Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC DOI Creative Commons
Byron J. Smith, Chunyu Zhao, Veronika Dubinkina

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 10, 2024

Abstract Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity bacterial species within and across individuals. Even single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for causes consequences this intraspecific diversity. The enormous size pangenome references, strain mixing samples, inconsistent sequencing depth present challenges existing tools analyze samples one at time. To address gap, we updated MIDAS profiler, now released version 3, developed StrainPGC, an approach strain-specific content estimation combines tracking correlations multiple samples. We validate integrated analysis using complex synthetic community from find StrainPGC outperforms approaches. Analyzing large, publicly available metagenome collection inflammatory bowel disease patients healthy controls, catalog repertoires thousands hundreds capturing extensive missing reference databases. Finally, apply metagenomes clinical trial fecal microbiota transplantation treatment ulcerative colitis. identify two Escherichia coli donors both frequently transmitted patients, but notable potential. v3 together enable precise, pangenomic investigations large collections without microbial isolation or de novo assembly.

Language: Английский

Valeriana jatamansi root extract a potent source for biosynthesis of silver nanoparticles and their biomedical applications, and photocatalytic decomposition DOI Creative Commons

Pradisha Prem,

Selvam Naveenkumar, Chinnaperumal Kamaraj

et al.

Green Chemistry Letters and Reviews, Journal Year: 2024, Volume and Issue: 17(1)

Published: Feb. 2, 2024

This study aimed to synthesize silver nanoparticles (VJ@AgNPs) using Valeriana jatamansi root extract and assess their antibacterial, antioxidant, antibiofilm properties against Escherichia coli, Staphylococcus aureus, Streptococcus mutans. Various chemical physical characterization methods were employed analyze the synthesized VJ@AgNPs. UV-Visible spectroscopy confirmed presence of VJ@AgNPs with a peak absorption at 426 nm, while FT-IR results indicated involvement phyto-compounds from V. in reduction stabilization these nanoparticles. High-resolution transmission electron microscopy revealed well-dispersed spherical nature an average size 29.1 ± 2.06 X-ray diffraction crystalline structure. The biosynthesized exhibited significant antibacterial activity all tested pathogens, substantial inhibition zones 50 100 μg/mL concentrations. Additionally, displayed potent antioxidant capacity scavenging assays. Furthermore, showed promise photocatalytic degradation, effectively removing 95% RhB dye within 75 minutes under solar light irradiation, following pseudo-first-order kinetics. suggests potential application wastewater treatment for organic removal. biocompatible environmentally friendly underscores as therapeutic agents bacterial infections oxidative stress-related diseases.

Language: Английский

Citations

18

Sesamin Alleviates Allergen-Induced Diarrhea by Restoring Gut Microbiota Composition and Intestinal Barrier Function DOI

Li Yu,

Fan Wu, Yongli Wang

et al.

Journal of Agricultural and Food Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Food allergens are the key triggers of allergic diarrhea, causing damage to immune-rich ileum. This weakens mucosal barrier and tight junctions, increases intestinal permeability, exacerbates allergen exposure, thereby worsening condition. Sesamin, a natural lignan isolated from sesame seed, has shown potential in regulating immune responses, but its effects on health remain unclear. In this study, we constructed an ovalbumin (OVA)-induced diarrhea mouse model, which demonstrated increased mast cell degranulation, reduced junction integrity, impaired function. Pro-inflammatory cytokines were significantly ileum, along with unbalanced cluster differentiation 4 (CD4

Language: Английский

Citations

2

Review of Escherichia coli O157:H7 Prevalence, Pathogenicity, Heavy Metal and Antimicrobial Resistance, African Perspective DOI Creative Commons
Sydney M. Gambushe, Oliver T. Zishiri, Mohamed E. El Zowalaty

et al.

Infection and Drug Resistance, Journal Year: 2022, Volume and Issue: Volume 15, P. 4645 - 4673

