Janet E. Hill

Bio: Janet E. Hill is an academic researcher from University of Saskatchewan. The author has contributed to research in topics: Microbiome & Bacterial vaginosis. The author has an hindex of 44, co-authored 172 publications receiving 5761 citations. Previous affiliations of Janet E. Hill include National Research Council & University of Illinois at Urbana–Champaign.

cpnDB: a chaperonin sequence database.

Abstract: The advent of genome-scale sequencing projects has led to the availability of full-genome sequences for a variety of organisms including eukaryotes, bacteria, and archaea. This data is an invaluable resource for studies of genome-scale evolutionary processes such as lateral gene transfer and organelle evolution, as well as providing fuel for debates surrounding topics such as the definition of “species,” particularly in the microbial world (Perna et al. 2001). NCBI currently lists 155 complete microbial genomes from 138 bacteria and 17 archaeal species. Obviously, this limited selection inadequately represents the vast microbial diversity present in the environment. As a result of this limitation, large collections of gene-specific sequence data, particularly from universal genes, are an important resource. Historically, small subunit ribosomal RNA (16S rRNA) sequences have been the primary resource for phylogenetic studies and for sequence-based taxonomy (Olsen et al. 1986; Woese et al. 1990; Cole et al. 2003). Given our current understanding of the dynamic nature of genomes and the impact of lateral gene transfer on genome evolution (Boucher et al. 2003), it is important that our view of taxonomy and phylogenetics be informed by more than one target. A comparison of the sequences of the Escherichia coli groEL gene, which encodes a protein identified as being essential for the posttranslational assembly of bacteriophage particles and the Rubisco subunit-binding protein of higher plant chloroplasts, led to the discovery that these two proteins represent a ubiquitous protein family now known as the type I chaperonins (CPN60; Hemmingsen et al. 1988). “CPN60” is our preferred term for the type I chaperonins that are variously referred to in the literature as “GroEL,” “MopA,” and “Hsp60.” Among the bacterial and eukaryal organisms for which complete genome sequences are available, only the intracellular organisms Mycoplasma pulmonis and Ureaplasma urealyticum have been found to lack cpn60 genes. These organisms also lack other genes previously considered essential for prokaryotic life (Glass et al. 2000; Chambaud et al. 2001). Originally thought to be confined to the bacteria and eukaryotes, cpn60 genes have recently been identified in two members of the archaeal genus, Methanosarcina (Klunker et al. 2003). Multiple functions have been ascribed to CPN60. Whereas the primary intracellular role of CPN60 is thought to be as a molecular chaperone in the processes of posttranslational protein folding and assembly of protein complexes (for review, see Saibil and Ranson 2002), CPN60 also appears to function as an intercellular signaling molecule (for review, see Maguire et al. 2002). Bacterial and mitochondrial CPN60 complexes consist of homo-14mers, whereas plastid CPN60 complexes contain two subunit types. Multiple cpn60 genes are rare in bacteria but commonplace in eukaryotes, particularly in plants where the genomes contain genes for the mitochondrial cpn60, as well as the two chloroplast cpn60 subunits. For example, the model plant Arabidopsis thaliana contains a total of nine cpn60 genes, three mitochondrial, two chloroplast cpn60-α, and four chloroplast cpn60-β subunit genes (Hill and Hemmingsen 2001). The universal nature of cpn60 genes makes them attractive targets for phylogenetic studies (Viale and Arakaki 1994; Viale et al. 1994; Viale 1995; Bush and Everett 2001; Jian et al. 2001), as well as clinical tools for detection and identification of organisms (Goh et al. 1997, 1998, 2000; Dale et al. 1998; Kwok et al. 2002; Kwok and Chow 2003; Lew et al. 2003). An analysis of the cpn60 sequences from a variety of bacterial and eukaryotic species led to the design of universal, degenerate PCR primers, which can be applied for the amplification of a 549- to 567-bp region of cpn60 corresponding to nucleotides 274–828 of the E. coli cpn60 sequence from virtually any genome (Goh et al. 1996). The utility of this cpn60 “universal target” (UT) for discriminating closely related bacterial species has been established, and it has been demonstrated that the cpn60 UT region generally provides more discriminating and phylogenetically informative data than the 16S rDNA target (Marston et al. 1999; Brousseau et al. 2001). The ability to amplify the cpn60 UT from any genomic template has also facilitated the study of complex microbial communities, in which the UT region is amplified from a complex template and libraries of cloned UT sequences are created and sequenced (Hill et al. 2002). A number of the characteristics of the cpn60 gene and of the UT region offer significant advantages over 16S rDNA for studies of complex microbial populations and for quantitative assays. As protein-coding genes, cpn60 sequences are less constrained from sequence variation than are structural RNA-encoding genes. Furthermore, sequence variation extends quite uniformly throughout the cpn60 coding region, whereas variable regions of 16S rRNA genes are dispersed between regions of highly conserved sequence. Highly stable secondary structure that is associated with 16S rRNA is not present in cpn60 genes or transcripts. Generally, cpn60 genes are single copy in prokaryotic genomes, and the relatively small size of the UT facilitates high-throughput sequencing approaches. Our ongoing efforts to exploit cpn60 as a target for phylogenetic studies, microbial detection and identification, and microbial ecology have led us to gather and curate a large collection of cpn60 (Type I chaperonin) sequence data, as well as sequence from the archaeal thermosome (Type II chaperonin), a homolog of cpn60. To share this resource with the scientific community, we have designed and implemented a Web interface for cpnDB, a curated collection of cpn60 sequence data that is available at http://cpndb.cbr.nrc.ca.

