RESUMO
The current food production system is negatively impacting planetary and human health. A transition to a sustainable and fair food system is urgently needed. Microorganisms are likely enablers of this process, as they can produce delicious and healthy microbial foods with low environmental footprints. We review traditional and current approaches to microbial foods, such as fermented foods, microbial biomass, and food ingredients derived from microbial fermentations. We discuss how future advances in science-driven fermentation, synthetic biology, and sustainable feedstocks enable a new generation of microbial foods, potentially impacting the sustainability, resilience, and health effects of our food system.
Assuntos
Alimentos Fermentados , Microbiologia de Alimentos , Humanos , Fermentação , Alimentos , Crescimento Sustentável , Conservação dos Recursos NaturaisRESUMO
According to the hygiene hypothesis, the increasing incidence of autoimmune diseases in western countries may be explained by changes in early microbial exposure, leading to altered immune maturation. We followed gut microbiome development from birth until age three in 222 infants in Northern Europe, where early-onset autoimmune diseases are common in Finland and Estonia but are less prevalent in Russia. We found that Bacteroides species are lowly abundant in Russians but dominate in Finnish and Estonian infants. Therefore, their lipopolysaccharide (LPS) exposures arose primarily from Bacteroides rather than from Escherichia coli, which is a potent innate immune activator. We show that Bacteroides LPS is structurally distinct from E. coli LPS and inhibits innate immune signaling and endotoxin tolerance; furthermore, unlike LPS from E. coli, B. dorei LPS does not decrease incidence of autoimmune diabetes in non-obese diabetic mice. Early colonization by immunologically silencing microbiota may thus preclude aspects of immune education.
Assuntos
Bacteroides/imunologia , Diabetes Mellitus Tipo 1/imunologia , Microbioma Gastrointestinal , Lipopolissacarídeos/imunologia , Animais , Estônia , Fezes/microbiologia , Finlândia , Microbiologia de Alimentos , Humanos , Lactente , Camundongos , Camundongos Endogâmicos NOD , Leite Humano/imunologia , Federação RussaRESUMO
Microbial communities of fermented foods have provided humans with tools for preservation and flavor development for thousands of years. These simple, reproducible, accessible, culturable, and easy-to-manipulate systems also provide opportunities for dissecting the mechanisms of microbial community formation. Fermented foods can be valuable models for processes in less tractable microbiota.
Assuntos
Ecossistema , Fermentação , Microbiologia de Alimentos , Interações Microbianas , PaladarRESUMO
The gut microbiota features important genetic diversity, and the specific spatial features of the gut may shape evolution within this environment. We investigate the fixation probability of neutral bacterial mutants within a minimal model of the gut that includes hydrodynamic flow and resulting gradients of food and bacterial concentrations. We find that this fixation probability is substantially increased, compared with an equivalent well-mixed system, in the regime where the profiles of food and bacterial concentration are strongly spatially dependent. Fixation probability then becomes independent of total population size. We show that our results can be rationalized by introducing an active population, which consists of those bacteria that are actively consuming food and dividing. The active population size yields an effective population size for neutral mutant fixation probability in the gut.
Assuntos
Bactérias , Biodiversidade , Microbioma Gastrointestinal , Hidrodinâmica , Bactérias/genética , Evolução Biológica , Alimentos , Microbiologia de Alimentos , Humanos , Densidade Demográfica , RNA Ribossômico 16S/genéticaRESUMO
Listeria monocytogenes is a Gram-positive facultative intracellular pathogen that can cause severe invasive infections upon ingestion with contaminated food. Clinically, listerial disease, or listeriosis, most often presents as bacteremia, meningitis or meningoencephalitis, and pregnancy-associated infections manifesting as miscarriage or neonatal sepsis. Invasive listeriosis is life-threatening and a main cause of foodborne illness leading to hospital admissions in Western countries. Sources of contamination can be identified through international surveillance systems for foodborne bacteria and strains' genetic data sharing. Large-scale whole genome studies have increased our knowledge on the diversity and evolution of L. monocytogenes, while recent pathophysiological investigations have improved our mechanistic understanding of listeriosis. In this article, we present an overview of human listeriosis with particular focus on relevant features of the causative bacterium, epidemiology, risk groups, pathogenesis, clinical manifestations, and treatment and prevention.