Published: Aug. 1, 2022

Abstract: Escherichia coli O157:H7 is an important food-borne and water-borne pathogen that causes hemorrhagic colitis the hemolytic-uremic syndrome in humans may cause serious morbidity large outbreaks worldwide. People with bloody diarrhea have increased risk of developing complications such as acute renal failure neurological damage. The (HUS) a condition, up to 50% HUS patients can develop long-term dysfunction or blood pressure-related complications. Children aged two six years HUS. Clinical enteropathogenic (EPEC) infections show fever, vomiting, diarrhea. EPEC reservoir unknown but suggested be asymptomatic symptomatic child adult carrier. Spreading often through fecal-oral route. prevalence infants low, highly contagious children. disease children tends clinically more severe than other diarrheal infections. Some experience persistent lasts for 14 days. Enterotoxigenic (ETEC) strains are compelling problem disease. ETEC global concern bacteria leading watery traveler's It chronic affect development well-being Infections diarrheagenic E. common African countries. Antimicrobial agents should avoided phase since studies showed antimicrobial increase South National Veterinary Surveillance Monitoring Programme Resistance Drugs has reported resistance . Pathogenic bacterial developed variety due misuse. induced heavy metal tolerance also enhance resistance. depends on type agent, strain, dose, time, mode administration. Developing countries severely affected by poverty, lack proper hygiene, clean water, which lead limited treatment options Keywords: , O157:H, Shiga-toxins, hemolysin, LEE, metagenomic, PhiG17, verotoxin, zoonosis, One health, resistance, acid

Language: Английский

Citations

59

Antimicrobial Resistance: Two-Component Regulatory Systems and Multidrug Efflux Pumps DOI Creative Commons
Giuseppe Valerio De Gaetano, Germana Lentini, Agata Famà

et al.

Antibiotics, Journal Year: 2023, Volume and Issue: 12(6), P. 965 - 965

Published: May 26, 2023

The number of multidrug-resistant bacteria is rapidly spreading worldwide. Among the various mechanisms determining resistance to antimicrobial agents, multidrug efflux pumps play a noteworthy role because they export extraneous and noxious substrates from inside outside environment bacterial cell contributing (MDR) and, consequently, failure anti-infective therapies. expression can be under control transcriptional regulators two-component systems (TCS). TCS are major mechanism by which microorganisms sense reply external and/or intramembrane stimuli coordinating genes involved not only in pathogenic pathways but also antibiotic resistance. In this review, we describe influence on pump activity some Gram-negative Gram-positive bacteria. Taking into account strict correlation between pumps, development drugs targeting TCS, alone or together with already discovered inhibitors, may represent beneficial strategy contribute fight against growing

Language: Английский

Citations

41

Molecular Mechanisms of Shigella Pathogenesis; Recent Advances DOI Open Access
Babak Pakbin, Wolfram Manuel Brück, Thomas Brück

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(3), P. 2448 - 2448

Published: Jan. 26, 2023

Shigella species are the main cause of bacillary diarrhoea or shigellosis in humans. These organisms inhabitants human intestinal tract; however, they one concerns public health both developed and developing countries. In this study, we reviewed summarised previous studies recent advances molecular mechanisms pathogenesis Dysenteriae non-Dysenteriae species. Regarding presence virulence factor encoding genes strains, bacteria categorised into clinical groups. uses attachment, invasion, intracellular motility, toxin secretion host cell interruption mechanisms, causing mild diarrhoea, haemorrhagic colitis haemolytic uremic syndrome diseases humans through expression effector delivery systems, protein effectors, toxins, immune system evasion iron uptake genes. The investigation these can help us to develop design new methods detect differentiate food samples determine appropriate strategies prevent treat extraintestinal infections caused by enteric pathogens.

Language: Английский

Citations

28

Etiology and risk factors of hemorrhagic abomasitis in goat kids DOI Creative Commons
Hossein Esmaeili,

Saba Almasi Chegeni,

Seyed Mehdi Joghataei

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Feb. 20, 2025

Hemorrhagic abomasitis, also known as Salivary Abomasum Disease (SAD), is a largely under-researched condition affecting young lambs and kids, often leading to high mortality rates significant economic losses. The disease's etiopathogenesis, risk factors, clinical features remain poorly understood. Existing studies have been limited fragmented, misdiagnoses confusion about its true nature. Given the lack of comprehensive investigation into SAD's incidence, causative agents, this study aims provide thorough analysis through clinical, necropsy, histopathological, microbiological, molecular examinations. This involved 633 with 323 in SAD group 310 control group. A multifaceted approach was utilized, encompassing evaluations, necropsies, histopathological assessments, microbiological analyses, focusing on investigating virulence genes. During kidding season, deaths were linked SAD, mean disease duration 1.34 ± 0.54 days. highest incidence occurred 8–14 day age group, accounting for 51.7% cases (p < 0.05). dominant symptoms included weakness, lethargy, depression, failure suckle, reluctance move, significantly reduced mobility, unsteady gait, withdrawn demeanor. Necropsy findings consistently showed dark hemorrhagic content abomasum characteristic "coffee grain" lesions, no abnormalities other organs. Escherichia coli isolated 63% sampled more than controls 0.03), confirmed analysis. Examination genes highlighted presence hlyA, stx1, cnf1, stx2, eaeA complex combinations severe damage. Poor bed bottle hygiene identified primary factors 0.001), escalating later stages season farm conditions deteriorated. thoroughly re-evaluates abomasitis delivering valuable reliable insights fatal disease. Based it strongly indicates E. agent.

