Natural Animal Reservoir Research Articles

Cross-Species Susceptibility of Emerging Variants of SARS-CoV-2 Spike.

The continuous evolution of SARS-CoV-2 and the emergence of novel variants with numerous mutations have heightened concerns surrounding the possibility of cross-species transmission and the establishment of natural animal reservoirs for the virus, but the host range of emerging SARS-CoV-2 variants has not been fully explored yet. We employed an in vitro model comprising VSV∆G* pseudotyped viruses bearing SARS-CoV-2 spike proteins to explore the plausible host range of SARS-CoV-2 emerging variants. The overall host tropism of emerging SARS-CoV-2 variants are consistent with that of the SARS-CoV-2 wuhan-hu-1 strain with minor difference. Pseudotyped viruses bearing spike protein from RaTG13 and RmYN02 can enter cell cultures from a broad range of mammalian species, revealing that mink and hamsters may act as potential intermediate hosts. We further investigated 95 potential site-specific mutations in the SARS-CoV-2 spike protein that could impact viral infectivity across different species. The results showed that 13 of these mutations notably increased the transduction rates by more than two-fold when compared to the wild-type spike protein. Further examination of these 13 mutations within cell cultures from 31 different species revealed heightened sensitivity in cells derived from palm civets, minks, and Chinese horseshoe bats to the VSV∆G*-SARS2-S mutants. Specific mutations, such as L24F, R158G, and L212I, were seen to significantly enhance the capacity for SARS-CoV-2 of cross-species transmission. This study offers critical insights for the ongoing surveillance and monitoring efforts of SARS-CoV-2 evolution, emphasizing the need for the vigilant monitoring of specific mutations in both human and animal populations.

Predicting hosts and cross-species transmission of Streptococcus agalactiae by interpretable machine learning

BackgroundStreptococcus agalactiae, commonly known as Group B Streptococcus (GBS), exhibits a broad host range, manifesting as both a beneficial commensal and an opportunistic pathogen across various species. In humans, it poses significant risks, causing neonatal sepsis and meningitis, along with severe infections in adults. Additionally, it impacts livestock by inducing mastitis in bovines and contributing to epidemic mortality in fish populations. Despite its wide host spectrum, the mechanisms enabling GBS to adapt to specific hosts remain inadequately elucidated. Therefore, the development of a rapid and accurate method differentiates GBS strains associated with particular animal hosts based on genome-wide information holds immense potential. Such a tool would not only bolster the identification and containment efforts during GBS outbreaks but also deepen our comprehension of the bacteria's host adaptations spanning humans, livestock, and other natural animal reservoirs. Methods and resultsHere, we developed three machine learning models—random forest (RF), logistic regression (LR), and support vector machine (SVM) based on genome-wide mutation data. These models enabled precise prediction of the host origin of GBS, accurately distinguishing between human, bovine, fish, and pig hosts. Moreover, we conducted an interpretable machine learning using SHapley Additive exPlanations (SHAP) and variant annotation to uncover the most influential genomic features and associated genes for each host. Additionally, by meticulously examining misclassified samples, we gained valuable insights into the dynamics of host transmission and the potential for zoonotic infections. ConclusionsOur study underscores the effectiveness of random forest (RF) and logistic regression (LR) models based on mutation data for accurately predicting GBS host origins. Additionally, we identify the key features associated with each GBS host, thereby enhancing our understanding of the bacteria's host-specific adaptations.

Transmission, seroprevalence, and maternal-fetal impact of lymphocytic choriomeningitis virus.

Congenital infections can have devastating short- and long-term impacts on the developing fetus. Lymphocytic choriomeningitis virus (LCMV) is a zoonotic pathogen of concern that causes a severe congenital syndrome but is under-recognized and under-studied. Herein we review data on the natural animal reservoirs of LCMV, modes of transmission to humans, seroprevalence of LCMV worldwide in both pregnant and non-pregnant individuals, mechanisms of viral dissemination to placenta and fetus, and impact of climate change on viral transmission. We highlight opportunities to enhance awareness of congenital LCMV and provide recommendations for prevention and monitoring among at-risk pregnant people. IMPACT: Key message of the article: LCMV is a zoonotic virus that poses a major threat to maternal-fetal health. Adds to the existing literature: We comprehensively address transmission of LCMV from the natural reservoir to the pregnant individual, placenta, and fetus. Impact: Available data call for enhanced patient and provider awareness about congenital LCMV during pregnancy, as well as a need for efforts to better define the seroprevalence and impact of congenital LCMV worldwide.

