Gary A Toranzos

University of Puerto Rico at Rio Piedras | UPR-RP · Department of Biology

Coprolites, or mummified feces, are valuable sources of information on ancient cultures as they contain ancient DNA (aDNA). In this study, we analyzed ancient plant DNA isolated from coprolites belonging to two pre-Columbian cultures (Huecoid and Saladoid) from Vieques, Puerto Rico, using shotgun metagenomic sequencing to reconstruct diet and lifes...

Constructed wetlands are an efficient and cost-effective system for the treatment of wastewater that can be reused for diverse purposes, including irrigation; however, few studies have determined the efficiency of microbial removal by constructed wetlands in tropical regions. Therefore, the present study aimed to determine the microbial quality of...

Parasites have affected and coevolved with humans and animals throughout history. Evidence of ancient parasitic infections, particularly, reside in archeological remains originating from different sources dating to various periods of times. The study of ancient parasites preserved in archaeological remains is known as paleoparasitology, and it init...

“Omics” is becoming an increasingly recognizable term, even to the general public, as it is used more and more often in everyday scientific research [...]

A recent publication evaluates microbial genome sequences from DNA isolated from ancient bones and compares these DNA sequences to those found in the surrounding soil. Although we need to be aware of environmental contamination when carrying out paleomicrobiological analyses, we should also realize that some samples do not contain their own microbi...

A water recycling system with improved efficiencies to satisfy the water demand in a closed-loop environment is required in the Environmental Control and Life Support Systems (ECLSS) for the National Aeronautics and Space Administration (NASA). The wastewater recycling system in the ECLSS has a water reclamation efficiency limitation of 90%. Theref...

The development of nuclear science and technology has led to increasing nuclear waste containing uranium. The contamination associated with nuclear activity, especially uranium, is a significant concern for human and environmental health. Due to the high toxicity, radioactivity, and extensive half-life of uranium, it is necessary to find a way to r...

Few data exist on the human gut mycobiome in relation to lifestyle, ethnicity, and dietary habits. To understand the effect of these factors on the structure of the human gut mycobiome, we analyzed sequences belonging to two extinct pre-Columbian cultures inhabiting Puerto Rico (the Huecoid and Saladoid) and compared them to coprolite samples found...

The present Special Issue focuses on the latest approaches to health and public health microbiology using multiomics [...]

A wastewater recycling system with enhanced efficiencies is needed to satisfy the water need in a closed-loop environment required by NASA's Environmental Control and Life Support Systems (ECLSS). Wastewater treatment and water-recovery system within the ECLSS has an efficiency limitation of approximately 90% of water reclamation. To provide self-s...

It has been called ‘the next plague’ and has raised many eyebrows from both sides of the topic; namely, those who stand on the ‘we are all going to die’ side and those who simply state: ‘What is the problem?’ The facts are actually somewhere in the middle of these extreme statements. On the one hand, we cannot simply overlook the fact that some pat...

Human activities provoke drastic changes in aquatic ecosystems that result in events such as eutrophication, algal blooms, massive fauna mortality, and, in extreme cases, the complete loss of the aquatic resources. Some of these events were registered at Laguna Alalay Lake in Cochabamba, Bolivia in 2016. We present a case study with the aim of dete...

The pre-Columbian Huecoid and Saladoid cultures were agricultural ethnic groups that supplemented their diets by fishing, hunting and scavenging. Archaeological deposits associated to these cultures contained a variety of faunal osseous remains that hinted at the cultures’ diets. The present study identified zoonotic parasites that may have infecte...

Malaria is one of the most important human diseases throughout tropical and sub-tropical regions of the world. Global distribution and ample host range have contributed to the genetic diversity of the etiological agent, Plasmodium. Phylogeographical analyses demonstrated that Plasmodium falciparum and Plasmodium vivax follow an Out of Africa (OOA)...

Soil microbial communities are an important component of biological diversity and terrestrial ecosystems which is responsible for processes such as decomposition, mineralization of nutrients, and accumulation of organic matter. One of the factors that provide information on the mechanisms regulating biodiversity is spatial scaling. We characterized...

