Where Next for Microbiome Research?

The development of high-throughput sequencing technologies has transformed our capacity to investigate the composition and dynamics of the microbial communities that populate diverse habitats. Over the past decade, these advances have yielded an avalanche of metagenomic data. The current stage of “van Leeuwenhoek”–like cataloguing, as well as functional analyses, will likely accelerate as DNA and RNA sequencing, plus protein and metabolic profiling capacities and computational tools, continue to improve. However, it is time to consider: what’s next for microbiome research? The short pieces included here briefly consider the challenges and opportunities awaiting microbiome research

Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences

Shotgun metagenomic sequencing reveals the potential in microbial communities. However, lower-cost 16S ribosomal RNA (rRNA) gene sequencing provides taxonomic, not functional, observations. To remedy this, we previously introduced Piphillin, a software package that predicts functional metagenomic content based on the frequency of detected 16S rRNA gene sequences corresponding to genomes in regularly updated, functionally annotated genome databases. Piphillin (and similar tools) have previously been evaluated on 16S rRNA data processed by the clustering of sequences into operational taxonomic units (OTUs). New techniques such as amplicon sequence variant error correction are in increased use, but it is unknown if these techniques perform better in metagenomic content prediction pipelines, or if they should be treated the same as OTU data in respect to optimal pipeline parameters

Strain level and comprehensive microbiome analysis in inflammatory bowel disease via multi-technology meta-analysis identifies key bacterial influencers of disease

Inflammatory bowel disease (IBD) is a heterogenous disease in which the microbiome has been shown to play an important role. However, the precise homeostatic or pathological functions played by bacteria remain unclear. Most published studies report taxa-disease associations based on single-technology analysis of a single cohort, potentially biasing results to one clinical protocol, cohort, and molecular analysis technology. To begin to address this key question, precise identification of the bacteria implicated in IBD across cohorts is necessary. We sought to take advantage of the numerous and diverse studies characterizing the microbiome in IBD to develop a multi-technology meta-analysis (MTMA) as a platform for aggregation of independently generated datasets, irrespective of DNA-profiling technique, in order to uncover the consistent microbial modulators of disease. We report the largest strain-level survey of IBD, integrating microbiome profiles from 3,407 samples from 21 datasets spanning 15 cohorts, three of which are presented for the first time in the current study, characterized using three DNA-profiling technologies, mapping all nucleotide data against known, culturable strain reference data. We identify several novel IBD associations with culturable strains that have so far remained elusive, including two genome-sequenced but uncharacterized Lachnospiraceae strains consistently decreased in both the gut luminal and mucosal contents of patients with IBD, and demonstrate that these strains are correlated with inflammation-related pathways that are known mechanisms targeted for treatment. Furthermore, comparative MTMA at the species versus strain level reveals that not all significant strain associations resulted in a corresponding species-level significance and conversely significant species associations are not always re-captured at the strain level. We propose MTMA for uncovering experimentally testable strain-disease associations that, as demonstrated here, are beneficial in discovering mechanisms underpinning microbiome impact on disease or novel targets for therapeutic interventions

Global, regional, and national burden of disorders affecting the nervous system, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021

