Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life

The human gut microbiome matures toward the adult composition during the first years of life and is implicated in early immune development. Here, we investigate the effects of microbial genomic diversity on gut microbiome development using integrated early childhood datasets collected in the DIABIMMUNE study in Finland, Estonia and Russian Karelia. We show that gut microbial diversity is associated with household location and linear growth of children. Single nucleotide polymorphism (SNP)- and metagenomic assembly-based strain tracking revealed large and highly dynamic microbial pangenomes, especially in the genus Bacteroides, in which we identified evidence of variability deriving from Bacteroides-targeting bacteriophages. Our analyses revealed functional consequences of strain diversity; only 10% of Finnish infants harbored Bifidobacterium longum subsp. infantis, a subspecies specialized in human milk metabolism, whereas Russian infants commonly maintained a probiotic Bifidobacterium bifidum strain in infancy. Groups of bacteria contributing to diverse, characterized metabolic pathways converged to highly subject-specific configurations over the first two years of life. This longitudinal study extends the current view of early gut microbial community assembly based on strain-level genomic variation.

Host genetic variation and its microbiome interactions within the Human Microbiome Project

Background

Despite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities. Although host genetic factors play a role in these interactions, these factors have remained relatively unexplored given the requirement for large population-based cohorts in which both genotyping and microbiome characterization have been performed.

Methods

We performed whole-genome sequencing of 298 donors from the Human Microbiome Project (HMP) healthy cohort study to accompany existing deep characterization of their microbiomes at various body sites. This analysis yielded an average sequencing depth of 32x, with which we identified 27 million (M) single nucleotide variants and 2.3 M insertions-deletions.

Results

Taxonomic composition and functional potential of the microbiome covaried significantly with genetic principal components in the gastrointestinal tract and oral communities, but not in the nares or vaginal microbiota. Example associations included validation of known associations between FUT2 secretor status, as well as a variant conferring hypolactasia near the LCT gene, with Bifidobacterium longum abundance in stool. The associations of microbial features with both high-level genetic attributes and single variants were specific to particular body sites, highlighting the opportunity to find unique genetic mechanisms controlling microbiome properties in the microbial communities from multiple body sites.

Conclusions

This study adds deep sequencing of host genomes to the body-wide microbiome sequences already extant from the HMP healthy cohort, creating a unique, versatile, and well-controlled reference for future studies seeking to identify host genetic modulators of the microbiome.

Electronic supplementary material

The online version of this article (10.1186/s13073-018-0515-8) contains supplementary material, which is available to authorized users.

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

BACKGROUND

Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes.

METHODS

We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn.

RESULTS

We found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of Ruminococcus gnavus in IBD patients, often co-occurring with increased disease activity. We identified two distinct clades of R. gnavus strains, one of which is enriched in IBD patients. To study functional differences between these two clades, we augmented the R. gnavus pangenome by sequencing nine isolates from IBD patients. We identified 199 IBD-specific, strain-specific genes involved in oxidative stress responses, adhesion, iron-acquisition, and mucus utilization, potentially conferring an adaptive advantage for this R. gnavus clade in the IBD gut.

CONCLUSIONS

This study adds further evidence to the hypothesis that increased oxidative stress may be a major factor shaping the dysbiosis of the microbiome observed in IBD and suggests that R. gnavus may be an important member of the altered gut community in IBD.

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

BACKGROUND

Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes.

METHODS

We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn.

RESULTS

We found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of Ruminococcus gnavus in IBD patients, often co-occurring with increased disease activity. We identified two distinct clades of R. gnavus strains, one of which is enriched in IBD patients. To study functional differences between these two clades, we augmented the R. gnavus pangenome by sequencing nine isolates from IBD patients. We identified 199 IBD-specific, strain-specific genes involved in oxidative stress responses, adhesion, iron-acquisition, and mucus utilization, potentially conferring an adaptive advantage for this R. gnavus clade in the IBD gut.

CONCLUSIONS

This study adds further evidence to the hypothesis that increased oxidative stress may be a major factor shaping the dysbiosis of the microbiome observed in IBD and suggests that R. gnavus may be an important member of the altered gut community in IBD.