Current urine recycling treatments are unable to completely recover clean water free of toxic metabolic products such as urea. Urea is a small and uncharged molecule, diffulting its removal from wastewater. Previous publications from our research group reported the use of immobilized urease enzyme on carbon matrix as a urea bioreactor to convert ur...

The concept of the human oral microbiome was applied to understand health and disease, lifestyles, and dietary habits throughout part of human history. In the present study, we augment the understanding of ancient oral microbiomes by characterizing human dental calculus samples recovered from the ancient Abbey of Badia Pozzeveri (central Italy), wi...

In the following comment, we reply to Eisenhofer and Weyrich’s letter “Proper authentication of ancient DNA is still essential” responding to the article “Gut Microbiome and Putative Resistome of Inca and Italian Nobility Mummies” by Santiago-Rodriguez et al. One of the concerns raised was the possibility that the patterns noted in the gut microbio...

Tetracyclines were discovered over 70 years ago and their use resulted in the emergence of tetracycline-resistance microorganisms; however, it has been hypothesized that tetracycline-resistance may have originated in the environment, and that determinants were transferred to the human gut microbiota. Ancient microbiomes represent an opportunity to...

One of the most challenging problems when trying to recycle urine for different purposes is the removal of urea. In this project we studied an ureolysis system using the bacterium Proteus vulgaris for the transformation of urea to ammonia and its subsequent oxidation to nitrogen at a Pt working electrode. Our system was tested under different pH, m...

In a world dominated by microbes, our ancestors evolved alongside an outstandingly diverse ancient microbiota (see Fig. 1 , Table 1 ). Symbiotic relationships between animals, microbes, and viruses have been observed as far back in animal evolutionary history as when hydras made their appearance, and these interactions currently span across all typ...

Environmental forensics has been previously described as the use of chemical, physical, and statistical techniques to investigate the sources and behavior of contaminants in the environment as a means to determine attribution for legal purposes. Although this definition still holds true, in environmental microbiology, metagenomics is increasingly b...

Microbiome analysis of environmental samples may represent the next frontier in environmental microbial forensics. The microbiome, defined as the sum total of all the genetic material present in a sample, contains evidence of the microbial communities in the sample at the time of collection. As such, it contains clues to past environmental events u...

Nucleic acids and modern sequencing analyses are the pivot for research in microbiology, as they provide insights into microbial gene pools and essential cellular processes. Particularly, the ability to isolate and sequence ancient DNA (aDNA) is of increasing importance, as it demonstrates gene evolution and also allows us to peek into the possible...

Bioterrorism is currently defined as the use of biological agents or pathogens (viruses, bacteria, fungi, parasites, and toxins) for the purpose of attacking and creating havoc in a population considered an enemy. Many of these agents can be isolated naturally from the environment or have been genetically manipulated to become more pathogenic. Addi...

Definitions and Historical Perspectives in Environmental Forensics, Page 1 of 2 Abstract Environmental forensics is a tool that uses chemical, physical, and statistical techniques to investigate contaminants in the environment as a means to determine attribution for legal purposes. Environmental microbiology is a branch of science that has benefi...

Future Technologies, Page 1 of 2 Abstract Microbiome analysis of environmental samples may represent the next frontier in environmental microbial forensics. Next-generation sequencing technologies significantly increased the available genetic data that could be used as evidentiary material. It is not clear, however, whether the microbiome can sca...

Little is still known about the microbiome resulting from the process of mummification of the human gut. In the present study, the gut microbiota, genes associated with metabolism, and putative resistome of Inca and Italian nobility mummies were characterized by using high-throughput sequencing. The Italian nobility mummies exhibited a higher bacte...

Little is still known about the microbiome resulting from the process of mummification of the human gut. In the present study, the gut microbiota, genes associated with metabolism, and putative resistome of Inca and Italian nobility mummies were characterized by using high-throughput sequencing. The Italian nobility mummies exhibited a higher bacte...

[This corrects the article DOI: 10.7717/peerj.3277.].