An update on current understanding of the epidemiology and management of the re-emerging endemic Lassa fever outbreaks

An update on current understanding of the epidemiology and management of the re-emerging endemic Lassa fever outbreaks

Monkeypox: Some Keys to Understand This Emerging Disease.

Simple SummaryMonkeypox has entered our lives when we have not yet fully recovered from the SARS-CoV-2 pandemic. This close relative of the smallpox virus was restricted to tropical Africa, except on rare occasions when it caused human cases in the US, UK, Singapore, or Israel. Cases have recently been identified in multiple countries in at least the Americas, Europe, Asia and Australia. Fortunately, it produces much milder clinical symptoms and a much lower mortality rate than smallpox, but even so, we have learned not to overlook any possible pathogen, and there are many unknowns about the disease. What population groups does it affect? Could it cause a pandemic? What is the animal reservoir? Do animals suffer from monkeypox as much as humans?In 1958, several monkeys in a Copenhagen laboratory developed a skin rash from which an orthopoxvirus could be isolated, which was named monkeypox virus (MPXV). However, the natural animal reservoir for MPXV is thought to be a rodent. The first human case occurred in 1970, and the incidence has increased progressively throughout the years. Starting May 2022, the number of cases outside Africa has soared, especially in Western Europe. There are two clades of MPXV, Congo Basin, with higher virulence and mortality, and Western Africa (WA). MPXV from the present outbreak has been proposed to be classified as Clade 3, distinct from the WA clade by at least 50 substitutions, which may increase human-to-human transmissibility. Most cases correspond to men in their 30s who have sex with men, and the possibility of sexual transmission is under investigation. Though there is no evidence of human-to-animal transmission, pets of positive human cases may be classified as low risk, including dogs, cats, and birds, who can be quarantined at home, and high risk, such as pet rabbits or mice, who should be isolated in official laboratories for observation. The current epidemiological data do not support the risk of a pandemic.

Recently spreading human monkeypox virus infection and its transmission during COVID-19 pandemic period: A travelers' prospective

Presently, monkeypox has emerged in multiple countries with many confirmed cases, posing a global public health threat. A link has been found between air travel and the international spread of infectious diseases including the previous spread of monkeypox.This article highlights the spread of COVID-19 through air travel, and then monkeypox spread from one country to another. Scientists are trying to establish the air travel and monkeypox spread. Any travel link from an endemic country has not been proven yet to describe the rising number of current monkeypox cases in non-endemic countries. Due to the quantification method, the direct link of the diseases with air travel might be difficult to establish. However, we have also developed different statistical models of the confirmed cases and the number of air travelers per year (noted in countries where monkeypox has spread). As there is no direct link, these models might show a probability of an indirect association of air travel. However, more strong evidence is needed in this direction.Although, the sudden appearance of monkeypox cases in multiple countries in a few days demands comprehensive epidemiological investigations, genome sequencing, and phylogenetic analysis of viral isolates to prove the travel link from an endemic country. At the same time, it is also necessary to know the real cause while also exploring any direct and/or indirect travel links between different countries. Similarly, the possibility of any zoonotic event should find out to understand the more about natural animal reservoir(s) for the monkeypox virus, which is unknown until now. However, this report will help researchers for conducting further explorative research and investigations for understanding transmission patterns and guide policymakers to make proactive policies to limit the spread of monkeypox.

Human Monkeypox-An Update

Human monkeypox disease, a rare zoonosis endemic in Western and central Africa emerged in 56 different countries around the world with an increase of 77% in cases is a global concern. Natural animal reservoir of monkeypox virus is still unknown; rodents and primates except human are the probable source of virus introduction to human. A clear and sufficient data about the virulence and transmissibility of human monkeypox disease is limited due to inconsistence in the epidemiological studies. As per World Health Organisation and Centre for Disease Control status report smallpox vaccine is found to provide 85% immunity against human monkeypox disease. There is currently no specific treatment available and two antibiotic drugs tecovirimat and brincidofovir can be used as supportive treatment for time being. ©2022iGlobal Research and PublishingFoundation. All rights reserved.

SARS-CoV-2 infection in free-ranging white-tailed deer.