Human genetic variation and the gut microbiome in disease

Taxonomic and functional changes to the composition of the gut microbiome have been implicated in multiple human diseases. Recent microbiome genome-wide association studies reveal that variants in many human genes involved in immunity and gut architecture are associated with an altered composition of the gut microbiome. Although many factors can affect the microbial organisms residing in the gut, a number of recent findings support the hypothesis that certain host genetic variants predispose an individual towards microbiome dysbiosis. This condition, in which the normal microbiome population structure is disturbed, is a key feature in disorders of metabolism and immunity.

Single molecule RNA sequencing uncovers trans-splicing and improves annotations in Anopheles stephensi

Single molecule real-time (SMRT) sequencing has recently been used to obtain full-length cDNA sequences that improve genome annotation and reveal RNA isoforms. Here, we used one such method called isoform sequencing from Pacific Biosciences (PacBio) to sequence a cDNA library from the Asian malaria mosquito Anopheles stephensi. More than 600 000 full-length cDNAs, referred to as reads of insert, were identified. Owing to the inherently high error rate of PacBio sequencing, we tested different approaches for error correction. We found that error correction using Illumina RNA sequencing (RNA-seq) generated more data than using the default SMRT pipeline. The full-length error-corrected PacBio reads greatly improved the gene annotation of Anopheles stephensi: 4867 gene models were updated and 1785 alternatively spliced isoforms were added to the annotation. In addition, six trans-splicing events, where exons from different primary transcripts were joined together, were identified in An. stephensi. All six trans-splicing events appear to be conserved in Culicidae, as they are also found in Anopheles gambiae and Aedes aegypti. The proteins encoded by trans-splicing events are also highly conserved and the orthologues of these proteins are cis-spliced in outgroup species, indicating that trans-splicing may arise as a mechanism to rescue genes that broke up during evolution.

Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes

Y chromosomes control essential male functions in many species, including sex determination and fertility. However, because of obstacles posed by repeat-rich heterochromatin, knowledge of Y chromosome sequences is limited to a handful of model organisms, constraining our understanding of Y biology across the tree of life. Here, we leverage long single-molecule sequencing to determine the content and structure of the nonrecombining Y chromosome of the primary African malaria mosquito, Anopheles gambiae We find that the An. gambiae Y consists almost entirely of a few massively amplified, tandemly arrayed repeats, some of which can recombine with similar repeats on the X chromosome. Sex-specific genome resequencing in a recent species radiation, the An. gambiae complex, revealed rapid sequence turnover within An. gambiae and among species. Exploiting 52 sex-specific An. gambiae RNA-Seq datasets representing all developmental stages, we identified a small repertoire of Y-linked genes that lack X gametologs and are not Y-linked in any other species except An. gambiae, with the notable exception of YG2, a candidate male-determining gene. YG2 is the only gene conserved and exclusive to the Y in all species examined, yet sequence similarity to YG2 is not detectable in the genome of a more distant mosquito relative, suggesting rapid evolution of Y chromosome genes in this highly dynamic genus of malaria vectors. The extensive characterization of the An. gambiae Y provides a long-awaited foundation for studying male mosquito biology, and will inform novel mosquito control strategies based on the manipulation of Y chromosomes.

Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution

The Asian tiger mosquito, Aedes albopictus, is a highly successful invasive species that transmits a number of human viral diseases, including dengue and Chikungunya fevers. This species has a large genome with significant population-based size variation. The complete genome sequence was determined for the Foshan strain, an established laboratory colony derived from wild mosquitoes from southeastern China, a region within the historical range of the origin of the species. The genome comprises 1,967 Mb, the largest mosquito genome sequenced to date, and its size results principally from an abundance of repetitive DNA classes. In addition, expansions of the numbers of members in gene families involved in insecticide-resistance mechanisms, diapause, sex determination, immunity, and olfaction also contribute to the larger size. Portions of integrated flavivirus-like genomes support a shared evolutionary history of association of these viruses with their vector. The large genome repertory may contribute to the adaptability and success of Ae. albopictus as an invasive species.

