Farm-to-fork profiling of bacterial communities associated with an artisan cheese production facility.

The various stages of the cheese-making process harbor distinct bacterial communities which may influence the sensory characteristics of artisanal cheeses. The objective of this study was to investigate the microbiota from dairy farm to final cheeses along an artisanal cheese-making continuum. Environmental and food samples were collected from 21 sites, including the dairy farm, milk, cheese plant, and finished cheeses. The microbiota of these samples were analyzed using 16S rRNA amplicon sequencing, with sequences grouped into operational taxonomic units (OTUs) by phylotype at the genus level. Alpha diversity decreased from dairy farm to finished cheese. Firmicutes was the dominant phylum, ranging from 31% to 92% between the dairy farm and finished cheeses, respectively, with Proteobacteria, Actinobacteria, and Bacteroides also present (25%, 11%, and 9% overall relative abundance, respectively). Of the 37 core OTUs (>5 reads in >80% of site replicates) observed in cheese, 32 were shared with the dairy farm. Starter-related genera (i.e., Lactococcus, Lactobacillus, Streptococcus, and Leuconostoc) represented between 69% and 98% relative abundance in final cheeses depending on style, with the remainder likely acquired from various environmental sources on the farm and during the cheese-making process.

Citrobacter rodentium: infection, inflammation and the microbiota.

Citrobacter rodentium is a mucosal pathogen of mice that shares several pathogenic mechanisms with enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC), which are two clinically important human gastrointestinal pathogens. Thus, C. rodentium has long been used as a model to understand the molecular basis of EPEC and EHEC infection in vivo. In this Review, we discuss recent studies in which C. rodentium has been used to study mucosal immunology, including the deregulation of intestinal inflammatory responses during bacteria-induced colitis and the role of the intestinal microbiota in mediating resistance to colonization by enteric pathogens. These insights should help to elucidate the roles of mucosal inflammatory responses and the microbiota in the virulence of enteric pathogens.

Effects of antibiotics on human microbiota and subsequent disease.

Although antibiotics have significantly improved human health and life expectancy, their disruption of the existing microbiota has been linked to significant side effects such as antibiotic-associated diarrhea, pseudomembranous colitis, and increased susceptibility to subsequent disease. By using antibiotics to break colonization resistance against Clostridium, Salmonella, and Citrobacter species, researchers are now exploring mechanisms for microbiota-mediated modulation against pathogenic infection, revealing potential roles for different phyla and family members as well as microbiota-liberated sugars, hormones, and short-chain fatty acids in regulating pathogenicity. Furthermore, connections are now being made between microbiota dysbiosis and a variety of different diseases such as rheumatoid arthritis, inflammatory bowel disease, type 1 diabetes, atopy, and obesity. Future advances in the rapidly developing field of microbial bioinformatics will enable researchers to further characterize the mechanisms of microbiota modulation of disease and potentially identify novel therapeutics against disease.

Recent advances in understanding enteric pathogenic Escherichia coli.

Although Escherichia coli can be an innocuous resident of the gastrointestinal tract, it also has the pathogenic capacity to cause significant diarrheal and extraintestinal diseases. Pathogenic variants of E. coli (pathovars or pathotypes) cause much morbidity and mortality worldwide. Consequently, pathogenic E. coli is widely studied in humans, animals, food, and the environment. While there are many common features that these pathotypes employ to colonize the intestinal mucosa and cause disease, the course, onset, and complications vary significantly. Outbreaks are common in developed and developing countries, and they sometimes have fatal consequences. Many of these pathotypes are a major public health concern as they have low infectious doses and are transmitted through ubiquitous mediums, including food and water. The seriousness of pathogenic E. coli is exemplified by dedicated national and international surveillance programs that monitor and track outbreaks; unfortunately, this surveillance is often lacking in developing countries. While not all pathotypes carry the same public health profile, they all carry an enormous potential to cause disease and continue to present challenges to human health. This comprehensive review highlights recent advances in our understanding of the intestinal pathotypes of E. coli.

Microbiology: EHEC downregulates virulence in response to intestinal fucose.

Recent work has revealed that enterohaemorrhagic Escherichia coli encodes a two-component system, termed FusKR, which responds to fucose and represses expression of virulence genes. Furthermore, a representative member of the microbiota appears to cleave fucose from host glycans, indicating that the microbiota and EHEC may act in concert to suppress virulence gene expression.

Enteric pathogen exploitation of the microbiota-generated nutrient environment of the gut.