Humans have infected a wide range of animals with SARS-CoV-21-5, but the establishment of a new natural animal reservoir has not been observed. Here we document that free-ranging white-tailed deer (Odocoileus virginianus) are highly susceptible to infection with SARS-CoV-2, are exposed to multiple SARS-CoV-2 variants from humans and are capable of sustaining transmission in nature. Using real-time PCR with reverse transcription, we detected SARS-CoV-2 in more than one-third (129 out of 360, 35.8%) of nasal swabs obtained from O. virginianus in northeast Ohio in the USA during January to March 2021. Deer in six locations were infected with three SARS-CoV-2 lineages (B.1.2, B.1.582 and B.1.596). The B.1.2 viruses, dominant in humans in Ohio at the time, infected deer in four locations. We detected probable deer-to-deer transmission of B.1.2, B.1.582 and B.1.596 viruses, enabling the virus to acquire amino acid substitutions in the spike protein (including the receptor-binding domain) and ORF1 that are observed infrequently in humans. No spillback to humans was observed, but these findings demonstrate that SARS-CoV-2 viruses have been transmitted in wildlife in the USA, potentially opening new pathways for evolution. There is an urgent need to establish comprehensive 'One Health' programmes to monitor the environment, deer and other wildlife hosts globally.

Leptospira interrogans biofilm formation in Rattus norvegicus (Norway rats) natural reservoirs.

Rattus norvegicus (Norway rat) is the main reservoir host of pathogenic Leptospira, the causative agent of leptospirosis, in urban environments. Pathogenic Leptospira forms biofilms in the environment, possibly contributing for bacterial survival and maintenance. Nonetheless, biofilms have not yet been studied in natural animal reservoirs presenting leptospiral renal carriage. Here, we described biofilm formation by pathogenic Leptospira inside the renal tubules of R. norvegicus naturally infected and captured in an urban slum endemic for leptospirosis. From the 65 rats carrying Leptospira in their kidneys, 24 (37%) presented biofilms inside the renal tubules. The intensity of leptospiral colonization in the renal tubules (OR: 1.00; 95% CI 1.05–1.1) and the type of occlusion pattern of the colonized renal tubules (OR: 3.46; 95% CI 1.20–9.98) were independently associated with the presence of Leptospira biofilm. Our data showed that Leptospira interrogans produce biofilms during renal chronic colonization in rat reservoirs, suggesting a possible role for leptospiral biofilms in the pathogenesis of leptospirosis and bacterial carriage in host reservoirs.

A review of Cyclospora cayetanensis in animals.

Cyclosporiasis is a global, emerging disease in humans caused by Cyclospora cayetanensis. The role of animals in the epidemiology of cyclosporiasis is not fully understood. We conducted a narrative review of the published literature on C. cayetanensis in animals. MEDLINE® (Web of Science™ ), Agricola (ProQuest), CABI Global Health (1979 to December 2020) and Food Science and Technology Abstracts (EBSCOhost) (1979 to February 2020) were searched. Studies of C. cayetanensis in or on any species of animal were eligible. Thirteen relevant studies were found. C. cayetanensis was found in wild and farmed Mediterranean mussels (Mytilus galloprovincialis), wild grooved carpet shell clams (Ruditapes decussatus) and in the faeces of dogs (domestic and street), wild chickens, wild rhesus macaques (Macaca mulatta), chimpanzees (Pan troglodytes) from a wildlife research centre, and Cynomolgus monkeys (Macaca fascicularis) from an experimental primate research centre. As the small intestines of the naturally exposed animals were not biopsied, existence of a natural animal reservoir of C. cayetanensis could not be confirmed. Animals shedding oocysts in their faeces may be paratenic hosts. Investigators were able to successfully infect the following animals with C. cayetanensis: oysters, Asian freshwater clams (Corbicula fluminea), Swiss albino mice and guinea pigs. Future non-laboratory studies of animals should use PCR coupled with DNA sequencing to confirm that the species found is C. cayetanensis. The potential role of animals in the transport of oocysts and contamination of food, water, and soil could be explored through future primary research.