Assuntos
Bacteriemia , Listeria monocytogenes , Listeriose , Gravidez , Feminino , Recém-Nascido , Humanos , Listeriose/epidemiologia , Listeriose/microbiologia , Listeriose/prevenção & controle , Listeria monocytogenes/genética , Fatores de Risco , Microbiologia de AlimentosRESUMO
Food irradiation can reduce foodborne illnesses but is rarely used in the United States. We determined whether outbreaks related to Campylobacter, Salmonella, Escherichia coli, and Listeria monocytogenes were linked to irradiation-eligible foods. Of 482 outbreaks, 155 (32.2%) were linked to an irradiation-eligible food, none of which were known to be irradiated.
Assuntos
Surtos de Doenças , Irradiação de Alimentos , Microbiologia de Alimentos , Doenças Transmitidas por Alimentos , Humanos , Estados Unidos/epidemiologia , Doenças Transmitidas por Alimentos/epidemiologia , Doenças Transmitidas por Alimentos/microbiologia , História do Século XXIRESUMO
The bacterial genus Hafnia has recently attracted attention due to its complex metabolic features and host-interaction capabilities, which are associated with health benefits, primarily weight loss. However, significant gaps remain in our understanding of the genomic characteristics of this emerging microbial group. In this study, we utilized all available high-quality genomes of Hafnia alvei and Hafnia paralvei to uncover the broad distribution of Hafnia in human and honeybee guts, as well as in dairy products, by analysing 1068 metagenomic datasets. We then investigated the genetic traits related to Hafnia's production of vitamins and short-chain fatty acids (SCFAs) through a comparative genomics analysis that included all dominant bacterial species in the three environments under study. Our findings underscore the extensive metabolic capabilities of Hafnia, particularly in the production of vitamins such as thiamine (B1), nicotinate (B3), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and menaquinone (K2). Additionally, Hafnia demonstrated a conserved genetic makeup associated with SCFA production, including acetate, propanoate, and butanoate. These metabolic traits were further confirmed using RNAseq analyses of a newly isolated H. paralvei strain T10. Overall, our study illuminates the ecological distribution and genetic attributes of this bacterial genus, which is of increasing scientific and industrial relevance.
Assuntos
Microbioma Gastrointestinal , Microbioma Gastrointestinal/genética , Humanos , Animais , Abelhas/microbiologia , Ácidos Graxos Voláteis/metabolismo , Genoma Bacteriano , Microbiologia de Alimentos , Metagenômica , Vitaminas/metabolismo , FilogeniaRESUMO
Pathogenic diseases that trigger food safety remain a noteworthy concern due to substantial public health, economic, and social burdens worldwide. It is vital for developing an integrated diagnosis and treatment strategy for bacteria, which could achieve quick detection of pathogenic bacteria and the inhibition of multidrug-resistant bacteria. Herein, we reported an organic molecule (M-3) possessed strong light capture capacity, emerging a low energy gap and ΔEST. Subsequently, M-3 was integrated into a nanostructured system (BTBNPs) with excellent ROS generation, light absorption capability, and photothermal performance. Reactive oxygen species (ROS) generated by BTBNPs were mainly free radicals from a type I mechanism, and the high photothermal conversion efficiency of BTBNPs was 41.26%. Benefiting from these advantages of BTBNPs, BTBNPs could achieve a â¼99% antibacterial effect for Escherichia coli O157:H7 with 20 µM dosage and 5 min of irradiation. Furthermore, the limit of detection (LoD) of the proposed BTBNPs-LFIA (colorimetric and photothermal modalities) for detecting E. coli O157:H7 was 4105 and 419 CFU mL-1, respectively. Overall, this work is expected to provide a new and sophisticated perspective for integrated diagnosis and treatment systems regarding pathogenic bacteria.
