About
34
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Introduction
Melissa does research in Microbiology, Ecology and Evolutionary Biology. Her current projects focus on functional specialization of the microbiome in dietary specialists.
Current institution
Additional affiliations
January 2018 - May 2018
Position
- Research Assistant
Description
- Evolution; graduate level course in which I led lab exercises, prepared R exercises to emphasize core concepts, and facilitated lectures.
August 2016 - October 2020
August 2015 - August 2016
Position
- Research Assistant
Description
- Microbiology Laboratory; my duties ranged from media and culture prep to designing and leading laboratory lectures and grading assignments. I taught this course a total of 3 semesters.
Education
September 2016 - October 2020
American Museum of Natural History, Richard Gilder Graduate School
Field of study
- Comparative Biology
August 2014 - May 2016
August 2011 - May 2015
Publications
Publications (34)
We present a genome assembly from a specimen of Barbarea vulgaris (winter-cress or yellow rocket; Streptophyta; Magnoliopsida; Brassicales; Brassicaceae). The genome sequence has a total length of 246.25 megabases. Most of the assembly (99.45%) is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have le...
We present a genome assembly from an individual male Artibeus lituratus (Chordata; Mammalia; Chiroptera; Phyllostomidae). The genome sequence is 2.15 in span. The majority of the assembly is scaffolded into 30 chromosomal pseudomolecules, with the X and Y sex chromosomes assembled.
Global biodiversity and ecosystem function are the result of complex networks of interactions and feedbacks between animals and their environments, which in turn are affected by the interactions and feedbacks between animals and the organisms they host. Understanding these complex networks, including the main drivers of and responses to ecological...
We present a genome assembly from an individual female Molossus alvarezi (Chordata; Mammalia; Chiroptera; Molossidae). The genome sequence is 2.490 Gb in span. The majority of the assembly is scaffolded into 24 chromosomal pseudomolecules, with the X sex chromosomes assembled.
Frugivory evolved multiple times in mammals, including bats. However, the cellular and molecular components driving it remain largely unknown. Here, we use integrative single-cell sequencing (scRNA-seq and scATAC-seq) on insectivorous (Eptesicus fuscus; big brown bat) and frugivorous (Artibeus jamaicensis; Jamaican fruit bat) bat kidneys and pancre...
We present a genome assembly from an individual male Molossus nigricans (Chordata; Mammalia; Chiroptera; Molossidae). The genome sequence is 2.41 gigabases in span. The majority of the assembly is scaffolded into 24 chromosomal pseudomolecules, with the X sex chromosome assembled.
Frugivory evolved multiple times in mammals, including bats. However, the cellular and molecular components driving it remain largely unknown. Here, we used integrative single-cell sequencing on insectivorous and frugivorous bat kidneys and pancreases and identified key cell population, gene expression and regulatory element differences associated...
Environmental DNA (eDNA) sequencing—DNA collected from the environment from living cells or shed DNA—was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine dive...
Suitable habitat fragment size, isolation, and distance from a source are important variables influencing community composition of plants and animals, but the role of these environmental factors in determining composition and variation of host-associated microbial communities is poorly known. In parasite-associated microbial communities, it is hypo...
Suitable habitat fragment size, isolation, and distance from a source are important variables influencing community composition of plants and animals, but the role of these environmental factors in determining composition and variation of host-associated microbial communities is poorly known. In parasite-associated microbial communities, it is hypo...
In this data paper, we describe environmental DNA (eDNA) cytochrome c oxidase (COI) amplicon sequence data from New York City’s Bronx River Estuary. As urban systems continue to expand, describing and monitoring their biodiversity is increasingly important for sustainability. Once polluted and overexploited, New York City’s Bronx River Estuary is u...
Background
Animals evolved in a microbial world, and their gut microbial symbionts have played a role in their ecological diversification. While many recent studies report patterns of phylosymbiosis between hosts and their gut bacteria, fewer studies examine the potentially adaptive functional contributions of these microbes to the dietary habits o...
Background
Changes in wild animal gut microbiotas may influence host health and fitness. While many studies have shown correlations between gut microbiota structure and external factors, few studies demonstrate causal links between environmental variables and microbiota shifts. Here, we use a fully factorial experiment to test the effects of elevat...
Characterising and monitoring biological diversity to foster sustainable ecosystems is highly recommended as urban centres rapidly expand. However, much of New York City’s biodiversity remains undescribed, including in the historically degraded, but recovering Bronx River Estuary. In a pilot study to identify organisms and characterise biodiversity...
Background: Changes in wild animal gut microbiotas may influence host health and fitness. While many studies have shown correlations between gut microbiota structure and external factors, few studies demonstrate causal links between environmental variables and microbiota shifts. Here, we use a fully factorial experiment to test the effects of eleva...
Bat communities in the Neotropics are some of the most speciose assemblages of mammals on Earth, with regions supporting more than 100 sympatric species with diverse feeding ecologies. Because bats are small, nocturnal, and volant, it is difficult to directly observe their feeding habits, which has resulted in their classification into broadly defi...