Complete Dosage Compensation in Anopheles stephensi and the Evolution of Sex-Biased Genes in Mosquitoes

Complete dosage compensation refers to hyperexpression of the entire X or Z chromosome in organisms with heterogametic sex chromosomes (XY male or ZW female) in order to compensate for having only one copy of the X or Z chromosome. Recent analyses suggest that complete dosage compensation, as in Drosophila melanogaster, may not be the norm. There has been no systematic study focusing on dosage compensation in mosquitoes. However, analysis of dosage compensation in Anopheles mosquitoes provides opportunities for evolutionary insights, as the X chromosome of Anopheles and that of its Dipteran relative, D. melanogaster formed independently from the same ancestral chromosome. Furthermore, Culicinae mosquitoes, including the Aedes genus, have homomorphic sex-determining chromosomes, negating the need for dosage compensation. Thus, Culicinae genes provide a rare phylogenetic context to investigate dosage compensation in Anopheles mosquitoes. Here, we performed RNA-seq analysis of male and female samples of the Asian malaria mosquito Anopheles stephensi and the yellow fever mosquito Aedes aegypti. Autosomal and X-linked genes in An. stephensi showed very similar levels of expression in both males and females, indicating complete dosage compensation. The uniformity of average expression levels of autosomal and X-linked genes remained when An. stephensi gene expression was normalized by that of their Ae. aegypti orthologs, strengthening the finding of complete dosage compensation in Anopheles. In addition, we comparatively analyzed the differentially expressed genes between adult males and adult females in both species, investigated sex-biased gene chromosomal distribution patterns in An. stephensi and provided three examples where gene duplications may have enabled the acquisition of sex-specific expression during mosquito evolution.

SEX DETERMINATION. A male-determining factor in the mosquito Aedes aegypti

Sex determination in the mosquito Aedes aegypti is governed by a dominant male-determining factor (M factor) located within a Y chromosome-like region called the M locus. Here, we show that an M-locus gene, Nix, functions as an M factor in A. aegypti. Nix exhibits persistent M linkage and early embryonic expression, two characteristics required of an M factor. Nix knockout with clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 resulted in largely feminized genetic males and the production of female isoforms of two key regulators of sexual differentiation: doublesex and fruitless. Ectopic expression of Nix resulted in genetic females with nearly complete male genitalia. Thus, Nix is both required and sufficient to initiate male development. This study provides a foundation for mosquito control strategies that convert female mosquitoes into harmless males.

Insights into the preservation of the homomorphic sex-determining chromosome of Aedes aegypti from the discovery of a male-biased gene tightly linked to the M-locus

The preservation of a homomorphic sex-determining chromosome in some organisms without transformation into a heteromorphic sex chromosome is a long-standing enigma in evolutionary biology. A dominant sex-determining locus (or M-locus) in an undifferentiated homomorphic chromosome confers the male phenotype in the yellow fever mosquito Aedes aegypti. Genetic evidence suggests that the M-locus is in a nonrecombining region. However, the molecular nature of the M-locus has not been characterized. Using a recently developed approach based on Illumina sequencing of male and female genomic DNA, we identified a novel gene, myo-sex, that is present almost exclusively in the male genome but can sporadically be found in the female genome due to recombination. For simplicity, we define sequences that are primarily found in the male genome as male-biased. Fluorescence in situ hybridization (FISH) on A. aegypti chromosomes demonstrated that the myo-sex probe localized to region 1q21, the established location of the M-locus. Myo-sex is a duplicated myosin heavy chain gene that is highly expressed in the pupa and adult male. Myo-sex shares 83% nucleotide identity and 97% amino acid identity with its closest autosomal paralog, consistent with ancient duplication followed by strong purifying selection. Compared with males, myo-sex is expressed at very low levels in the females that acquired it, indicating that myo-sex may be sexually antagonistic. This study establishes a framework to discover male-biased sequences within a homomorphic sex-determining chromosome and offers new insights into the evolutionary forces that have impeded the expansion of the nonrecombining M-locus in A. aegypti.

Six novel Y chromosome genes in Anopheles mosquitoes discovered by independently sequencing males and females

Background

Y chromosomes are responsible for the initiation of male development, male fertility, and other male-related functions in diverse species. However, Y genes are rarely characterized outside a few model species due to the arduous nature of studying the repeat-rich Y.