Assuntos
Escherichia coli O157 , Nanopartículas Multifuncionais , Microbiologia de Alimentos , Espécies Reativas de Oxigênio , Limite de DetecçãoRESUMO
Fully integrated devices that enable full functioning execution without or with minimum external accessories or equipment are deemed to be one of the most desirable and ultimate objectives for modern device design and construction. Escherichia coli O157:H7 (E. coli O157:H7) is often linked to outbreaks caused by contaminated water and food. However, the sensors that are currently used for point-of-care E. coli O157:H7 (E. coli O157:H7) detection are often large and cumbersome. Herein, we demonstrate the first example of a handheld and pump-free fully integrated electrochemical sensing platform with the capability to point-of-care test E. coli O157:H7 in the actual samples of E. coli O157:H7-spiked tap water and E. coli O157:H7-spiked watermelon juice. This platform was made possible by overcoming major engineering challenges in the seamless integration of a microfluidic module for pump-free liquid sample collection and transportation, a sensing module for efficient E. coli O157:H7 testing, and an electronic module for automatically converting and wirelessly transmitting signals into a single and compact electrochemical sensing platform that retains its inimitable stand-alone, handheld, pump-free, and cost-effective feature. Although our primary emphasis in this study is on detecting E. coli O157:H7, this pump-free fully integrated handheld electrochemical sensing platform may also be used to monitor other pathogens in food and water by including specific antipathogen antibodies.
Assuntos
Escherichia coli O157 , Anticorpos , Testes Imediatos , Sistemas Automatizados de Assistência Junto ao Leito , Água , Microbiologia de AlimentosRESUMO
Cronobacter sakazakii (C. sakazakii) is a widely existing opportunistic pathogen and thus threatens people with low immunity, especially infants. To prevent the outbreak, a rapid and accurate on-site testing method is required. The current standard culture-based method is time-consuming (3-4 days), while the nucleic acid amplification (PCR)-based detection is mostly carried out in central laboratories. Herein, isothermal recombinase polymerase amplification (RPA) coupled with a photosensitization colorimetric assay (PCA) was adopted for the on-site detection of C. sakazakii in powdered infant formulas (PIFs). The lowest visual detection concentration of C. sakazakii is 800 cfu/mL and 2 cfu/g after 8 h bacteria pre-enrichment. Furthermore, to avoid typical cap opening-resulted aerosol pollution, the PCA reagents were lyophilized onto the cap of the RPA tube (containing lyophilized RPA reagents). After amplification, the tube was subjected to simple shaking to mix the PCA reagents with the amplification products for light-driven color development. Such a one-tube assay offered a lowest concentration of 1000 copies of genomic DNA of C. sakazakii within 1 h. After 8 h of bacterial enrichment, the lowest detecting concentration could be pushed down to 5 cfu/g bacteria in PIF. To facilitate on-site monitoring, a portable, battery-powered PCA device was designed to mount the typical RPA 8-tube strip, and a color analysis cellphone APP was further employed for facile readout.
Assuntos
Cronobacter sakazakii , Lactente , Humanos , Animais , Pós , Colorimetria , Microbiologia de Alimentos , Recombinases , Leite/microbiologia , Fórmulas Infantis , NucleotidiltransferasesRESUMO
How timely identification and determination of pathogen species in pathogen-contaminated foods are responsible for rapid and accurate treatments for food safety accidents. Herein, we synthesize four aggregation-induced emissive nanosilicons with different surface potentials and hydrophobicities by encapsulating four tetraphenylethylene derivatives differing in functional groups. The prepared nanosilicons are utilized as receptors to develop a nanosensor array according to their distinctive interactions with pathogens for the rapid and simultaneous discrimination of pathogens. By coupling with machine-learning algorithms, the proposed nanosensor array achieves high performance in identifying eight pathogens within 1 h with high overall accuracy (93.75-100%). Meanwhile, Cronobacter sakazakii and Listeria monocytogenes are taken as model bacteria for the quantitative evaluation of the developed nanosensor array, which can successfully distinguish the concentration of C. sakazakii and L. monocytogenes at more than 103 and 102 CFU mL-1, respectively, and their mixed samples at 105 CFU mL-1 through the artificial neural network. Moreover, eight pathogens at 1 × 104 CFU mL-1 in milk can be successfully identified by the developed nanosensor array, indicating its feasibility in monitoring food hazards.
