Yun Kit Yeoh

Australian Institute of Marine Science

The microbiota-gut-brain axis has been suggested to play an important role in Parkinson’s disease (PD). Here we performed a cross-sectional study to profile gut microbiota across early PD, REM sleep behavior disorder (RBD), first-degree relatives of RBD (RBD-FDR), and healthy controls, which could reflect the gut-brain staging model of PD. We show...

Aims: Sub-therapeutic use of antibiotics as a growth promoter in animal diets has either been banned or voluntarily withdrawn from use in many countries to help curb the emergence of antibiotic-resistant pathogens. Probiotics may be an alternative to antibiotics as a growth promoter. We investigated the effects of a novel probiotic strain Bacillus...

Obesity is associated with altered gut microbiome composition but data across different populations remain inconsistent. We meta-analyzed publicly available 16S-rRNA sequence datasets from 18 different studies and identified differentially abundant taxa and functional pathways of the obese gut microbiome. Most differentially abundant genera (Odorib...

Wolbachia are among the most prevalent and widespread endosymbiotic bacteria on earth. Wolbachia's success in infecting an enormous number of arthropod species is attributed to two features: the range of phenotypes they induce in their hosts, and their ability to switch between host species. Whilst much progress has been made in elucidating their i...

Irritable bowel syndrome (IBS) is a heterogeneous condition with multifactorial pathogenesis. We studied deeply phenotyped individuals with microbiota sequencing enrolled in the American Gut Project. The IBS subjects were matched by age, gender, body mass index, geography, and dietary patterns with non-IBS controls. A total of 942 subjects with IBS...

Systemic characterisation of the human faecal microbiome provides the opportunity to develop non-invasive approaches in the diagnosis of a major human disease. However, shared microbial signatures across different diseases make accurate diagnosis challenging in single-disease models. Herein, we present a machine-learning multi-class model using fae...

Objective We investigate interrelationships between gut microbes, metabolites, and cytokines that characterize COVID-19 and its complications, and validate the results with follow-up, Japanese 4D microbiome cohort, and non-Japanese datasets. Design We performed shotgun metagenomic sequencing and metabolomics on stools and cytokine measurements on...

Microplastics are recognised as a ubiquitous and hazardous pollutant worldwide. These small-sized particles have been detected in human faeces collected from a number of cities, providing evidence of human ingestion of microplastics and their presence in the gastrointestinal tract. Here, using Raman spectroscopy, we identified an average of 50 part...

Understanding the role of fecal microbiota transplantation (FMT) in the decolonization of multidrug-resistant organisms (MDRO) is critical. Specifically, little is known about virome changes in MDRO-infected subjects treated with FMT. Using shotgun metagenomic sequencing, we characterized longitudinal dynamics of the gut virome and bacteriome in th...

Prevotella species in the human gut microbiome are primarily comprised of Prevotella copri , and its diversity and function were recently investigated in detail. Much less is known about other Prevotella species in the human gut. Here, we examined the composition of Prevotella species in human guts by mapping publicly available gut metagenomes to a...

We report the antimicrobial resistance of 191 fish and 61 pork Group B Streptococcus (GBS) procured from Hong Kong wet markets. Two-hundred-and-fifty-two GBS strains were isolated from 992 freshwater fish and 361 pig offal during 2016–2019. The strains were isolated from homogenised samples and plated on selective media, followed by identification...

Wolbachia are among the most prevalent and widespread endosymbiotic bacteria on earth. Wolbachia’s success in infecting an enormous number of arthropod species is attributed to two features: the range of phenotypes they induce in their hosts, and their ability to switch between host species. Whilst much progress has been made in elucidating their i...

Background Long-term complications after COVID-19 are common, but the potential cause for persistent symptoms after viral clearance remains unclear. Objective To investigate whether gut microbiome composition is linked to post-acute COVID-19 syndrome (PACS), defined as at least one persistent symptom 4 weeks after clearance of the SARS-CoV-2 virus...

Background & aims: SARS-CoV-2 infection is associated with altered gut microbiota composition. Phylogenetic groups of gut bacteria involved in the metabolism of short chain fatty acids were depleted in SARS-CoV-2-infected patients. We aimed to characterize functional profile of gut microbiome in patients with COVID-19 before and after disease reso...

Eczema is a prevalent skin inflammatory disorder among paediatric populations in the globe. While recent studies suggested the importance of various skin microbes including S. aureus in the flare-up of childhood eczema, most of the studies were cross-sectional and it remains inconclusive if similar changes of the microbial composition govern the on...

Wolbachia are among the most prevalent and widespread endosymbiotic bacteria on earth. Wolbachia's success in infecting an enormous number of arthropod species is attributed to two features: the range of phenotypes they induce in their hosts, and their ability to switch to new host species. Whilst much progress has been made in elucidating the phen...

