Author
Julia M. Maritz
Other affiliations: Merck & Co.
Bio: Julia M. Maritz is an academic researcher from New York University. The author has contributed to research in topics: Microbiome & Metagenomics. The author has an hindex of 11, co-authored 17 publications receiving 606 citations. Previous affiliations of Julia M. Maritz include Merck & Co..
Topics: Microbiome, Metagenomics, Population, Human virome, Vaccination
Papers
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City University of New York1, Cornell University2, Hunter College3, New York University4, Brooklyn College5, Fordham University6, State University of New York System7, University of Vermont8, Icahn School of Medicine at Mount Sinai9, Rockefeller University10, University College Dublin11, Boston Children's Hospital12, York College, City University of New York13, IBM14
TL;DR: This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.
Abstract: The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station's history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.
275 citations
San Diego State University1, Charles University in Prague2, Cairo University3, Monash University4, University of Notre Dame5, Delft University of Technology6, University of Liverpool7, Utrecht University8, Kavli Institute of Nanoscience9, Aix-Marseille University10, New York University11, University of California, Davis12, University of Otago13, University of Groningen14, Katholieke Universiteit Leuven15, University of Los Andes16, Norwegian Institute of Public Health17, Universidad Mayor18, Saint Petersburg State University of Information Technologies, Mechanics and Optics19, National Autonomous University of Mexico20, Technical University of Denmark21, University of Jordan22, University of Alicante23, University of Illinois at Urbana–Champaign24, Autonomous University of Barcelona25, Pontifical Catholic University of Chile26, University of Warsaw27, Dartmouth College28, University of Khartoum29, University of Chicago30, University of Barcelona31, Scripps Research Institute32, University College Cork33, University of Tampere34, Northern Illinois University35, University of Sydney36, Columbus Zoo and Aquarium37, McGill University38, University of Western Australia39, University of Colorado Boulder40, Virginia Tech41, Tel Aviv University42, Instituto Superior Técnico43, Makerere University44, University of California, San Diego45, Hawaii Pacific University46, Stockholm University47, University of California, Irvine48, University of Buenos Aires49, Fudan University50, University of Padua51, University of Pittsburgh52, Ebonyi State University53, Andrés Bello National University54, University of Copenhagen55, Radboud University Nijmegen56
TL;DR: It is concluded that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
Abstract: Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
167 citations
TL;DR: It is the opinion that several phylogenetic analyses have identified animal-derived trichomonads as close sister taxa of the two human-specific species, and prompt further investigation into the importance of zoonotic trICHomonads for human health.
87 citations
San Diego State University1, Charles University in Prague2, Cairo University3, Monash University4, University of Notre Dame5, Delft University of Technology6, University of Liverpool7, Utrecht University8, Aix-Marseille University9, New York University10, University of California, Berkeley11, University of Otago12, University Medical Center Groningen13, Katholieke Universiteit Leuven14, University of Los Andes15, Norwegian Institute of Public Health16, Universidad Mayor17, Saint Petersburg State University of Information Technologies, Mechanics and Optics18, National Autonomous University of Mexico19, Technical University of Denmark20, University of Jordan21, University of Alicante22, University of Illinois at Urbana–Champaign23, Autonomous University of Barcelona24, Pontifical Catholic University of Chile25, University of Warsaw26, Dartmouth College27, University of Khartoum28, University of Chicago29, University of Barcelona30, Scripps Research Institute31, University College Cork32, University of Tampere33, Northern Illinois University34, University of Sydney35, Columbus Zoo and Aquarium36, National Scientific and Technical Research Council37, University of Western Australia38, University of Colorado Boulder39, Virginia Tech40, Stockholm University41, Tel Aviv University42, Instituto Superior Técnico43, Makerere University44, Hawaii Pacific University45, University of Buenos Aires46, Fudan University47, University of Padua48, University of Pittsburgh49, Ebonyi State University50, Andrés Bello National University51, Radboud University Nijmegen52
TL;DR: It is concluded that crAssphage is a benign globetrotter virus that may have co-evolved with the human lineage and an integral part of the normal human gut virome.
Abstract: Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared to other environments. Here we investigate the origin, evolution, and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboratory, we obtained DNA sequences of crAssphage from over one-third of the world’s countries, and showed that its phylogeography is locally clustered within countries, cities, and individuals. We also found colinear crAssphage-like genomes in both Old-World and New-World primates, challenging genomic mosaicism and suggesting that the association of crAssphage with primates may be millions of years old. We conclude that crAssphage is a benign globetrotter virus that may have co-evolved with the human lineage and an integral part of the normal human gut virome.