Recovering influenza genomes from wild bird habitats for better avian flu surveillance

Background: Avian influenza viruses (AIVs) cause severe disease in poultry and dangerous zoonotic infections in humans. Outbreaks disrupt trade, threaten food security, and jeopardize public health. They also allow novel flu viruses to adapt to human hosts, threatening future pandemics and new types of seasonal flu. A cornerstone of outbreak prevention and pandemic preparedness is surveillance of AIVs in wild waterfowl, their natural animal reservoir. Current surveillance efforts focus on testing dead or captured birds, but rarely provide warning of dangerous strains. We have developed an alternative surveillance strategy using sediment specimens from wild bird habitats; since this is where virus-laden feces from the whole wild bird community accumulate, it likely contains an extensive collection of locally-circulating viruses. Here, we report a custom laboratory method to recover influenza genomes from sediment using targeted genomic sequencing. Methods and materials: A proof-of-concept experiment was conducted on 4 sediment specimens collected near Vancouver, Canada during the fall of 2016. Total RNA was extracted from these sediments and prepared into metagenomic sequencing libraries. Hemagglutinin, neuraminidase, and matrix segments of the influenza A virus genome were enriched using 600 custom hybridization probes, then sequenced on an Illumina MiSeq. qPCR targeting the matrix gene was used to estimate the fold-enrichment provided by the probes. Consensus sequences of hemagglutinin and neuraminidase genome segments were generated by mapping sequencing reads to subtype-specific references using the Burrows-Wheeler Aligner. Reference sequences were selected by querying the reads from each library against a BLAST database containing 8555 AIV sequences. Results: Influenza genome targets were enriched 19 million-fold following two sequential captures using our custom hybridization probe method. 17 haemagglutinin and neuraminidase genome segments were recovered from these sediment samples, 9 of which were at least 80% complete. Sequence analysis identified 6 subtypes of haemagglutinin (H3, H4, H6, H9, H10, H11) and 4 subtypes of neuraminidase (N1, N2, N6, N8, and N9). Phylogenetic analysis revealed they were closely-related to other AIV sequences previously isolated from wild birds in the same region of North America in recent years. Conclusion: Targeted genomic sequencing of wetlands sediment has demonstrated its potential as a viable complement to current AIV surveillance practices.

Rousette Bat Dendritic Cells Overcome Marburg Virus-Mediated Antiviral Responses by Upregulation of Interferon-Related Genes While Downregulating Proinflammatory Disease Mediators.

Dysregulated and maladaptive immune responses are at the forefront of human diseases caused by infection with zoonotic viral hemorrhagic fever viruses. Elucidating mechanisms of how the natural animal reservoirs of these viruses coexist with these agents without overt disease, while permitting sufficient replication to allow for transmission and maintenance in a population, is important for understanding the viral ecology and spillover to humans. The Egyptian rousette bat (ERB) has been identified as a reservoir for Marburg virus (MARV), a filovirus and the etiological agent of the highly lethal Marburg virus disease. Little is known regarding how these bats immunologically respond to MARV infection. In humans, macrophages and dendritic cells (DCs) are primary targets of infection, and their dysregulation is thought to play a central role in filovirus diseases, by disturbing their normal functions as innate sensors and adaptive immune response facilitators while serving as amplification and dissemination agents for the virus. The infection status and responses to MARV in bat myeloid-lineage cells are uncharacterized and likely represent an important modulator of the bat's immune response to MARV infection. Here, we generate DCs from the bone marrow of rousette bats. Infection with a bat isolate of MARV resulted in a low level of transcription in these cells and significantly downregulated DC maturation and adaptive immune-stimulatory pathways while simultaneously upregulating interferon-related pathogen-sensing pathways. This study provides a first insight into how the bat immune response is directed toward preventing aberrant inflammatory responses while mounting an antiviral response to defend against MARV infection.IMPORTANCE Marburg viruses (MARVs) cause severe human disease resulting from aberrant immune responses. Dendritic cells (DCs) are primary targets of infection and are dysregulated by MARV. Dysregulation of DCs facilitates MARV replication and virus dissemination and influences downstream immune responses that result in immunopathology. Egyptian rousette bats (ERBs) are natural reservoirs of MARV, and infection results in virus replication and shedding, with asymptomatic control of the virus within weeks. The mechanisms that bats employ to appropriately respond to infection while avoiding disease are unknown. Because DC infection and modulation are important early events in human disease, we measured the transcriptional responses of ERB DCs to MARV. The significance of this work is in identifying cell type-specific coevolved responses between ERBs and MARV, which gives insight into how bat reservoirs are able to harbor MARV and permit viral replication, allowing transmission and maintenance in the population while simultaneously preventing immunopathogenesis.

Detection of Hepatitis E Virus in Raw Pork and Pig Viscera As Food in Hebei Province of China.