Objective The gut microbiota has been suggested to play a role in autism spectrum disorder (ASD). We postulate that children with ASD harbour an altered developmental profile of the gut microbiota distinct from that of typically developing (TD) children. Here, we aimed to characterise compositional and functional alterations in gut microbiome in as...

Background & aims: Obesity and type 2 diabetes mellitus (T2DM) are associated with changes in the gut bacterial composition, but little is known about the role of the viral community (virome) in disease development. This study aims to characterize the gut virome alterations in obese subjects with or without T2DM. Methods: 128 obese subjects (Bod...

Background Coronavirus disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from fecal samples, and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively kn...

Background: Legume crop rotation in sugarcane cropping systems can improve soil health and fertility. However, their impacts on soil microbial community composition and function have not been clearly understood to date. Aims: This study aimed to assess responses of soil biochemical properties and composition of microbial communities driving C and N...

Objective Although COVID-19 is primarily a respiratory illness, there is mounting evidence suggesting that the GI tract is involved in this disease. We investigated whether the gut microbiome is linked to disease severity in patients with COVID-19, and whether perturbations in microbiome composition, if any, resolve with clearance of the SARS-CoV-2...

Fecal microbiota transplant (FMT) has emerged as a potential treatment for severe colitis associated with graft-versus-host disease (GvHD) following hematopoietic stem cell transplant. Bacterial engraftment from FMT donor to recipient has been reported, however the fate of fungi and viruses after FMT remains unclear. Here we report longitudinal dyn...

DNA sequencing has become a common tool in environmental microbial ecology, facilitating characterization of microbial populations as well as complex microbial communities by circumventing culture bottlenecks. However, certain samples especially from host-associated environments (rhizosphere, human tissue) or complex communities (soils) can contain...

Colorectal cancer is the fourth most common cancer and the fifth leading cause of cancer death worldwide. Two important hallmarks of the disease are faulty tumor suppressor genes and altered composition of the community of microbes that live in the colon. That prompted researchers to explore whether there is a connection between the two. They exami...

Background & aims: Beyond bacteria, the human gastrointestinal tract is host to a vast diversity of fungi, collectively known as the gut mycobiome. Little is known of the impact of geography, ethnicity and urbanization on the gut mycobiome at a large population level. We aim to delineate the variation of human gut mycobiome and its association wit...

The human-gut-DNA virome is highly diverse and individual specific, but little is known of its variation at a population level. Here, we report the fecal DNA virome of 930 healthy adult subjects from two regions in China (Hong Kong and Yunnan) spanning six ethnicities (Han, Zang, Miao, Bai, Dai, and Hani), and including urban and rural residents fo...

Background: Coronavirus Disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from faecal samples and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively k...

Background: Coronavirus Disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from faecal samples and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively k...

Objective Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was detected in faeces of patients with COVID-19, the activity and infectivity of the virus in the GI tract during disease course is largely unknown. We investigated temporal transcriptional activity of SARS-CoV-2 and its association with longitudinal faecal microbi...

Background: Altered microbiome composition and aberrant promoter hypermethylation of tumor suppressor genes (TSGs) are two important hallmarks of colorectal cancer (CRC). Here we performed concurrent 16S rRNA gene sequencing and methyl-CpG binding domain-based capture sequencing in 33 tissue biopsies (5 normal colonic mucosa tissues, 4 pairs of ad...

Background: Hong Kong (HK) is a densely populated city near the epicentre of the coronavirus disease 2019 (COVID-19) outbreak. Stringent border control together with aggressive case finding, contact tracing, social distancing and quarantine measures were implemented to halt the importation and spread of the virus. Methods: We performed an epidem...

We report a SCCmec II, ST39 methicillin-resistant Staphylococcus aureus isolate from pigs that harbored toxic-shock syndrome toxin gene (tsst-1). The gene was located in a rare pathogenicity island SaPI68111, which also carried enterotoxin genes that can cause fatal infections. Pigs may potentially serve as a reservoir for MRSA dissemination.

We report a SCCmec II, ST39 methicillin-resistant Staphylococcus aureus isolate from pigs that harbored toxic-shock syndrome toxin gene (tsst-1). The gene was located in a rare pathogenicity island SaPI68111, which also carried enterotoxin genes that can cause fatal infections. Pigs may potentially serve as a reservoir for MRSA dissemination.

Background: Non-typeable H. Influenzae (NTHi) is increasingly recognized to play an important role in respiratory tract infections. Increasing reports of ampicillin- and β-lactamase-negative ampicillin-resistance are also noted. We aimed to study the epidemiology and characteristics of NTHi from a collection of archived Haemophilus influenzae (HI)...

