic mice.

High prevalence of ST5-SCC mec II-t311 clone of methicillin-resistant Staphylococcus aureus isolated from bloodstream infections in East China

Methicillin-resistant Staphylococcus aureus (MRSA) is a challenging global health threat, resulting in significant morbidity and mortality worldwide. This study aims to determine the molecular characteristics and...

Characteristics of the oral and gastric microbiome in patients with early-stage intramucosal esophageal squamous cell carcinoma

Oral microbiome dysbacteriosis has been reported to be associated with the pathogenesis of advanced esophageal cancer. However, few studies investigated the potential role of oral and gastric microbiota in ear...

The potential role of Listeria monocytogenes in promoting colorectal adenocarcinoma tumorigenic process

Listeria monocytogenes is a foodborne pathogen, which can cause a severe illness, especially in people with a weakened immune system or comorbidities. The interactions between host and pathogens and between patho...

Evaluation of clinical characteristics and risk factors associated with Chlamydia psittaci infection based on metagenomic next-generation sequencing

Psittacosis is a zoonosis caused by Chlamydia psittaci , the clinical manifestations of Psittacosis range from mild illness to fulminant severe pneumonia with multiple organ failure. This study aimed to evaluate t...

Characterization of the broad-spectrum antibacterial activity of bacteriocin-like inhibitory substance-producing probiotics isolated from fermented foods

Antimicrobial peptides, such as bacteriocin, produced by probiotics have become a promising novel class of therapeutic agents for treating infectious diseases. Selected lactic acid bacteria (LAB) isolated from...

Metagenomic gut microbiome analysis of Japanese patients with multiple chemical sensitivity/idiopathic environmental intolerance

Although the pathology of multiple chemical sensitivity (MCS) is unknown, the central nervous system is reportedly involved. The gut microbiota is important in modifying central nervous system diseases. Howeve...

The effect of in vitro simulated colonic pH gradients on microbial activity and metabolite production using common prebiotics as substrates

The interplay between gut microbiota (GM) and the metabolization of dietary components leading to the production of short-chain fatty acids (SCFAs) is affected by a range of factors including colonic pH and ca...

Gut microbial network signatures of early colonizers in preterm neonates with extrauterine growth restriction

Extrauterine growth restriction (EUGR) represents a prevalent condition observed in preterm neonates, which poses potential adverse implications for both neonatal development and long-term health outcomes. The...

Early transcriptional changes of heavy metal resistance and multiple efflux genes in Xanthomonas campestris pv. campestris under copper and heavy metal ion stress

Copper-induced gene expression in Xanthomonas campestris pv. campestris (Xcc) is typically evaluated using targeted approaches involving qPCR. The global response to copper stress in Xcc and resistance to metal i...

Whole-genome sequencing and analysis of Chryseobacterium arthrosphaerae from Rana nigromaculata

Chryseobacterium arthrosphaerae strain FS91703 was isolated from Rana nigromaculata in our previous study. To investigate the genomic characteristics, pathogenicity-related genes, antimicrobial resistance, and ph...

Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study

To explore the changes and potential mechanisms of microbiome in different parts of the upper airway in the development of pediatric OSA and observe the impact of surgical intervention on oral microbiome for p...

Unveiling biological activities of biosynthesized starch/silver-selenium nanocomposite using Cladosporium cladosporioides CBS 174.62

Microbial cells capability to tolerate the effect of various antimicrobial classes represent a major worldwide health concern. The flexible and multi-components nanocomposites have enhanced physicochemical cha...

Characterization of the major autolysin ( AtlC ) of Staphylococcus carnosus

Autolysis by cellular peptidoglycan hydrolases (PGH) is a well-known phenomenon in bacteria. During food fermentation, autolysis of starter cultures can exert an accelerating effect, as described in many studi...

Exploring Aeromonas dhakensis in Aldabra giant tortoises: a debut report and genetic characterization

Aeromonas dhakensis (A. dhakensis) is becoming an emerging pathogen worldwide, with an increasingly significant role in animals and human health. It is a ubiquitous bacteria found in terrestrial and aquatic milie...