Hepatitis E virus (HEV) is an important human pathogen with pigs serving as the main natural animal reservoir. In China, pork is the most popular meat, while pig viscera are also widely consumed. The aim of this study was to evaluate the prevalence of HEV among pigs at slaughter, and assess the presence of HEV in raw pork and pig viscera as food. Samples of pig blood, raw pork, liver, kidney, and blood curd were collected from slaughterhouse or (and) retail market. Anti-HEV antibody in serum samples was detected using enzyme-linked immunosorbent assay based on an ORF2 antigen sandwich kit. HEV RNA was tested by reverse transcription nested polymerase chain reaction (RT-nested PCR) and the viral load was further assessed using quantitative real-time PCR. The final amplicons of RT-nested PCR were sequenced and undergone phylogenetic analysis. Prevalence of antibodies to HEV was 90.4% (104/115) in pigs at slaughtered level, and one serum sample was HEV RNA positive (0.9%, 1/115). HEV RNA was detected in liver, kidney, and blood samples with positivity of 6.1% (7/114), 3.1% (4/129), and 1.2% (2/170) respectively with viral loads ranged 102.4-104.4 (2.4Log-4.4Log) genome equivalents per gram, but not in pork. The HEV RNA prevalence in both liver and kidney were statistically higher than in pork. Phylogenetic analysis showed that all obtained sequences belonged to HEV genotype 4, which were divided into subtypes 4a, 4b, 4d, and 4i, highly identical to the known human and swine HEV sequences in China. The results indicate that raw pig viscera are more likely to harbor HEV than pork, suggesting a higher transmission risk related to consuming pig organs.

Hepatitis E virus was not detected in feces and milk of cows in Hebei province of China: No evidence for HEV prevalence in cows

Hepatitis E virus (HEV) is an important human pathogen, with pigs and other species serving as natural animal reservoirs. Recently, the report of detection of genotype 4 HEV in dairy milk with high positive rate in Yunnan province of China has attracted extensive attention. To assess the zoonotic risk of cows as HEV reservoir and transmission of HEV through dairy milk, 467 fecal samples of cows, 276 fresh milk samples, and 140 retail milk samples were collected across Hebei Province, China, from March 2017 to May 2018, and detected for HEV RNA. Fecal samples of rabbit or pig were also collected for HEV detection from farms of mixed farming with cows or farms neighboring cow farms. HEV RNA was not detected in any cow feces or in any milk samples, but 9.3% feces of pigs and 18.9% feces of rabbits were positive for HEV RNA. In addition, all of the dairy milk samples undergone HEV antigen and anti-HEV antibody detections, but none was positive. Phylogenetic analysis showed that all of the HEV isolates from pigs belonged to genotype 4 and those from rabbits were genotype 3-rabbit HEV. The results indicate that, currently in Hebei province of China, HEV is not apparently prevalent in cows and hence there is no zoonotic transmission risk through dairy milk towards humans, albeit the genotype 4 and 3 (rabbit) HEV are prevalent in pigs and rabbits respectively.

Risk factors and sources of foodborne hepatitis E virus infection in the United States.

Hepatitis E virus (HEV) is an important human pathogen with pigs and other species serving as natural animal reservoirs. Ample evidence documents sporadic cases of hepatitis E acquired via consumption of undercooked meat. Chronic hepatitis E cases in immunosuppressed individuals are mostly caused by zoonotic HEV of swine origin. We report here the identification of genotype 3 HEV from non-liver commercial pork from local grocery stores in southwest Virginia, and association of HEV seropositivity to the consumption of undercooked meat in healthy young adults at a university in the United States. These results raise concerns about foodborne HEV transmission in the United States. J. Med. Virol. 88:1641-1645, 2016. © 2016 Wiley Periodicals, Inc.

Serologic Survey of Plague in Animals, Western Iran

Serologic Survey of Plague in Animals, Western Iran

From SARS coronavirus to novel animal and human coronaviruses.