En esta nota reportamos una nueva especie de Peropteryx para Bolivia, P. leucoptera Peters, 1867, el murciélago peróptero aliblanco. Los especímenes de esta especie fueron anteriormente identificados como P. kappleri y P. macrotis. También brindamos datos morfométricos de P. leucoptera de Bolivia y P. kappleri de otros países. Los registros de esta...
Animals evolved in a microbial world, and their gut microbial symbionts have played a role in their ecological diversification. While many recent studies have reported patterns of co-diversification of hosts and their gut microbes, few studies have directly examined the functional contributions of these microbes to the dietary habits of their hosts...
Animals evolved in a microbial world, and their gut microbial symbionts have played a role in their ecological diversification. While many recent studies have reported patterns of co-diversification of hosts and their gut microbes, few studies have directly examined the functional contributions of these microbes to the dietary habits of their hosts...
Biodiversity monitoring is an essential component of restoration efforts. We sequenced 16S rRNA gene amplicons from sediments and waters of Hunts Point Riverside Park and Soundview Park, located in a historically degraded but recovering urban estuary in New York. In total, 508,352 unique amplicon sequence variants were recovered, and Proteobacteria...
Host ecological factors and external environmental factors are known to influence the structure of gut microbial communities, but few studies have examined the impacts of environmental changes on microbiotas in free-ranging animals. Rapid land-use change has the potential to shift gut microbial communities in wildlife through exposure to novel bact...
Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies...
Numerous free fatty acids (FFAs) are known to have potent antifungal effects. The mammalian epidermis contains both FFAs and multiple classes of fatty acid esters, including 1-monoacylglycerols and wax esters. We thus hypothesized that wax esters and 1-monoacylglycerols composed of antifungal fatty acids would also have antifungal properties. We te...
The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the contex...
White Nose Syndrome (WNS) greatly increases the over-winter mortality of little brown (Myotis lucifugus), Indiana (M. sodalis), northern (M. septentrionalis), and tricolored (Perimyotis subflavus) bats, and is caused by cutaneous infections with Pseudogymnoascus destructans (Pd). Big brown bats (Eptesicus fuscus) are highly resistant to Pd infectio...
White Nose Syndrome (WNS) is a cutaneous infection caused by the psychrophilic fungus Pseudogymnoascus destructans (Pd). WNS has caused extensive mortality in hibernating North American bats, particularly Myotis lucifugus, M. septentrionalis, M. sodalis, and Perimyotis subflavus. The epidermis of M. lucifugus contains free fatty acids (FFAs) that h...
White Nose Syndrome (WNS) greatly increases the over-winter mortality of little brown (Myotis lucifugus), Indiana (Myotis sodalis), northern (Myotis septentrionalis), and tricolored(Perimyotis subflavus) bats. It is caused by a cutaneous infection with the fungus Pseudogymnoascus destructans(Pd). Big brown bats (Eptesicus fuscus) are much more resi...
Questions
Questions (4)
Hello all,
I am currently preparing 16S amplicon libraries on fecal and gut tissue material from bats following Illumina's 16S Metagenomics protocol. I have performed triplicate reactions, then pooled the triplicate PCR products for each sample.
The problem is, when I run these samples on a gel, I get no bands. When I ran four samples on the Bioanalyzer, my highest yield for the expected fragment size (370 bp) was ~400 pg/uL.
It's not clear to me how little amplicon DNA you can have to proceed to the indexing PCR (adding barcodes for multiplexing). The Illumina indexes are quite expensive and I do not want to perform this step until I know my DNA yields are enough. Does anyone know/have experience with low yield amplicon products?
I am performing a study on the gut micro biome of Neotropical bats and have collected guano, intestinal tissue, and blood from each species. For comparability of results, I would like to use one extraction kit for all three sample types. Has anyone had success with a particular kit? I was thinking of using ThermoFisher's PureLink Microbiome kit, but haven't read any reviews for extraction from tissue.
Thanks in advance,
A recent paper by Shoemaker et al. (2016) [attached] has suggested that bacterial communities show patterns of diversity consistent with lognormal dynamics. Maximum entropy theory (underpinning of Maxent) predicts a log-series species abundance distribution, and predicted microbial abundances worse than lognormal or Zipf distributions. Therefore, is it even appropriate to use MaxEnt to model the distributions of these species, if they are not following the dynamics used to create the algorithm? Thanks in advance for the input!
I am currently investigating whether one species of Artibeus (leaf-nosed bat) is actually two. I started with mtDNA sequences (Cytb and COI) from GenBank and have Bayesian trees for both loci showing two distinct, well-supported clades. The pairwise distances are relatively high, so now I am wondering about the possibility that these sequences are pseudogenes of COI before I test any nuclear loci. The COI data are partial cd's.
What is the best method/software to test for pseudogenes in this situation? Thanks in advance!