Biotransformation of zearalenone to non-estrogenic compounds with two novel recombinant lactonases from Gliocladium

The mycotoxin zearalenone (ZEA) produced by toxigenic fungi is widely present in cereals and its downstream products. The danger of ZEA linked to various human health issues has attracted increasing attention....

Multidrug resistance among uropathogenic clonal group A E. Coli isolates from Pakistani women with uncomplicated urinary tract infections

Multi-drug resistance (MDR) has notably increased in community acquired uropathogens causing urinary tract infections (UTIs), predominantly Escherichia coli . Uropathogenic E. coli causes 80% of uncomplicated comm...

RpoS role in antibiotic resistance, tolerance and persistence in E. coli natural isolates

The intrinsic concentration of RpoS, the second most abundant sigma factor, varies widely across the E. coli species. Bacterial isolates that express high levels of RpoS display high resistance to environmental s...

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Microbiology

Viral Genetics Confirms What On-the-Ground Activists Knew Early in the Mpox Outbreak

Molecular biology could have changed the mpox epidemic—and could stop future outbreaks

Joseph Osmundson

Cannibal Cells Inspire Cancer Treatment Improvement

Giving cells an appetite for cancer could enhance treatments

Kate Graham-Shaw

Is Raw-Milk Cheese Safe to Eat?

Recent bacterial outbreaks from consuming cheese made from unpasteurized milk, or “raw milk,” raise questions about the safety of eating these artisanal products

Riis Williams

Many Pregnancy Losses Are Caused by Errors in Cell Division

Odd cell divisions could help explain why even young, healthy couples might struggle to get pregnant

Gina Jiménez

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Editorial: Rising stars in clinical microbiology: 2022

Rafael franco.

1 CiberNed Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, Madrid, Spain

2 Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain

3 School of Chemistry, Universitat de Barcelona, Barcelona, Spain

The objective of this Research Topic was to highlight “rising stars” in what concerns new approaches in microbiology research that address pending issues and, more importantly, that arise in response to new challenges such as the one posed by the SARS-CoV-2 pandemic. In addition, one of the articles, through a meta-analysis, underscores the possible relationship between the gram negative bacterium Porphyromonas gingivalis and a common age-related disease involving alterations in the immunological response, namely rheumatoid arthritis ( Li et al. ). Altered immunological responses caused by age, drug use, environmental factors, etc. may be incited and/or aggravated by microorganisms. One of the most popular articles, with >1800 views as of today (October 10, 2022), is devoted to the potential of vitamin D to combat inflammation in macrophages in patients with Crohn’s disease who are also infected with Mycobacterium avium subsp. paratuberculosis ( Vaccaro et al ). Another article, a review with >2,200 views, deals with the anti-cancer potential of oncolytic viruses. This review suggests that gastrointestinal tumors can be managed more effectively if immunotherapy takes into account the synergistic action of oncolytic viruses with immunoregulatory power ( Li et al. ).

In further confirmation of the correlation between the intestinal microbiota and disease risk and/or its impact on disease progression, the Research Topic contains multiple highly compelling studies and reviews on this subject. One of the reviews highlights the possibility that probiotics may decrease the risk of viral infection. Multiple mechanisms may be in operation, from the probiotic triggering of anti-viral immune cells to the production of antiviral metabolites and binding of these compounds to viruses to prevent cell infection. The article includes a table presenting the effects of common bacteria present in probiotic preparations in terms of preparing the human body to fight invading viral pathogens ( Wang et al. ). Akkermansia muciniphila , a commensal bacterium present in the intestine, is beneficial in the maintenance of a healthy microflora and a balanced gut immune system (see Rodrigues et al., 2022 , for a review). Interestingly, Lv et al. decipher the genomic architecture of Akkermansia species found in the human intestine, also identifying different phylogroups when comparing data obtained from Chinese and Western populations. The authors also demonstrate the presence of a strain, A. glicaniphila GP37 , previously described only in python ( Lv et al. ). The relevance of a proper microbiota is highlighted in another paper, in which alteration of bile acid metabolism is observed in patients with slow transit constipation. The authors conclude that their study “ provides an in-depth understanding of the relationship between the fecal microbiota, metabolites, and intestinal dysfunction in slow transit constipation patients ” ( Fan et al. ).