Results

The chromosome quotient (CQ) is a novel approach to systematically discover Y chromosome genes. In the CQ method, genomic DNA from males and females is sequenced independently and aligned to candidate reference sequences. The female to male ratio of the number of alignments to a reference sequence, a parameter called the chromosome quotient (CQ), is used to determine whether the sequence is Y-linked. Using the CQ method, we successfully identified known Y sequences from Homo sapiens and Drosophila melanogaster. The CQ method facilitated the discovery of Y chromosome sequences from the malaria mosquitoes Anopheles stephensi and An. gambiae. Comparisons to transcriptome sequence data with blastn led to the discovery of six Anopheles Y genes, three from each species. All six genes are expressed in the early embryo. Two of the three An. stephensi Y genes were recently acquired from the autosomes or the X. Although An. stephensi and An. gambiae belong to the same subgenus, we found no evidence of Y genes shared between the species.

Conclusions

The CQ method can reliably identify Y chromosome sequences using the ratio of alignments from male and female sequence data. The CQ method is widely applicable to species with fragmented genome assemblies produced from next-generation sequencing data. Analysis of the six Y genes characterized in this study indicates rapid Y chromosome evolution between An. stephensi and An. gambiae. The Anopheles Y genes discovered by the CQ method provide unique markers for population and phylogenetic analysis, and opportunities for novel mosquito control measures through the manipulation of sexual dimorphism and fertility.

Outcomes and reasons for dacryocystorhinostomy (DCR) at KCMC, a Tanzanian referral hospital, 2001-2006

BACKGROUND

External dacryocystorhinostomy (DCR) is a surgical intervention aimed to treat blocked nasolacrimal ducts of almost all causes. To date there is only limited data available from the Sub Saharan African setting.

OBJECTIVES

This study aimed to provide further information of the outcomes of DCR in Africa.

METHODS

Records of all patients undergoing external DCR operations from January 2001 to April 2006 were systematically searched. 55 patients were identified and notes were available for 45 patients.

RESULTS

Discharge and epiphora were resolved in 90.9% (30/33) and 84.4% (27/32) of patients respectively. Over half the cases (51.1%) were children. The commonest reason for operation was chronic dacryocystitis (51.1%). Outcomes for DCR were not significantly different for either children or adults and a clear improvement of symptoms was found in the vast majority of cases.

CONCLUSION

This study provides information on the outcomes of DCR in the African population. An 84.4% cure rate of epiphora and 90.9% cure rate of discharge is comparable with findings in other developing countries. This study supports the continued use of this intervention in skilled hands for treatment of blocked nasolacrimal duct.

Extent and economic effect of heat loads on dairy cattle production in Australia

OBJECTIVE

To investigate the extent of heat load problems, caused by the combination of excessive temperature and humidity, in Holstein-Friesian cows in Australia. Also, to outline how milk production losses and consequent costs from this can be estimated and minimised.

PROCEDURES

Long-term meteorological data for Australia were analysed to determine the distribution of hot conditions over space and time. Fifteen dairy production regions were identified for higher-resolution data analysis. Both the raw meteorological data and their integration into a temperature-humidity thermal index were compiled onto a computer program. This mapping software displays the distribution of climatic patterns, both Australia-wide and within the selected dairying regions. Graphical displays of the variation in historical records for 200 locations in the 15 dairying regions are also available. As a separate study, production data from research stations, on-farm trials and milk factory records were statistically analysed and correlated with the climatic indices, to estimate production losses due to hot conditions.

RESULTS

Both milk yields and milk constituents declined with increases in the temperature-humidity index. The onset and rate of this decline are dependent on a number of factors, including location, level of production, adaptation, and management regime. These results have been integrated into a farm-level economic analysis for managers of dairy properties.

CONCLUSION

By considering the historical patterns of hot conditions over time and space, along with expected production losses, managers of dairy farms can now conduct an economic evaluation of investment strategies to alleviate heat loads. These strategies include the provision of sprinklers, shade structures, or combinations of these.

Associations between lens features assessed in the Oxford Clinical Cataract Classification and Grading System

PURPOSE

To study the associations between eleven lens features graded according to the Oxford Clinical Cataract Classification and Grading System (OCCCGS).

METHOD

560 subjects taking part in the Melton Eye Study had their lenses graded according to the OCCCGS by one of two examiners. Associations between features were examined using log-linear models for categorised grades. Adjustment was made for age, sex and grader.