Assuntos
Microbiologia de Alimentos , Listeria monocytogenes , Aprendizado de Máquina , Listeria monocytogenes/isolamento & purificação , Cronobacter sakazakii/isolamento & purificação , Dióxido de Silício/química , Sistemas Automatizados de Assistência Junto ao Leito , Animais , Leite/microbiologia , Leite/química , Técnicas Biossensoriais , Redes Neurais de ComputaçãoRESUMO
The emergence of nanoenzymes has catalyzed the robust advancement of the lateral flow immunoassay (LFIA) in recent years. Among them, multifunctional nanocomposite enzymes with core-shell architectures are considered preferable for promoting the sensing ability due to their good biocompatibility, precise control over size, and surface properties etc. Herein, we developed a dual-channel ensured lateral flow immunoassay (DFLIA) platform utilizing a magnetic, colorimetric, and catalytic multifunctional nanocomposite enzyme (Fe3O4@TCPP@Pd) [TCPP, Tetrakis (4-carboxyphenyl) porphyrin] for the ultrasensitive and highly accurate rapid detection of Escherichia coli O157:H7 (E. coli O157:H7). Fe3O4@TCPP@Pd-mAb exhibits superior performance compared to traditional AuNPs, including enhanced sensitivity and an extended linear detection range, benefiting from its high brightness signal, strong magnetic separation ability, and high peroxidase activity (Vmax = 2.32 µM S1-). Moreover, the Fe3O4@TCPP@Pd-labeled mAb probe exhibited exceptional stability and high affinity toward E. coli O157:H7 (with an affinity constant of approximately 1.723 × 109 M-1), indicating its potential for the efficient capture of the pathogen. Impressively, the developed Fe3O4@TCPP@Pd-DFLIA achieved ultrasensitive detection for E. coli O157:H7 with pre- and postcatalytic naked-eye detection sensitivities of 255 cfu/mL and 77 cfu/mL, respectively, representing an approximately 41-fold improvement over the conventional AuNP-based LFIA and also possessed good specificity and reproducibility [relative standard deviation (RSD) < 10%]. Additionally, the established DFLIA exhibited satisfactory recoveries in detecting pork and milk samples, further validating the reliability of this platform for immunoassays and demonstrating its potential for utilization in bioassays and clinical diagnostics.
Assuntos
Escherichia coli O157 , Nanopartículas Metálicas , Nanocompostos , Animais , Leite , Reprodutibilidade dos Testes , Ouro/química , Colorimetria , Nanopartículas Metálicas/química , Imunoensaio/métodos , Nanocompostos/química , Fenômenos Magnéticos , Microbiologia de AlimentosRESUMO
Escherichia coli O157:H7 is one of the most susceptible foodborne pathogens, easily causing food poisoning and other health risks. It is of great significance to establish a quantitative method with higher sensitivity and less time consumption for foodborne pathogens analysis. The Raman-silent signal has a good performance for avoiding interference from the food matrix so as to achieve accurate signal differentiation. In this work, we presented a preparation-mapping all-in-one method for digital mapping analysis. We prepared a functionalized Raman-silent polymer label of Escherichia coli O157:H7, which was captured on a porous 4-mercaptophenylboric acid@Ag foam chip. To improve accuracy and widen the detection range, a digital mapping quantitative strategy was employed in data extraction and processing. By transfer mapping information into digitized statistical results, the limitation of obtaining reproducible intensity values just by randomly selected spots on the substrate can be addressed. With a wide linear range of 1.0 × 101-1.0 × 105 CFU mL-1 and a limit of detection of 4.4 CFU mL-1, this all-in-one method had good sensitivity performance. Also, this method achieved good precision and selectivity in a series of experiments and was successfully applied to the analysis of beverage samples.