Microbiology is a common source of novel techniques to detect infections. This calls to mind the difficulties of obtaining the virus causing hepatitis D via PCR. The causal factor for hepatitis D is a viroid with a high complementarity of RNA sequences, resulting in a compact structure with a high degree of complementarity: that is, with bases that form a tight double helix. This structure is so difficult to relax to allow the RNA polymerase to act in a PCR assay that it is necessary to boil the sample for 15 min to achieve success (F. Rodriguez-Frías, personal communication; see details in Schaper et al., 2010 and Homs et al., 2014 ). Although there are RNAs that are very fragile, that of the viroid that causes hepatitis D in fact remains undegraded under adverse conditions. In the single methodological article included in the Research Topic, a luciferase-based methodology is used to detect antibodies against swine fever virus. The method consists of immunoprecipitation and, to increase detection sensitivity, takes advantage of the high yield of Gaussia luciferase, which is obtained from Gaussia princeps , a marine copepod ( Ding et al., ).

The Research Topic also includes an original research article and a review related to SARS-CoV-2 coronavirus infection. The review summarizes the primary mechanisms involved in severe cases of respiratory distress in patients with COVID-19. Among the novel contributions of this article is a description of the involvement of vitamin D in its role as an immunomodulator. It seems that patients who have low levels of blood vitamin D have poor prognosis; however, it is not demonstrated whether vitamin supplementation helps patients with COVID-19 ( Zheng et al. ). The original research article reports on the isolation and testing of chimeric virus-like particles that contain proteins coded by the SARS-CoV-2 genome. The authors prepared a plasmid that contained the sequence of the spike protein, which interacts with the virus receptor at host cells, in two forms: one intact, and another as a spike–H5N1 protein fusion, H5N1 being a protein of the avian influenza A virus. Virus-like particles containing these proteins, produced in a “ baculovirus insect cell expression system ,” were found to be immunogenic in mice. These results indicate that the approach may be useful in the design of novel anti-SARS-CoV-2 vaccines ( Chen et al. ).

Finally, the Research Topic does not lack discussion of novel and sophisticated techniques: Dai et al. propose the popular CRISPR/Cas9 system as a method of preparing a defective form of BHV-1 bovine herpesvirus virus, which causes vulvovaginitis and rhinotracheitis in cattle. The defective virus could eventually be used to prepare a vaccine, but at present has served to demonstrate that the UL41 viral gene is important for replication. Bioinformatics approaches show value in the construction of a model of the Fiber protein (gene ON164651) of the CAdV-1 canine adenovirus. The model has served to predict KLGVKPTTY as the amino acid sequence that binds to the major histocompatibility complex-1 in lymphocytes, thus paving the way for the development of an epitope-based vaccine ( Wang et al. ).

Author contributions

The author confirms being the sole contributor of this work and has approved it for publication.

Conflict of interest

The author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Publisher’s note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

• Homs M., Giersch K., Blasi M., Luẗgehetmann M., Buti M., Esteban R., et al.. (2014). Relevance of a full-length genomic RNA standard and a thermal-shock step for optimal hepatitis delta virus quantification . J. Clin. Microbiol. 52 , 3334–3338. doi:  10.1128/JCM.00940-14 [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
• Rodrigues V. F., Elias-Oliveira J., Pereira Í.S., Pereira J. A., Barbosa S. C., Machado M. S. G., et al.. (2022). Akkermansia muciniphila and gut immune system: A good friendship that attenuates inflammatory bowel disease, obesity, and diabetes . Front. Immunol. 13 . doi:  10.3389/FIMMU.2022.934695 [ PMC free article ] [ PubMed ] [ CrossRef ] [ Google Scholar ]
• Schaper M, Rodriguez-Frias F, Jardi R, Tabernero D, Homs M, Ruiz G, et al.. (2010) J. Hepatol. 52 ( 5 ), 658–664. doi:  10.1016/j.jhep.2009.10.036 [ PubMed ] [ CrossRef ] [ Google Scholar ]

Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released.