80 citations
TL;DR: It is demonstrated that cockroaches disseminate their gut microbiome in their feces, and this work underscores the important contribution of the cockroach fecal microbiome to the microbial diversity of cockroach-infested homes.
Abstract: German cockroaches, Blattella germanica (Blattodea: Ectobiidae), are human commensals that move freely between food and waste, disseminating bacteria, including potential pathogens, through their feces. However, the relationship between the microbial communities of the cockroach gut and feces is poorly understood. We analyzed the V4 region of the 16S rRNA gene and the V9 region of the 18S rRNA gene by next-generation sequencing (NGS) to compare the bacterial and protist diversities in guts versus feces and males versus females, as well as assess variation across cockroach populations. Cockroaches harbored a diverse array of bacteria, and 80 to 90% of the operational taxonomic units (OTUs) were shared between the feces and gut. Lab-reared and field-collected cockroaches had distinct microbiota, and whereas lab-reared cockroaches had relatively conserved communities, considerable variation was observed in the microbial community composition of cockroaches collected in different apartments. Nonetheless, cockroaches from all locations shared some core bacterial taxa. The eukaryotic community in the feces of field-collected cockroaches was found to be more diverse than that in lab-reared cockroaches. These results demonstrate that cockroaches disseminate their gut microbiome in their feces, and they underscore the important contribution of the cockroach fecal microbiome to the microbial diversity of cockroach-infested homes.IMPORTANCE The German cockroach infests diverse human-built structures, including homes and hospitals. It produces potent allergens that trigger asthma and disseminates opportunistic pathogens in its feces. A comprehensive understanding of gut and fecal microbial communities of cockroaches is essential not only to understand their contribution to the biology of the cockroach, but also for exploring their clinical relevance. In this study, we compare the diversity of bacteria and eukaryotes in the cockroach gut and feces and assess the variation in the gut microbiota across cockroach populations.
50 citations
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
10,124 citations
TL;DR: In this article, a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation is described and validated, which addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities.
Abstract: This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.
3,060 citations
Journal Article•
TL;DR: FastTree as mentioned in this paper uses sequence profiles of internal nodes in the tree to implement neighbor-joining and uses heuristics to quickly identify candidate joins, then uses nearest-neighbor interchanges to reduce the length of the tree.
Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.
2,436 citations
TL;DR: Because MMseqs2 needs no random memory access in its innermost loop, its runtime scales almost inversely with the number of cores used, which enables sensitive protein sequence searching for the analysis of massive data sets.
Abstract: Sequencing costs have dropped much faster than Moore's law in the past decade, and sensitive sequence searching has become the main bottleneck in the analysis of large (meta)genomic datasets. While previous methods sacrificed sensitivity for speed gains, the parallelized, open-source software MMseqs2 overcomes this trade-off: In three-iteration profile searches it reaches 50% higher sensitivity than BLAST at 83-fold speed and the same sensitivity as PSI-BLAST at 270 times its speed. MMseqs2 therefore offers great potential to increase the fraction of annotatable (meta)genomic sequences.
1,371 citations
TL;DR: The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome and that some low-frequency taxa seemingly associated with preterm birth were contaminants.
Abstract: The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants—DNA sequences not truly present in the sample. Contaminants come from various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do not eliminate it. Here we introduce decontam (
https://github.com/benjjneb/decontam
), an open-source R package that implements a statistical classification procedure that identifies contaminants in MGS data based on two widely reproduced patterns: contaminants appear at higher frequencies in low-concentration samples and are often found in negative controls. Decontam classified amplicon sequence variants (ASVs) in a human oral dataset consistently with prior microscopic observations of the microbial taxa inhabiting that environment and previous reports of contaminant taxa. In metagenomics and marker-gene measurements of a dilution series, decontam substantially reduced technical variation arising from different sequencing protocols. The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome and that some low-frequency taxa seemingly associated with preterm birth were contaminants. Decontam improves the quality of metagenomic and marker-gene sequencing by identifying and removing contaminant DNA sequences. Decontam integrates easily with existing MGS workflows and allows researchers to generate more accurate profiles of microbial communities at little to no additional cost.
1,287 citations