Assuntos
Bebidas , Escherichia coli O157 , Polímeros , Análise Espectral Raman , Escherichia coli O157/isolamento & purificação , Análise Espectral Raman/métodos , Bebidas/análise , Bebidas/microbiologia , Polímeros/química , Compostos de Boro/química , Microbiologia de Alimentos/métodos , Contaminação de Alimentos/análise , Compostos de Sulfidrila/química , Compostos de Sulfidrila/análise , Ácidos BorônicosRESUMO
Sensitive and on-site discrimination of live and dead foodborne pathogenic strains remains a significant challenge due to the lack of appropriate assay and signal probes. In this work, a versatile platinum nanoparticle-decorated phage nanozyme (P2@PtNPs) that integrated recognition, bacteriolysis, and catalysis was designed to establish the bioluminescence/pressure dual-mode bioassay for on-site determination of the vitality of foodborne pathogenic strains. Benefiting from the bacterial strain-level specificity of phage, the target Salmonella typhimurium (S.T) was specially captured to form sandwich complexes with P2@PtNPs on another phage-modified glass microbead (GM@P1). As the other part of the P2@PtNPs nanozyme, the introduced PtNPs could not only catalyze the decomposition of hydrogen peroxide to generate a significant oxygen pressure signal but also produce hydroxyl radicals around the target bacteria to enhance the bacteriolysis of phage and adenosine triphosphate release. It significantly improved the bioluminescence signal. The two signals corresponded to the total and live target bacteria counts, so the dead target could be easily calculated from the difference between the total and live target bacteria counts. Meanwhile, the vitality of S.T was realized according to the ratio of live and total S.T. Under optimal conditions, the application range of this proposed bioassay for bacterial vitality was 102-107 CFU/mL, with a limit of detections for total and live S.T of 30 CFU/mL and 40 CFU/mL, respectively. This work provides an innovative and versatile nanozyme signal probe for the on-site determination of bacterial vitality for food safety.
Assuntos
Bacteriófagos , Medições Luminescentes , Nanopartículas Metálicas , Platina , Salmonella typhimurium , Platina/química , Nanopartículas Metálicas/química , Salmonella typhimurium/isolamento & purificação , Salmonella typhimurium/virologia , Salmonella typhimurium/química , Catálise , Bacteriófagos/química , Microbiologia de Alimentos , Bioensaio/métodos , Técnicas Biossensoriais/métodos , Pressão , Peróxido de Hidrogênio/químicaRESUMO
In this study, the covalently fixed "end-on" orientation of a monoclonal Listeria monocytogenes antibody (mAb-Lis) to amino terminated oligo (ethylene glycol)-capped gold nanoparticles (NH2-TEG-AuNPs) was used to fabricate an in-house lateral flow strip (LFS), namely, the fixed "end-on" Lis-mAb-NH-TEG-AuNPs LFS. The aim was to evaluate the performance of the fixed "end-on" Lis-mAb-NH-TEG-AuNPs LFS in detecting L. monocytogenes. The proposed LFS enabled the sensitive detection of L. monocytogenes in 15 min with a visual limit of detection of 102 CFU/mL. Quantitative analysis indicated an LOD at 10 CFU/mL. The fixed "end-on" Lis-mAb-NH-TEG-AuNPs LFS showed no cross-reactivity with other pathogenic bacteria and practical performance across different food matrices, including human blood, milk, and mushroom samples. Furthermore, the clinical performance of the fixed "end-on" Lis-mAb-NH-TEG-AuNPs LFS for detecting L. monocytogenes was evaluated by using 12 clinical samples validated by the hemoculture method. It demonstrated excellent concordance with the reference methods, with no false-positive or false-negative results observed. Therefore, the fixed "end-on" Lis-mAb-NH-TEG-AuNPs LFS serves as a promising candidate for a point-of-care test (POCT), enabling the rapid, precise, and highly sensitive detection of L. monocytogenes in clinical samples and contaminated food.
Assuntos
Anticorpos Monoclonais , Ouro , Listeria monocytogenes , Nanopartículas Metálicas , Listeria monocytogenes/isolamento & purificação , Listeria monocytogenes/imunologia , Ouro/química , Nanopartículas Metálicas/química , Anticorpos Monoclonais/imunologia , Anticorpos Monoclonais/química , Humanos , Limite de Detecção , Microbiologia de Alimentos , Leite/microbiologia , Leite/química , Anticorpos Antibacterianos/química , Anticorpos Antibacterianos/imunologia , Anticorpos Imobilizados/química , Anticorpos Imobilizados/imunologia , Animais , Listeriose/microbiologia , Listeriose/diagnósticoRESUMO
tGrowth of microorganisms and interpretation of growth data are core skills required by microbiologists. While science moves forward, it is of paramount importance that essential skills are not lost. The bacterial growth curve and the information that can gleaned from it is of great value to all of microbiology, whether this be a simple growth experiment, comparison of mutant strains or the establishment of conditions for a large-scale multi-omics experiment. Increasingly, the basics of plotting and interpreting growth curves and growth data are being overlooked. This primer article serves as a refresher for microbiologists on the fundamentals of microbial growth kinetics.