Volume 30, Number 5—May 2024

Covid-19 vaccination site accessibility, united states, december 11, 2020–march 29, 2022.

Main Article

Figure 3 . Walking accessibility for COVID-19 vaccination sites, by state, United States, December 11, 2020–March 29, 2022. A) 15 minutes; B) 30 minutes; C) 45 minutes; D) 60 minutes.

1 These first authors contributed equally to this article.

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ORIGINAL RESEARCH article

Modifying soil bacterial communities in saline mudflats with organic acids and substrates.

• 1 Nanjing Agricultural University, Nanjing, China
• 2 Nanjing University, Nanjing, Jiangsu Province, China

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In this paper, the effects of applying exogenous organic acids combined with biological substrate on the composition and diversity of soil bacterial community were studied in moderately saline mudflats in Jiangsu Province.Methods A combination of three exogenous organic acids (humic acid, fulvic acid, and citric acid) and four biological substrates (cottonseed hull, cow manure, grass charcoal, and pine needle) was set up set up on a coastal saline mudflat planted with a salt-tolerant forage grass, sweet sorghum. A total of 120 kg ha -1 of organic acids and 5000 kg ha -1 of substrates were used, plus two treatments, CK without application of organic acids and substrates and CK0 in bare ground, for a total of 14 treatments.No significant difference was found in the alpha diversity of soil bacterial community among all treatments (P ≥ 0.05), with the fulvic acid composite pine needle (FPN) treatment showing the largest increase in each index. The beta diversity differed significantly (P < 0.05) among all treatments, and the difference between citric acid-grass charcoal (CGC) and CK treatments was greater than that of other treatments. All treatments were effective in increasing the number of bacterial ASVs and affecting the structural composition of the community. Citric acid-cow manure (CCM), FPN, and CGC treatments were found to be beneficial for increasing the relative abundance of Proteobacteria, Chloroflexi, and Actinobacteria, respectively. By contrast, all treatments triggered a decrease in the relative abundance of Acidobacteria. Conclusions Among the 12 different combinations of exogenous organic acid composite biomass substrates applied to the coastal beach, the CGC treatment was more conducive to increasing the relative abundance of the salt-tolerant bacteria Proteobacteria, Chloroflexi and Actinobacteria, and improving the community structure of soil bacteria.The FPN treatment was more conducive to increase the species diversity of the soil bacterial community and adjust the species composition of the bacterial community.

Keywords: Mudflat soil, organic acid, Biological substrate, bacterial community structure, Soil microbial enhancement

Received: 27 Feb 2024; Accepted: 11 Apr 2024.

Copyright: © 2024 Liu, zhong, Yang, wang, Xinbao, xue, yang, Shen, Li and Sun. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Zhengguo Sun, Nanjing Agricultural University, Nanjing, China

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

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2022 National Healthcare Quality and Disparities Report

Introduction.

The  National Healthcare Quality and Disparities Re port  assesses the performance of our healthcare system and identifies areas of strengths and weaknesses, as well as disparities, for access to healthcare and quality of healthcare. Quality is described in terms of six priorities: patient safety, person-centered care, care coordination, effective treatment, healthy living, and care affordability. The report is based on more than 250 measures of quality and disparities covering a broad array of healthcare services and settings.

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Internet Citation: 2022 National Healthcare Quality and Disparities Report. Content last reviewed July 2023. Agency for Healthcare Research and Quality, Rockville, MD. https://www.ahrq.gov/research/findings/nhqrdr/nhqdr22/index.html