Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

/pdf/diet-rapidly-and-reproducibly-alters-the-human-gut-drvn0pi8vp.pdf

Diet rapidly and reproducibly alters the human gut microbiome

https://www.cell.com/trends/genetics/pdf/S0168-9525(08)00023-1.pdf

The impact of next-generation sequencing technology on genetics.

Viral diversity and life cycles are poorly understood in the human gut and other body habitats. Phages and their encoded functions may provide informative signatures of a human microbiota and of microbial community responses to various disturbances, and may indicate whether community health or dysfunction is manifest after apparent recovery from a disease or therapeutic intervention. Here we report sequencing of the viromes (metagenomes) of virus-like particles isolated from faecal samples collected from healthy adult female monozygotic twins and their mothers at three time points over a one-year period. We compared these data sets with data sets of sequenced bacterial 16S ribosomal RNA genes and total-faecal-community DNA. Co-twins and their mothers share a significantly greater degree of similarity in their faecal bacterial communities than do unrelated individuals. In contrast, viromes are unique to individuals regardless of their degree of genetic relatedness. Despite remarkable interpersonal variations in viromes and their encoded functions, intrapersonal diversity is very low, with >95% of virotypes retained over the period surveyed, and with viromes dominated by a few temperate phages that exhibit remarkable genetic stability. These results indicate that a predatory viral-microbial dynamic, manifest in a number of other characterized environmental ecosystems, is notably absent in the very distal intestine.

Viruses in the faecal microbiota of monozygotic twins and their mothers

Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct “marine-ness” quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied on a North-South latitudinal gradient. The marine regions had different assemblages of viruses. Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. However most viral species were found to be widespread. With a majority of shared species between oceanic regions, most of the differences between viral assemblages seemed to be explained by variation in the occurrence of the most common viral species and not by exclusion of different viral genomes. These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure.

/pdf/the-marine-viromes-of-four-oceanic-regions-39vuiiazh3.pdf

The marine viromes of four oceanic regions

Wastewater surveillance represents a complementary approach to clinical surveillance to measure the presence and prevalence of emerging infectious diseases like the novel coronavirus SARS-CoV-2. This innovative data source can improve the precision of epidemiological modeling to understand the penetrance of SARS-CoV-2 in specific vulnerable communities. Here, we tested wastewater collected at a major urban treatment facility in Massachusetts and detected SARS-CoV-2 RNA from the N gene at significant titers (57 to 303 copies per ml of sewage) in the period from 18 to 25 March 2020 using RT-qPCR. We validated detection of SARS-CoV-2 by Sanger sequencing the PCR product from the S gene. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of 25 March. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks. IMPORTANCE Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence.

SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases

The human gut is known to be a reservoir of a wide variety of microbes, including viruses. Many RNA viruses are known to be associated with gastroenteritis; however, the enteric RNA viral community present in healthy humans has not been described. Here, we present a comparative metagenomic analysis of the RNA viruses found in three fecal samples from two healthy human individuals. For this study, uncultured viruses were concentrated by tangential flow filtration, and viral RNA was extracted and cloned into shotgun viral cDNA libraries for sequencing analysis. The vast majority of the 36,769 viral sequences obtained were similar to plant pathogenic RNA viruses. The most abundant fecal virus in this study was pepper mild mottle virus (PMMV), which was found in high concentrations—up to 109 virions per gram of dry weight fecal matter. PMMV was also detected in 12 (66.7%) of 18 fecal samples collected from healthy individuals on two continents, indicating that this plant virus is prevalent in the human population. A number of pepper-based foods tested positive for PMMV, suggesting dietary origins for this virus. Intriguingly, the fecal PMMV was infectious to host plants, suggesting that humans might act as a vehicle for the dissemination of certain plant viruses.

https://digitalcommons.usf.edu/cgi/viewcontent.cgi?article=1787&context=msc_facpub

RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses

DNA microarrays used as 'genomic sensors' have great potential in clinical diagnostics. Biases inherent in random PCR-amplification, cross-hybridization effects, and inadequate microarray analysis, however, limit detection sensitivity and specificity. Here, we have studied the relationships between viral amplification efficiency, hybridization signal, and target-probe annealing specificity using a customized microarray platform. Novel features of this platform include the development of a robust algorithm that accurately predicts PCR bias during DNA amplification and can be used to improve PCR primer design, as well as a powerful statistical concept for inferring pathogen identity from probe recognition signatures. Compared to real-time PCR, the microarray platform identified pathogens with 94% accuracy (76% sensitivity and 100% specificity) in a panel of 36 patient specimens. Our findings show that microarrays can be used for the robust and accurate diagnosis of pathogens, and further substantiate the use of microarray technology in clinical diagnostics.

/pdf/optimization-and-clinical-validation-of-a-pathogen-detection-1pr61r9yi6.pdf

Optimization and clinical validation of a pathogen detection microarray

BACKGROUND: Although the epidemiology of respiratory syncytial virus (RSV) lower respiratory tract infections (LRI) is well known in industrialized countries, the burden in developing Asian countries is not well studied. 

METHODS: To define the burden of RSV disease in children <5 years of age in rural and urban Indonesia, infants and children were enrolled from peri-urban and rural subdistricts, in the following 2 cohorts: (a) a cross-sectional cohort of approximately 100 children from each of 2 subdistricts in the following 5 age groups: 3 to 5, 6 to 8, 9 to 11, 12 to 23, and 24 to 48 months; (b) a birth cohort of all newborns in both subdistricts during the 28 months of the study. All subjects were visited weekly at home. Children with World Health Organization-defined LRI or wheezing had a nasal wash for detection of RSV using an enzyme immunoassay and polymerase chain reaction. 

RESULTS: Of the 2014 children studied, 1074 were in the cross-sectional and 940 in the newborn cohorts. Of the 802 episodes of LRI, 163 were caused by RSV. The RSV LRI incidence per 1000 child-years (C-Y) was higher in rural areas (57.25 vs. 38.54), P < 0.05. No RSV LRI occurred in the first 2 months of life and the peak incidence was in the 6- to 8-month-old infants (103/1000 C-Y). The rates were lowest in those <6 months, 16.5 per 1000 C-Y, compared with 83.1 per 1000 C-Y in those 6 to 11 months of age (P < 0.001), 66.99 in those 12 to 23 months of age, and 28.1 in 2- to 5-year-olds. 

CONCLUSIONS: In Indonesia, the incidence of RSV LRI in the first 6 months of life is relatively low with most disease occurring in older children.

Shirlena Wee Ling Soh

Papers

RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses

Optimization and clinical validation of a pathogen detection microarray

The epidemiology of respiratory syncytial virus lower respiratory tract infections in children less than 5 years of age in Indonesia.