Assuntos
Microbiologia de Alimentos , CinéticaRESUMO
Salmonella enterica subsp. enterica Typhimurium and its monophasic variant I 1;4,[5],12:i:- (MVST) are responsible for thousands of reported cases of salmonellosis each year in Canada, and countries worldwide. We investigated S. Typhimurium and MVST isolates recovered from raw shellfish harvested in Atlantic Canada by the Canadian Food Inspection Agency (CFIA) over the past decade, to assess the potential impact of these isolates on human illness and to explore possible routes of shellfish contamination. Whole-genome sequence analysis was performed on 210 isolates of S. Typhimurium and MVST recovered from various food sources, including shellfish. The objective was to identify genetic markers linked to ST-99, a sequence type specifically associated with shellfish, which could explain their high prevalence in shellfish. We also investigated the genetic similarity amongst CFIA ST-99 isolates recovered in different years and geographical locations. Finally, the study aimed to enhance the molecular serotyping of ST-99 isolates, as they are serologically classified as MVST but are frequently misidentified as S. Typhimurium through sequence analysis. To ensure recovery of ST-99 from shellfish was not due to favourable growth kinetics, we measured the growth rates of these isolates relative to other Salmonella and determined that ST-99 did not have a faster growth rate and/or shorter lag phase than other Salmonella evaluated. The CFIA ST-99 isolates from shellfish were highly clonal, with up to 81 high-quality single nucleotide variants amongst isolates. ST-99 isolates both within the CFIA collection and those isolated globally carried numerous unique deletions, insertions and mutations in genes, including some considered important for virulence, such as gene deletions in the type VI secretion system. Interestingly, several of these genetic characteristics appear to be unique to North America. Most notably was a large genomic region showing a high prevalence in genomes from Canadian isolates compared to those from the USA. Although the functions of the majority of the proteins encoded within this region remain unknown, the genes umuC and umuD, known to be protective against UV light damage, were present. While this study did not specifically examine the effects of mutations and insertions, results indicate that these isolates may be adapted to survive in specific environments, such as ocean water, where wild birds and/or animals serve as the natural hosts. Our hypothesis is reinforced by a global phylogenetic analysis, which indicates that isolates obtained from North American shellfish and wild birds are infrequently connected to isolates from human sources. These findings suggest a distinct ecological niche for ST-99, potentially indicating their specialization and adaptation to non-human hosts and environments, such as oceanic habitats.
Assuntos
Tipagem de Sequências Multilocus , Salmonella typhimurium , Frutos do Mar , Frutos do Mar/microbiologia , Salmonella typhimurium/genética , Salmonella typhimurium/isolamento & purificação , Salmonella typhimurium/classificação , Canadá , Sequenciamento Completo do Genoma , Animais , Humanos , Genoma Bacteriano , Microbiologia de Alimentos , FilogeniaRESUMO
Introduction. Leclercia adecarboxylata is a member of Enterobacterales, often considered an opportunistic pathogen. Recent reports have highlighted L. adecarboxylata as an emerging pathogen harbouring virulence and resistance determinants.Gap statement. Little information exists on virulence and resistance determinants in L. adecarboxylata strains isolated from environmental, food, and clinical samples.Aim. To determine the presence of resistance and virulence determinants and plasmid features in L. adecarboxylata strains isolated from environmental, food, and clinical samples, as well as their phylogenetic relationship.Results. All strains tested showed resistance to ß-lactams and quinolones but were sensitive to aminoglycosides and nitrofurans. However, even though fosfomycin resistance is considered a characteristic trait of L. adecarboxylata, the resistance phenotype was only observed in 50â% of the strains; bla TEM was the most prevalent BLEE gene (70â%), while the quinolone qnrB gene was observed in 60â% of the strains. Virulence genes were differentially observed in the strains, with adhesion-related genes being the most abundant, followed by toxin genes. Finally, all strains carried one to seven plasmid bands ranging from 7 to 125 kbps and harboured several plasmid addiction systems, such as ParDE, VagCD, and CcdAB in 80â% of the strains.Conclusions. L. adecarboxylata is an important emerging pathogen that may harbour resistance and virulence genes. Additionally, it has mobilizable genetic elements that may contribute to the dissemination of genetic determinants to other bacterial genera.