Characterization of Intestinal Microbiota and Response to Dietary Virginiamycin Supplementation in the Broiler Chicken

Abstract: The inclusion of antibiotic growth promoters, such as virginiamycin, at subtherapeutic levels in poultry feeds has a positive effect on health and growth characteristics, possibly due to beneficial effects on the host gastrointestinal microbiota. To improve our understanding of the chicken gastrointestinal microbiota and the effect of virginiamycin on its composition, we characterized the bacteria found in five different gastrointestinal tract locations (duodenal loop, mid-jejunum, proximal ileum, ileocecal junction, and cecum) in 47-day-old chickens that were fed diets excluding or including virginiamycin throughout the production cycle. Ten libraries (five gastrointestinal tract locations from two groups of birds) of approximately 555-bp chaperonin 60 PCR products were prepared, and 10,932 cloned sequences were analyzed. A total of 370 distinct cpn60 sequences were identified, which ranged in frequency of recovery from 1 to 2,872. The small intestinal libraries were dominated by sequences from the Lactobacillales (90% of sequences), while the cecum libraries were more diverse and included members of the Clostridiales (68%), Lactobacillales (25%), and Bacteroidetes (6%). To assess the effects of virginiamycin on the gastrointestinal microbiota, 15 bacterial targets were enumerated using quantitative, real-time PCR. Virginiamycin was associated with increased abundance of many of the targets in the proximal gastrointestinal tract (duodenal loop to proximal ileum), with fewer targets affected in the distal regions (ileocecal junction and cecum). These findings provide improved profiling of the composition of the chicken intestinal microbiota and indicate that microbial responses to virginiamycin are most significant in the proximal small intestine.

Characterization of the vaginal microbiota of healthy Canadian women through the menstrual cycle

Abstract: The vaginal microbial community plays a vital role in maintaining women’s health. Understanding the precise bacterial composition is challenging because of the diverse and difficult-to-culture nature of many bacterial constituents, necessitating culture-independent methodology. During a natural menstrual cycle, physiological changes could have an impact on bacterial growth, colonization, and community structure. The objective of this study was to assess the stability of the vaginal microbiome of healthy Canadian women throughout a menstrual cycle by using cpn 60-based microbiota analysis. Vaginal swabs from 27 naturally cycling reproductive-age women were collected weekly through a single menstrual cycle. Polymerase chain reaction (PCR) was performed to amplify the universal target region of the cpn 60 gene and generate amplicons representative of the microbial community. Amplicons were pyrosequenced, assembled into operational taxonomic units, and analyzed. Samples were also assayed for total 16S rRNA gene content and Gardnerella vaginalis by quantitative PCR and screened for the presence of Mollicutes by using family and genus-specific PCR. Overall, the vaginal microbiome of most women remained relatively stable throughout the menstrual cycle, with little variation in diversity and only modest fluctuations in species richness. Microbiomes between women were more different than were those collected consecutively from individual women. Clustering of microbial profiles revealed the expected groupings dominated by Lactobacillus crispatus, Lactobacillus iners, and Lactobacillus jensenii. Interestingly, two additional clusters were dominated by either Bifidobacterium breve or a heterogeneous mixture of nonlactobacilli. Direct G. vaginalis quantification correlated strongly with its pyrosequencing-read abundance, and Mollicutes, including Mycoplasma hominis, Ureaplasma parvum, and Ureaplasma urealyticum, were detected in most samples. Our cpn 60-based investigation of the vaginal microbiome demonstrated that in healthy women most vaginal microbiomes remained stable through their menstrual cycle. Of interest in these findings was the presence of Bifidobacteriales beyond just Gardnerella species. Bifidobacteriales are frequently underrepresented in 16S rRNA gene-based studies, and their detection by cpn 60-based investigation suggests that their significance in the vaginal community may be underappreciated.

Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics

Abstract: With the continued interest in the role of the gut microbiota in health, attention has now turned to how to harness the microbiota for the benefit of the host. This Consensus Statement outlines the definition and scope of the term 'prebiotic' as determined by an expert panel convened by the International Scientific Association for Probiotics and Prebiotics in December 2016. In December 2016, a panel of experts in microbiology, nutrition and clinical research was convened by the International Scientific Association for Probiotics and Prebiotics to review the definition and scope of prebiotics. Consistent with the original embodiment of prebiotics, but aware of the latest scientific and clinical developments, the panel updated the definition of a prebiotic: a substrate that is selectively utilized by host microorganisms conferring a health benefit. This definition expands the concept of prebiotics to possibly include non-carbohydrate substances, applications to body sites other than the gastrointestinal tract, and diverse categories other than food. The requirement for selective microbiota-mediated mechanisms was retained. Beneficial health effects must be documented for a substance to be considered a prebiotic. The consensus definition applies also to prebiotics for use by animals, in which microbiota-focused strategies to maintain health and prevent disease is as relevant as for humans. Ultimately, the goal of this Consensus Statement is to engender appropriate use of the term 'prebiotic' by relevant stakeholders so that consistency and clarity can be achieved in research reports, product marketing and regulatory oversight of the category. To this end, we have reviewed several aspects of prebiotic science including its development, health benefits and legislation.

The role of the gut microbiota in nutrition and health

Abstract: The microbial communities that colonize different regions of the human gut influence many aspects of health. In the healthy state, they contribute nutrients and energy to the host via the fermentation of nondigestible dietary components in the large intestine, and a balance is maintained with the host's metabolism and immune system. Negative consequences, however, can include acting as sources of inflammation and infection, involvement in gastrointestinal diseases, and possible contributions to diabetes mellitus and obesity. Major progress has been made in defining some of the dominant members of the microbial community in the healthy large intestine, and in identifying their roles in gut metabolism. Furthermore, it has become clear that diet can have a major influence on microbial community composition both in the short and long term, which should open up new possibilities for health manipulation via diet. Achieving better definition of those dominant commensal bacteria, community profiles and system characteristics that produce stable gut communities beneficial to health is important. The extent of interindividual variation in microbiota composition within the population has also become apparent, and probably influences individual responses to drug administration and dietary manipulation. This Review considers the complex interplay between the gut microbiota, diet and health.

Food Animals and Antimicrobials: Impacts on Human Health

Abstract: Antimicrobials are valuable therapeutics whose efficacy is seriously compromised by the emergence and spread of antimicrobial resistance. The provision of antibiotics to food animals encompasses a wide variety of nontherapeutic purposes that include growth promotion. The concern over resistance emergence and spread to people by nontherapeutic use of antimicrobials has led to conflicted practices and opinions. Considerable evidence supported the removal of nontherapeutic antimicrobials (NTAs) in Europe, based on the "precautionary principle." Still, concrete scientific evidence of the favorable versus unfavorable consequences of NTAs is not clear to all stakeholders. Substantial data show elevated antibiotic resistance in bacteria associated with animals fed NTAs and their food products. This resistance spreads to other animals and humans-directly by contact and indirectly via the food chain, water, air, and manured and sludge-fertilized soils. Modern genetic techniques are making advances in deciphering the ecological impact of NTAs, but modeling efforts are thwarted by deficits in key knowledge of microbial and antibiotic loads at each stage of the transmission chain. Still, the substantial and expanding volume of evidence reporting animal-to-human spread of resistant bacteria, including that arising from use of NTAs, supports eliminating NTA use in order to reduce the growing environmental load of resistance genes.

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae.

Abstract: The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).