Background The study of ancient microorganisms in mineralized dental plaque or calculi is providing insights into microbial evolution, as well as lifestyles and disease states of extinct cultures; yet, little is still known about the oral microbial community structure and function of pre-Columbian Caribbean cultures. In the present study, we invest...

Background The study of ancient microorganisms in mineralized dental plaque or calculi is providing insights into microbial evolution, as well as lifestyles and disease states of extinct cultures; yet, little is still known about the oral microbial community structure and function of pre-Columbian Caribbean cultures. In the present study, we invest...

SourceTracker Filtered Unfiltered SourceTracker analyses of the dental calculi samples including D21 (A), E19 (B), E26 (C), F20 (D), G18 (E), G21 (F), G22 (G), I19 (H), I23A (I), I23B (J), I24A (K), I24B (L), F24 (M), H6 (N) and M8 (O). Dental calculi microbiomes were compared to stool, coprolite, saliva, soil from the archaeological site of Sorcé,...

Alphararefaction curves Filtered Unfiltered Alphararefaction curves of chao1 (A), and observed OTUs values (B) after filtering soil and blank control OTUs from the dental calculi, and chao1 (C), and observed OTUs (D) values prior filtering soil and blank control OTUs. Samples included dental calculi from loose teeth samples (yellow), dental calculi...

Taxa Plots Unfiltered Barplots representing the bacterial taxonomy based on 16S rRNA gene. Data are shown at the phylum level for dental calculi, supragingival plaque, subgingival plaque, saliva, coprolites, stool, soil from the archeological site of Sorcé, and a blank control. Soil and blank control OTUs were not filtered from the dental calculi p...

Data Set S1 OTU Table Blank Control

Data Set S4 Dental Calculi Genus Level Filtered

PCoA Unfiltered Principal Coordinates Analysis (PCoA) 2D plots of ancient and modern oral and gut microbiomes, as well as that of soil from the archaeological site of Sorcé. Dental calculi (yellow), dental calculi of teeth attached to bones that enabled the identification of gender or age (Dental calculi (Bone)) (red), coprolites (light blue), stoo...

PICRUSt Unfiltered Heatmap of the relative abundances of the predicted functional categories (level 2) of microbiomes of dental calculi, coprolites, supragingival and subgingival plaque, saliva, stool and soil from the archeological site of Sorcé. Functional categories were predicted using PICRUSt. Soil and blank control OTUs were not filtered from...

Data Set S2 OTU Table Soil

Data Set S7 Group Significance Dental Calculi Unfiltered

Data Set S9 Core OTUs 25% Modern Oral Microbiome

Alpha Diversity Unfiltered Bar plots of alpha diversity indices. Bar plots representing the chao 1 (A) and observed OTUs (B) indices for the bacterial taxonomy based on 16S rRNA gene of the dental calculi, modern supragingival and subgingival plaque, saliva, coprolites, stool and soil from the archaeological site of Sorcé microbiomes. Alpha diversi...

LefSe Unfiltered Linear discriminatory analyses. Effect size (LEfSe) plots of predicted functional categories (level 2). Functional categories of dental calculi (ancient oral microbiomes, green), supragingival plaque, subgingival plaque and saliva (modern oral microbiomes, purple), coprolites (ancient gut microbiomes, red), stool (modern gut microb...

Data Set S3 Taxa found in blank control

Data Set S5 Dental Calculi Genus Level

Data Set S8 Core OTUs 25% Dental Calculi

Chao1 Alpha Compare Unfiltered

Observed OTUs Alpha Compare Filtered

Observed OTUs Alpha Compare Unfiltered

Data Set S6 Group Significance Dental Calculi Filtered

All Samples

Chao1 Alpha Compare Filtered

Forensic Approaches to Detect Possible Agents of Bioterror, Page 1 of 2 Abstract Many biological agents have been strategic pathogenic agents throughout history. Some have even changed history as a consequence of early discoveries of their use as weapons of war. Many of these bioagents can be easily isolated from the environment, and some have re...

From Evolutionary Advantage to Disease Agents: Forensic Reevaluation of Host-Microbe Interactions and Pathogenicity, Page 1 of 2 Abstract As the “human microbiome era” continues, there is an increasing awareness of our resident microbiota and its indispensable role in our fitness as holobionts. However, the host-microbe relationship is not so cle...