Assuntos
Antibacterianos , Enterobacteriaceae , Testes de Sensibilidade Microbiana , Filogenia , Plasmídeos , Fatores de Virulência , Antibacterianos/farmacologia , Plasmídeos/genética , Virulência/genética , Enterobacteriaceae/genética , Enterobacteriaceae/efeitos dos fármacos , Enterobacteriaceae/patogenicidade , Enterobacteriaceae/isolamento & purificação , Enterobacteriaceae/classificação , Fatores de Virulência/genética , Humanos , Infecções por Enterobacteriaceae/microbiologia , Fenótipo , Farmacorresistência Bacteriana/genética , Quinolonas/farmacologia , beta-Lactamas/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Microbiologia de AlimentosRESUMO
There is currently a transformed interest toward understanding the impact of fermentation on functional food development due to growing consumer interest on modified health benefits of sustainable foods. In this review, we attempt to summarize recent findings regarding the impact of Next-generation sequencing and other bioinformatics methods in the food microbiome and use prediction software to understand the critical role of microbes in producing fermented foods. Traditionally, fermentation methods and starter culture development were considered conventional methods needing optimization to eliminate errors in technique and were influenced by technical knowledge of fermentation. Recent advances in high-output omics innovations permit the implementation of additional logical tactics for developing fermentation methods. Further, the review describes the multiple functions of the predictions based on docking studies and the correlation of genomic and metabolomic analysis to develop trends to understand the potential food microbiome interactions and associated products to become a part of a healthy diet.
Assuntos
Alimentos Fermentados , Microbiota , Biologia Computacional , Fermentação , Microbiologia de Alimentos , Microbiota/genéticaRESUMO
Even though differences in methodology (e.g., sample volume and detection method) have been shown to affect observed microbial water quality, multiple sampling and laboratory protocols continue to be used for water quality monitoring. Research is needed to determine how these differences impact the comparability of findings to generate best management practices and the ability to perform meta-analyses. This study addresses this knowledge gap by compiling and analyzing a data set representing 2,429,990 unique data points on at least one microbial water quality target (e.g., Salmonella presence and Escherichia coli concentration). Variance partitioning analysis was used to quantify the variance in likelihood of detecting each pathogenic target that was uniquely and jointly attributable to non-methodological versus methodological factors. The strength of the association between microbial water quality and select methodological and non-methodological factors was quantified using conditional forest and regression analysis. Fecal indicator bacteria concentrations were more strongly associated with non-methodological factors than methodological factors based on conditional forest analysis. Variance partitioning analysis could not disentangle non-methodological and methodological signals for pathogenic Escherichia coli, Salmonella, and Listeria. This suggests our current perceptions of foodborne pathogen ecology in water systems are confounded by methodological differences between studies. For example, 31% of total variance in likelihood of Salmonella detection was explained by methodological and/or non-methodological factors, 18% was jointly attributable to both methodological and non-methodological factors. Only 13% of total variance was uniquely attributable to non-methodological factors for Salmonella, highlighting the need for standardization of methods for microbiological water quality testing for comparison across studies.IMPORTANCEThe microbial ecology of water is already complex, without the added complications of methodological differences between studies. This study highlights the difficulty in comparing water quality data from projects that used different sampling or laboratory methods. These findings have direct implications for end users as there is no clear way to generalize findings in order to characterize broad-scale ecological phenomenon and develop science-based guidance. To best support development of risk assessments and guidance for monitoring and managing waters, data collection and methods need to be standardized across studies. A minimum set of data attributes that all studies should collect and report in a standardized way is needed. Given the diversity of methods used within applied and environmental microbiology, similar studies are needed for other microbiology subfields to ensure that guidance and policy are based on a robust interpretation of the literature.