Residing within the intestine is a large community of commensal organisms collectively termed the microbiota. This community generates a complex nutrient environment by breaking down indigestible food products into metabolites that are used by both the host and the microbiota. Both the invading intestinal pathogen and the microbiota compete for these metabolites, which can shape both the composition of the flora, as well as susceptibility to infection. After infection is established, pathogen mediated inflammation alters the composition of the microbiota, which further shifts the makeup of metabolites in the gastrointestinal tract. A greater understanding of the interplay between the microbiota, the metabolites they generate, and susceptibility to enteric disease will enable the discovery of novel therapies against infectious disease.

Generation of branched-chain fatty acids through lipoate-dependent metabolism facilitates intracellular growth of Listeria monocytogenes.

The gram-positive bacterial pathogen Listeria monocytogenes has evolved mechanisms to rapidly replicate in the host cytosol, implying efficient utilization of host-derived nutrients. However, the contribution of host nutrient scavenging versus that of bacterial biosynthesis toward rapid intracellular growth remains unclear. Nutrients that contribute to growth of L. monocytogenes include branched-chain fatty acids (BCFAs), amino acids, and other metabolic intermediates generated from acyl-coenzyme A, which is synthesized using lipoylated metabolic enzyme complexes. To characterize which biosynthetic pathways support replication of L. monocytogenes inside the host cytosol, we impaired lipoate-dependent metabolism by disrupting two lipoate ligase genes that are responsible for bacterial protein lipoylation. Interrupting lipoate-dependent metabolism modestly impaired replication in rich broth medium but strongly inhibited growth in defined medium and host cells and impaired the generation of BCFAs. Addition of short BCFAs and amino acids restored growth of the A1A2-deficient (A1A2-) mutant in minimal medium, implying that lipoate-dependent metabolism generates amino acids and BCFAs. BCFAs alone rescued intracellular growth and spread in L2 fibroblasts of the A1A2- mutant. Lipoate-dependent metabolism was also required in vivo, as a wild-type strain robustly outcompeted the lipoylation-deficient mutant in a murine model of listeriosis. The results of this study suggest that lipoate-dependent metabolism contributes to both amino acid and BCFA biosynthesis and that BCFA biosynthesis is preferentially required for intracellular growth of L. monocytogenes.

LplA1-dependent utilization of host lipoyl peptides enables Listeria cytosolic growth and virulence.

The bacterial pathogen Listeria monocytogenes replicates within the cytosol of mammalian cells. Mechanisms by which the bacterium exploits the host cytosolic environment for essential nutrients are poorly defined. L. monocytogenes is a lipoate auxotroph and must scavenge this critical cofactor, using lipoate ligases to facilitate attachment of the lipoyl moiety to metabolic enzyme complexes. Although the L. monocytogenes genome encodes two putative lipoate ligases, LplA1 and LplA2, intracellular replication and virulence require only LplA1. Here we show that LplA1 enables utilization of host-derived lipoyl peptides by L. monocytogenes. LplA1 is dispensable for growth in the presence of free lipoate, but necessary for growth on low concentrations of mammalian lipoyl peptides. Furthermore, we demonstrate that the intracellular growth defect of the DeltalplA1 mutant is rescued by addition of exogenous lipoic acid to host cells, suggesting that L. monocytogenes dependence on LplA1 is dictated by limiting concentrations of available host lipoyl substrates. Thus, the ability of L. monocytogenes and other intracellular pathogens to efficiently use host lipoyl peptides as a source of lipoate may be a requisite adaptation for life within the mammalian cell.

Phenotypic characterization of a glucose transporter null mutant in Leishmania mexicana.

Glucose is a major source of energy and carbon in promastigotes of Leishmania mexicana, and its uptake is mediated by three glucose transporters whose genes are encoded within a single cluster. A null mutant in which the glucose transporter gene cluster was deleted by homologous gene replacement was generated previously and shown to grow more slowly than wild type promastigotes but not to be viable as amastigotes in primary tissue culture macrophages or in axenic culture. Further phenotypic characterization demonstrates that the null mutant is unable to import glucose, mannose, fructose, or galactose and that each of the three glucose transporter isoforms, LmGT1, LmGT2, and LmGT3, is capable of transporting each of these hexoses. Complementation of the null mutant with each isoform is able to restore growth in each of the four hexoses to wild type levels. Null mutant promastigotes are reduced in size to about 2/3 the volume of wild type parasites. In addition, the null mutants are significantly more sensitive to oxidative stress than their wild type counterparts. These results underscore the importance of glucose transporters in the parasite life cycle and suggest reasons for their non-viability in the disease-causing amastigote stage.