Language: Английский

Citations

1

Microplastic polymer properties as deterministic factors driving terrestrial plastisphere microbiome assembly and succession in the field DOI Creative Commons
Stephan Rohrbach, Gerasimos Gkoutselis, Linda Hink

et al.

Environmental Microbiology, Journal Year: 2022, Volume and Issue: 25(12), P. 2681 - 2697

Published: Oct. 13, 2022

Abstract Environmental microplastic (MP) is ubiquitous in aquatic and terrestrial ecosystems providing artificial habitats for microbes. Mechanisms of MP colonization, polymer impacts, effects on soil microbiomes are largely unknown systems. Therefore, we experimentally tested the hypothesis that type an important deterministic factor affecting community assembly by incubating common types situ landfill 14 months. 16S rRNA gene amplicon sequencing indicated polymers have specific impacts plastisphere microbiomes, which subsets microbiome. Chloroflexota, Gammaproteobacteria, certain Nitrososphaerota, Nanoarchaeota explained differences among time points. Plastisphere microbial composition derived from different diverged over was enriched potential pathogens. PICRUSt predictions pathway abundances quantitative PCR functional marker genes exerted ambivalent effect genetic potentials biogeochemical cycles. Overall, data indicate (i) as rather than stochastic factors drives assembly, (ii) greenhouse gas metabolism, xenobiotic degradation pathogen distribution, (iii) serves ideal model system studying fundamental questions ecology such mechanisms environments.

Language: Английский

Citations

36

Orally delivered single-domain antibodies against gastrointestinal pathogens DOI Creative Commons
Marcus Petersson, Sandra Wingaard Thrane, Lone Gram

et al.

Trends in biotechnology, Journal Year: 2023, Volume and Issue: 41(7), P. 875 - 886

Published: Feb. 9, 2023

Single-domain antibodies (sdAbs) are exceptionally stable fragments derived from the antigen-binding domains of immunoglobulins. They can withstand extreme pH, high temperature, and proteolysis, making them suitable for controlling gastrointestinal (GI) infections in humans animals. sdAbs may function their native soluble form, although different protein formats use delivery vehicles be useful improved oral delivery. We discuss selected examples orally delivered protecting animals against GI caused by pathogenic bacteria, viruses, parasites. finally provide perspectives on how applied industrially what challenges should overcome to reach market.

Language: Английский

Citations

21

Impact of short chain fatty acids (SCFAs) on antimicrobial activity of new β-lactam/β-lactamase inhibitor combinations and on virulence of Escherichia coli isolates DOI Creative Commons

Ashraf A. Kadry,

May A. El-Antrawy,

Amira M. El-Ganiny

et al.

The Journal of Antibiotics, Journal Year: 2023, Volume and Issue: 76(4), P. 225 - 235

Published: Feb. 1, 2023

Abstract In a healthy gut microbiota, short chain fatty acids (SCFAs) are produced. The antibacterial action of SCFAs against intestinal pathogens makes them useful for ensuring the safety food and human health. this study, we aimed to assess in vitro inhibitory activity SCFAs, report, first time, their impact on new β-lactam/β-lactamase inhibitor combinations. minimum concentrations acetic, propionic, butyric were determined E. coli clinical isolates recovered from gastrointestinal infections. Cefoperazone/sulbactam, ceftazidime/avibactam cefepime/enmetazobactam combinations that studied combined therapeutic effects. Also, effects pH concentration evaluated bacterial growth expression genes encoding motility, adhesion, invasion, biofilm formation. tested at 12 mM 7.4 (ileum-conditions), addition 60 123 mM, 6.5 (colon-conditions). showed same MIC (3750 μg ml −1 ≃ mM) all isolates. Furthermore, greatly restored susceptibility had significant effect virulence concentration-dependent manner; low ileal potentiated growth, while higher colonic significantly suppressed down-regulated ( fliC, ipaH, FimH, BssS ). Therefore, might lead development promising treatment strategies.

Language: Английский

Citations

18

Insights into antibiotic and heavy metal resistance interactions in Escherichia coli isolated from livestock manure and fertilized soil DOI

Yulan Tan,

Ke Zhao,

Shengzhi Yang

et al.

Journal of Environmental Management, Journal Year: 2023, Volume and Issue: 351, P. 119935 - 119935

Published: Dec. 27, 2023

Language: Английский

Citations

18