BackgroundDisorders affecting the nervous system are diverse and include neurodevelopmental disorders, late-life neurodegeneration, and newly emergent conditions, such as cognitive impairment following COVID-19. Previous publications from the Global Burden of Disease, Injuries, and Risk Factor Study estimated the burden of 15 neurological conditions in 2015 and 2016, but these analyses did not include neurodevelopmental disorders, as defined by the International Classification of Diseases (ICD)-11, or a subset of cases of congenital, neonatal, and infectious conditions that cause neurological damage. Here, we estimate nervous system health loss caused by 37 unique conditions and their associated risk factors globally, regionally, and nationally from 1990 to 2021.MethodsWe estimated mortality, prevalence, years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs), with corresponding 95% uncertainty intervals (UIs), by age and sex in 204 countries and territories, from 1990 to 2021. We included morbidity and deaths due to neurological conditions, for which health loss is directly due to damage to the CNS or peripheral nervous system. We also isolated neurological health loss from conditions for which nervous system morbidity is a consequence, but not the primary feature, including a subset of congenital conditions (ie, chromosomal anomalies and congenital birth defects), neonatal conditions (ie, jaundice, preterm birth, and sepsis), infectious diseases (ie, COVID-19, cystic echinococcosis, malaria, syphilis, and Zika virus disease), and diabetic neuropathy. By conducting a sequela-level analysis of the health outcomes for these conditions, only cases where nervous system damage occurred were included, and YLDs were recalculated to isolate the non-fatal burden directly attributable to nervous system health loss. A comorbidity correction was used to calculate total prevalence of all conditions that affect the nervous system combined.FindingsGlobally, the 37 conditions affecting the nervous system were collectively ranked as the leading group cause of DALYs in 2021 (443 million, 95% UI 378–521), affecting 3·40 billion (3·20–3·62) individuals (43·1%, 40·5–45·9 of the global population); global DALY counts attributed to these conditions increased by 18·2% (8·7–26·7) between 1990 and 2021. Age-standardised rates of deaths per 100 000 people attributed to these conditions decreased from 1990 to 2021 by 33·6% (27·6–38·8), and age-standardised rates of DALYs attributed to these conditions decreased by 27·0% (21·5–32·4). Age-standardised prevalence was almost stable, with a change of 1·5% (0·7–2·4). The ten conditions with the highest age-standardised DALYs in 2021 were stroke, neonatal encephalopathy, migraine, Alzheimer's disease and other dementias, diabetic neuropathy, meningitis, epilepsy, neurological complications due to preterm birth, autism spectrum disorder, and nervous system cancer.InterpretationAs the leading cause of overall disease burden in the world, with increasing global DALY counts, effective prevention, treatment, and rehabilitation strategies for disorders affecting the nervous system are needed

Effect of thrombin and alpha-1-antitrypsin on mesenchymal cell proliferation and procollagen production

The mechanisms of tissue repair following injury are partially understood. Disruption of blood vessels results in the extravasation of blood derived proteins with subsequent platelet aggregation and fibrin clot formation. The repair processes that follow involve acute phase and inflammatory reactions, accompanied by extracellular matrix synthesis and remodelling. Mesenchymal cells are responsible for the latter processes which are thought to be co-ordinated by cytokines and growth factors. Aberrations in the proliferation and connective tissue metabolism by these cells can lead to the development of fibroproliferative disorders. Proteases and antiproteases play key roles in blood coagulation, inflammatory reactions and the subsequent repair processes. Two such molecules are thrombin and α1-antitrypsin (AAT). Thrombin, a serine protease involved in blood coagulation, also promotes mesenchymal cell chemotaxis and proliferation. It is therefore believed to play a role in tissue repair processes and fibrotic disorders in organs such as the lung, kidney and blood vessels. AAT on the other hand, is an acute phase serine protease inhibitor which protects tissues from the effects of neutrophil elastase. Increased levels of AAT have been associated with liver fibrosis, and its absence in the inflamed lung results in destruction of the connective tissue and emphysema. At present, AAT has not been reported to directly influence mesenchymal cell behaviour, and the effect of thrombin on collagen metabolism by these cells remains unexplored. The aim of this thesis was therefore to address the hypothesis that thrombin and AAT can play roles in tissue repair processes by directly activating mesenchymal cells. More specifically, the effects of thrombin and AAT on mesenchymal cell proliferation and procollagen metabolism were investigated. The results showed that thrombin stimulated fibroblast and smooth muscle cell procollagen production in a dose- and time-dependent manner. This stimulation occurs via increases in ?1(I) procollagen mRNA levels and requires de novo protein synthesis. Further, the mechanisms which mediate these stimulatory effects involve the proteolytic activation of the PAR-1 thrombin receptor, and preliminary experiments investigating the intracellular signalling pathways showed that tyrosine kinase- and PKC-linked pathways play a role in mediating these effects. In addition, this thesis reports for the first time, that AAT stimulated fibroblast proliferation and procollagen production. AAT also induced rapid protein tyrosine phosphorylation and the stimulatory effects on fibroblast proliferation were mediated via tyrosine kinase- and MAP kinase-linked pathways, suggesting that AAT exerts these stimulatory effects via a receptor mediated mechanism. In summary, this thesis demonstrates for the first time that thrombin stimulates mesenchymal cell procollagen production, and that AAT promotes fibroblast proliferation and procollagen production. It also partially characterises the mechanisms which mediate these stimulatory effects. These data support the hypothesis that thrombin and AAT can play a role in tissue repair processes by influencing mesenchymal cell proliferation and procollagen metabolism. This supports the view that proteases and antiproteases can exert similar effects to cytokines and growth factors and may form an additional mechanism by which connective tissue repair can be regulated