We previously isolated and characterized an Enterococcus faecalis ATCC 19433 siphovirus 15 from raw domestic sewage as a viral indicator of human fecal pollution. Here, we report 16 the draft genome sequence of this bacteriophage.

Characterization of naturally-mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10–15th centuries using 16S rRNA gene high-throughput sequencing an...

Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology, Page 1 of 2 Abstract Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is prov...

. The most important hypersaline environment in Bolivia is the Uyuni salt flat. It is the largest salt flat in the world and, it presents certain unique chemical characteristics and composition on its surface such as a gradient of ion concentrations from south to north. The autochthonous microbial communities in these salt flats have yet to be stud...

Urbanization affects the microbial loading into tropical streams, but its impact on water quality varies across watersheds. Rainfall in tropical environments also complicates microbial dynamics due to high seasonal and annual variations. Understanding the dynamics of fecal contamination in tropical surface waters may be further hindered by limitati...

The natural mummification process of the human gut represents a unique opportunity to study the resulting microbial community structure and composition. While results are providing insights into the preservation of bacteria, fungi, pathogenic eukaryotes and eukaryotic viruses, no studies have demonstrated that the process of natural mummification a...

Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing an...

For ages, specialists from varying fields have studied the diets of the primeval inhabitants of our planet, detecting diet remains in archaeological specimens using a range of morphological and biochemical methods. As of recent, metagenomic ancient DNA studies have allowed for the comparison of the fecal and gut microbiomes associated to archaeolog...

Description of eukaryote diet-associated genes detected after conducting a translated-nucleotide query of coprolite DNA from both cultures. 1gi| NCBI gene identification number. 2Identification code of the corresponding DNA sequence detected in Huecoid (H-A4LNU…) and Saladoid (S-A4LNU…) coprolite samples. (See S1 Dataset for complete DNA sequences)...

DNA and library concentrations. 1Indicates whole genome amplified and purified DNA. Reported size includes sequencing adaptors, measuring approximately 120bp each. (DOCX)

Fasta format file containing the trimmed, post-QC ancient DNA sequences described in this study. These sequences correspond to the genes identified through blast query search. (DOCX)

Virus genes detected by translated-nucleotide query of coprolite DNA from both cultures. 1gi| NCBI gene identification number. 2Identification code of the corresponding DNA sequence detected in Huecoid (H-A4LNU…) and Saladoid (S-A4LNU…) coprolite samples. (See S1 Dataset for complete DNA sequences). (DOCX)

The natural mummification process of the human gut represents a unique opportunity to study the resulting microbial community structure and composition. While results are providing insights into the preservation of bacteria, fungi, pathogenic eukaryotes and eukaryotic viruses, no studies have demonstrated that the process of natural mummification a...

The natural mummification process of the human gut represents a unique opportunity to study the resulting microbial community structure and composition. While results are providing insights into the preservation of bacteria, fungi, pathogenic eukaryotes and eukaryotic viruses, no studies have demonstrated that the process of natural mummification a...

The process of natural mummification is a rare and unique process from which little is known about the resulting microbial community structure. In the present study, we characterized the microbiome of paleofeces, and ascending, transverse and descending colon of an 11 th century A.D. pre-Columbian Andean mummy by 16S rRNA gene high-throughput seque...

Fecal contamination of freshwaters and drinking waters may result in serious risks to public health that include gastrointestinal and respiratory illnesses, eye and skin infections, many caused by enteric pathogens. The microbiological quality of freshwaters and drinking waters is usually monitored by the detection of traditional indicators that in...

Coprolites are fossilized feces that can be used to provide information on the composition of the intestinal microbiota and,as we show, possibly on diet. We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement onVieques Island, Puerto Rico. While more is known about the Saladoid culture, it is believed that both societ...

There still exists an indisputable growing demand for water around the world, therefore is of major interest to recycle and reuse water. One of the effective measures to help solve the water shortage problem involves recycling of urine. Urea is one of the most common compounds found in urine, and its degradation has been a matter of study for sever...