In 2003, severe acute respiratory syndrome coronavirus (SARS-CoV) caused one of the most devastating epidemics known to the developed world. There were two important lessons from this epidemic. Firstly, coronaviruses, in addition to influenza viruses, can cause severe and rapidly spreading human infections. Secondly, bats can serve as the origin and natural animal reservoir of deadly human viruses. Since then, researchers around the world, especially those in Asia where SARS-CoV was first identified, have turned their focus to find novel coronaviruses infecting humans, bats, and other animals. Two human coronaviruses, HCoV-HKU1 and HCoV-NL63, were identified shortly after the SARS-CoV epidemic as common causes of human respiratory tract infections. In 2012, a novel human coronavirus, now called Middle East respiratory syndrome coronavirus (MERS-CoV), has emerged in the Middle East to cause fatal human infections in three continents. MERS-CoV human infection is similar to SARS-CoV in having a high fatality rate and the ability to spread from person to person which resulted in secondary cases among close contacts including healthcare workers without travel history to the Middle East. Both viruses also have close relationships with bat coronaviruses. New cases of MERS-CoV infection in humans continue to occur with the origins of the virus still unknown in many cases. A multifaceted approach is necessary to control this evolving MERS-CoV outbreak. Source identification requires detailed epidemiological studies of the infected patients and enhanced surveillance of MERS-CoV or similar coronaviruses in humans and animals. Early diagnosis of infected patients and appropriate infection control measures will limit the spread in hospitals, while social distancing strategies may be necessary to control the outbreak in communities if it remained uncontrolled as in the SARS epidemic.

A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa

Deep sequencing was used to discover a novel rhabdovirus (Bas-Congo virus, or BASV) associated with a 2009 outbreak of 3 human cases of acute hemorrhagic fever in Mangala village, Democratic Republic of Congo (DRC), Africa. The cases, presenting over a 3-week period, were characterized by abrupt disease onset, high fever, mucosal hemorrhage, and, in two patients, death within 3 days. BASV was detected in an acute serum sample from the lone survivor at a concentration of 1.09×106 RNA copies/mL, and 98.2% of the genome was subsequently de novo assembled from ∼140 million sequence reads. Phylogenetic analysis revealed that BASV is highly divergent and shares less than 34% amino acid identity with any other rhabdovirus. High convalescent neutralizing antibody titers of >1∶1000 were detected in the survivor and an asymptomatic nurse directly caring for him, both of whom were health care workers, suggesting the potential for human-to-human transmission of BASV. The natural animal reservoir host or arthropod vector and precise mode of transmission for the virus remain unclear. BASV is an emerging human pathogen associated with acute hemorrhagic fever in Africa.

Ebola and Marburg Viruses

Ebola and Marburg viruses, members of the filovirus family, cause severe hemorrhagic fever in human and nonhuman primates and are classified as biosafety level 4 agents. No effective filovirus-specific prophylaxis or treatment is yet commercially available. Filovirus species vary genetically, with one in the Marburg virus group and five in the Ebola virus group. Epidemiological efforts to prevent outbreaks lie mainly in identifying natural animal reservoirs. Increasingly frequent outbreaks in Africa and concerns about bioterrorism and imported cases in nonendemic areas point to the importance of public health in two ways – finding strategies to control disease outbreak and developing effective vaccines and drugs.

Chemical sensing in mammalian host-bacterial commensal associations.

The mammalian gastrointestinal (GI) tract is colonized by a complex consortium of bacterial species. Bacteria engage in chemical signaling to coordinate population-wide behavior. However, it is unclear if chemical sensing plays a role in establishing mammalian host-bacterial commensal relationships. Enterohemorrhagic Escherichia coli (EHEC) is a deadly human pathogen but is a member of the GI flora in cattle, its main reservoir. EHEC harbors SdiA, a regulator that senses acyl-homoserine lactones (AHLs) produced by other bacteria. Here, we show that SdiA is necessary for EHEC colonization of cattle and that AHLs are prominent within the bovine rumen but absent in other areas of the GI tract. We also assessed the rumen metagenome of heifers, and we show that it is dominated by Clostridia and/or Bacilli but also harbors Bacteroidetes. Of note, some members of the Bacteroidetes phyla have been previously reported to produce AHLs. SdiA-AHL chemical signaling aids EHEC in gauging these GI environments, and promotes adaptation to a commensal lifestyle. We show that chemical sensing in the mammalian GI tract determines the niche specificity for colonization by a commensal bacterium of its natural animal reservoir. Chemical sensing may be a general mechanism used by commensal bacteria to sense and adapt to their mammalian hosts. Additionally, because EHEC is largely prevalent in cattle herds, interference with SdiA-mediated cattle colonization is an exciting alternative to diminish contamination of meat products and cross-contamination of produce crops because of cattle shedding of this human pathogen.