RESULTS

Within subjects, the two nuclear features, white nuclear scatter and brunescence, are closely related with one another, as are coronary flakes and focal-dots, but these two groupings are negatively associated. Cortical spoke, fibrefolds and waterclefts are all associated with one another and this group is positively associated with coronary flakes and focal-dots. Posterior subcapsular and anterior subcapsular opacity are associated with one another and with cortical spokes. A within-eye analysis gives similar results.

CONCLUSION

These associations may be important in defining cataract subtypes and in identifying minor features that indicate early cataract development.

LOCS III versus the Oxford Clinical Cataract Classification and Grading System for the assessment of nuclear, cortical and posterior subcapsular cataract

PURPOSE

To compare two methods of cataract grading for nuclear cataract, cortical cataract and posterior subcapsular cataract.

METHODS

The Melton Eye Study is an English community-based epidemiological study of the natural history of eye disease in people aged 55 to 74 years. The lenses of both eyes of 560 subjects were graded at the slit lamp using two cataract grading systems. The Oxford Clinical Cataract Classification and Grading System (OCCCGS) employs standard diagrams and Munsell colour samples for the grading of cortical, posterior subcapsular and nuclear cataract. The Lens Opacities Classification System III (LOCS III) uses photographic transparencies of the lens as standards. In both systems a decimalised score is assigned. We also graded the LOCS III standard images using the OCCCGS. Interobserver variation was calculated for both grading systems. Linear calibration lines are plotted for each type of lens opacity.

RESULTS

The relationship between LOCS III and OCCCGS for nuclear cataract and posterior subcapsular cataract is linear. The relationship for cortical cataract is linear once the LOCS III scores are squared. The intervals between the LOCS III images when ranked by the human eye using the OCCCGS are linear. Interobserver variation for both systems is good.

CONCLUSIONS

The linear calibration lines may be used to convert from one system to another and will be useful in comparing studies or performing meta-analysis. These results show that data from cataract studies using different clinical grading schemes can be compared.

Prevalence of lenticular abnormalities in a population-based study: Oxford Clinical Cataract Grading in the Melton Eye Study

PURPOSE

To describe the distribution of the 11 features assessed by the Oxford Clinical Cataract Classification and Grading System (OCCCGS) in a population-based study.

METHODS

The Melton Eye Study is an English community-based epidemiological study of the natural history of eye disease in people aged 55 to 74 years. Both lenses of 560 subjects were graded at the slit lamp using a decimalised version of the OCCCGS. Subject prevalences were estimated by logistic regression and the extent, when present, against normal errors regression.

RESULTS

White nuclear scatter (WNS), brunescence, cortical spoke (CS), anterior subcapsular opacity (ASC), fibre folds (FF), waterclefts (WC) and perinuclear retro-dots all increased with age (p < 0.05). Posterior subcapsular opacity (PSC), vacuoles, focal dots (FD) and coronary flakes (CF) did not significantly increase with age. Subject prevalences of the features and the mean Oxford scores when present were: WNS (1.33), brunescence (0.88), CS 36% (0.34), PSC 11% (0.52), ASC 2% (0.53), FF 18% (0.53), WC 17% (0.29), retro-dots 11% (1.15), vacuoles 59% (0.43), FD 98% (1.79) and CF 39% (1.24). Significantly more common in women were both coronary flakes (p < 0.001) and waterclefts (p < 0.05).

CONCLUSIONS

These are the first data on the distribution of these minor lesions in a population-based study. Coronary flakes and waterclefts are more common in women.

Innovative clinical teaching

Participating faculty are entering their third year using this type of student rotation and have found that it continues to be a positive teaching-learning experience for faculty, staff, and students. It has enabled a greater number of students to enjoy a positive clinical experience in areas that previously were limited to a smaller number of students. Perhaps this strategy, or a part of it, may be of benefit to other nurse educators as a method of improving undergraduate clinical experiences.

A thermodynamic view of polymer degradation, and its application to extensive sonication of DNA

A simple thermodynamic theory is developed, which predicts (in agreement with a wide variety of other theoretical approaches and experimental results) that for simple polymers the most probable Schulz distribution of fragments will be obtained in a polymer degradation process that is allowed to proceed to a dynamic equilibrium. When the same method is applied to a double-stranded polymer like DNA, however, it predicts that some narrowing of this distribution may occur in conjunction with a limited amount of base unpairing at the fragment termini. The compatibility of this prediction with the experimental results of long-time sonication of DNA is considered.