Background: Streptococcus agalactiae (GBS) is an important pathogen with a wide host range, causing sepsis and meningitis in humans, mastitis in cattle and streptococcosis in fish. This results in much medical and veterinary morbidities and a huge economic burden to both livestock and aquaculture industries worldwide. The outbreak of adult sepsis d...

BACKGROUD & AIMS: Although SARS-CoV-2 infects gastrointestinal tissues, little is known about the roles of gut commensal microbes in susceptibility to and severity of infection. We investigated changes in fecal microbiomes of patients with SARS-CoV-2 infection during hospitalization and associations with severity and fecal shedding of virus. METHO...

Objective Fusobacteria are not common nor relatively abundant in non-colorectal cancer (CRC) populations, however, we identified multiple Fusobacterium taxa nearly absent in western and rural populations to be comparatively more prevalent and relatively abundant in southern Chinese populations. We investigated whether these represented known or nov...

Background: Microbial culture-based investigations of inflamed tonsil tissues have previously indicated enrichment of several microorganisms such as Streptococcus, Staphylococcus and Prevotella. These taxa were also largely reflected in DNA sequencing studies performed using tissue material. In comparison, less is known about the response of the o...

In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 month...

Objective The underlying microbial basis, predictors of therapeutic outcome and active constituent(s) of faecal microbiota transplantation (FMT) mediating benefit remain unknown. An international panel of experts presented key elements that will shape forthcoming FMT research and practice. Design Systematic search was performed, FMT literature was...

Background Fecal microbiota transplant (FMT) has emerged as a potential treatment for severe colitis associated with graft-versus-host disease (GvHD) following hematopoietic stem cell transplant. Bacteria engraftment has been reported, however, the fate of fungi and viruses and their relationship with treatment response after FMT remains unclear. H...

Large-scale human microbiota studies require specimens collected from multiple sites and/or time points to maximize detection of the small effects in microbe-host interactions. However, batch biases caused by experimental protocols, such as sample collection, massively parallel sequencing, and bioinformatics analyses, remain critical and should be...

Stools are commonly used as proxies for studying human gut microbial communities as sample collection is straightforward, cheap and non-invasive. In large-scale human population surveys, however, sample integrity becomes an issue as it is not logistically feasible for researchers to personally collect stools from every participant. Instead, partici...

Supplementary tables S1 to S6 Table S1: Sample metadata. Table S2: ESVs enriched in preservative medium samples determined using GLM (three subjects combined). Table S3: ESVs enriched in preservative medium samples determined using GLM (subjects analysed separately). Table S4: Effect of storage temperature and duration on stool community compositio...

Supplementary figures 1–4 Respective figure legends are underneath each figure.

otu table OTU counts generated by 16S rRNA gene amplicon sequencing.

Sample metadata Sample metadata for community composition analysis.

R commands for community profile analysis Commands used in R for analysing community profile counts data.

Representative fasta sequence Representative fasta sequences from each exact sequence variance (ESV) detected in this study.

Studies on the microbial communities in non-human primate hosts provide unique insights in both evolution and function of microbes related to human health and diseases. Using 16S rRNA gene amplicon profiling, we examined the oral, anal and vaginal microbiota in a group of non-captive rhesus macaques (N = 116) and compared the compositions with the...

The World Health Organization selects influenza vaccine compositions biannually to cater to peaks in temperate regions. In tropical and subtropical regions, where influenza seasonality varies and epidemics can occur year-round, the choice of vaccine remains uncertain. Our 17-year molecular epidemiologic survey showed that most influenza A(H3N2) (9/...

GenBank accession numbers of hemagglutinin sequences of circulating influenza A and B strains, Hong Kong, China, 1996–2012; pairwise hemagglutinin amino acid distances between circulating and vaccine strains of influenza A(H3N2) and influenza B.

Nitrifying microorganisms play an important role in nitrogen (N) cycling in agricultural soils as nitrification leads to accumulation of nitrate (NO3⁻) that is readily lost through leaching and denitrification, particularly in high rainfall regions. Legume crop rotation in sugarcane farming systems can suppress soil pathogens and improve soil healt...

Culture-independent molecular surveys of plant root microbiomes indicate that soil type generally has a stronger influence on microbial communities than host phylogeny. However, these studies have mostly focussed on model plants and crops. Here, we examine the root microbiomes of multiple plant phyla including lycopods, ferns, gymnosperms, and angi...

In the article 'Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database GigaScience 2016 5:21' [1] the authorship list should have included Leon Court, who was responsible for sample collection and preparation, sampling design and sequencing method design. The authors regret this omission.

Contribution of the gastrointestinal microbiota to animal health, overall wellbeing and productivity is well appreciated. The chicken gastrointestinal microbiome has been studied for more than four decades to understand its characteristics and function. Its microbial community composition is dependent mainly on diet (Apajalahti et al., 2001), and t...