Francesco Cicala Murolo - Academia.edu (original) (raw)
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Papers by Francesco Cicala Murolo
PeerJ, 2021
The shrimp gut is a long digestive structure that includes the Foregut (stomach), Midgut (hepatop... more The shrimp gut is a long digestive structure that includes the Foregut (stomach), Midgut (hepatopancreas) and Hindgut (intestine). Each component has different structural, immunity and digestion roles. Given these three gut digestive tract components’ significance, we examined the bacterial compositions of the Foregut, Hindgut, and Midgut digestive fractions. Those bacterial communities’ structures were evaluated by sequencing the V3 hypervariable region of the 16S rRNA gene, while the functions were predicted by PICRUSt2 bioinformatics workflow. Also, to avoid contamination with environmental bacteria, shrimp were maintained under strictly controlled conditions. The pairwise differential abundance analysis revealed differences among digestive tract fractions. The families Rhodobacteraceae and Rubritalaceae registered higher abundances in the Foregut fraction, while in the Midgut, the families with a higher proportion were Aeromonadaceae, Beijerinckiaceae and Propionibacteriaceae. F...
Fish physiology and biochemistry, 2021
The aquaculture industry's rapid growth to meet commercial demand can trigger an outbreak of ... more The aquaculture industry's rapid growth to meet commercial demand can trigger an outbreak of infectious diseases due to high-density farming. Antibiotic overuse and misuse in fish farming and its global health consequences have led to searching for more natural alternatives such as medicinal plants. In this sense, garlic (Allium sativum) has different bioactive compounds with biological properties for animal health. Among them are the ajoene, alliin, and allicin, which confer biological properties such as growth promotion, antimicrobial, antiviral, antioxidant, and antiparasitic. Ways to use garlic in aquaculture include oil, fresh mash, aqueous extract, and garlic powder. The powder presentation is the most used in aquaculture; it is generally applied by oral administration, adding to the feed, and the dose used ranges from 0.05 to 40 g/kg of feed. Garlic has been used in the aquaculture of different species such as rainbow trout (Oncorhynchus mykiss), spotted grouper (Epinephe...
Molecular Ecology
Zooplankton plays a pivotal role in sustaining the majority of marine ecosystems. The distributio... more Zooplankton plays a pivotal role in sustaining the majority of marine ecosystems. The distribution patterns and diversity of zooplankton provide key information for understanding the functioning of these ecosystems. Nevertheless, due to the numerous cryptic and sibling species and the lack of diagnostic characteristics for early developmental stages, the identification of the global-to-local patterns of zooplankton biodiversity and biogeography remains challenging in different research fields. The spatial and temporal changes in the zooplankton community in the open waters of the southern Gulf of Mexico were assessed using metabarcoding analysis of the V9 region of 18S rRNA and mitochondrial cytochrome oxidase c subunit I (COI). Additionally, a multi-scale analysis was implemented to evaluate which environmental predictors may explain the variability in the structure of the zooplankton community. Our findings suggest that the synergistic effects of dissolved oxygen concentration, temperature, and longitude (intended as a proxy for still unidentified predictors) may explain both spatial and temporal zooplankton variability even with low contribution. Furthermore, the zooplankton distribution likely reflects the coexistence of three heterogeneous ecoregions and a bio-physical partitioning of the studied area. Finally, some taxa were either exclusive or predominant with either 18S or COI markers. This may suggest that comprehensive assessments of the zooplankton community may be more accurately met by the use of multi-locus approaches.
Aquaculture International
This study aimed to evaluate the structural changes in the microbiota of Penaeus monodon during i... more This study aimed to evaluate the structural changes in the microbiota of Penaeus monodon during its ontogenetic development and evaluate functional shifts in metabolic pathways. To address these questions, shrimp were maintained under isolated conditions to avoid cross-contamination with other environmental bacteria and reared in twelve 50 L plastic tanks connected to a recirculation system. The replicates of pooled intestine specimens from 15 shrimp were analyzed at postlarvae, juvenile, and adult phases for nucleic acid extraction. We tested the V3 region of the 16S rRNA gene from the postlarvae, juvenile, and adult stages. Resulting amplicon sequence variants (ASVs) were used to evaluate both structural and functional shifts during tiger shrimp development. Although the richness and diversity of microbiota were only slightly affected, the phylum Proteobacteria (genus Vibrio) was significantly predominant in the earliest stages of life, while Actinobacteria (genus Actinotalea) significantly increased in adult shrimp. Moreover, functional predictions by PICRUSt suggested that microbiota is primarily involved in metabolic activities during each developmental stage. Overall, these results suggest that each ontogenetic stage may provide specific conditions for the proliferation of certain bacterial taxa. Nerveless, alternative microbiota maintains similar ecological activities; thus, we posit that “stage-specific” changes in microbiota may be regulated to guarantee pivotal host functions.
The gastro-intestinal (GI) microbiota of abalone contains a highly complex bacterial assemblage p... more The gastro-intestinal (GI) microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA 454 pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings reveal...
PeerJ
The GI microbiota of abalone contains a highly complex bacterial assemblage playing an essential ... more The GI microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities of abalone species characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their abalone host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA gene pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our finding...
Journal of invertebrate pathology, Jan 23, 2018
Withering syndrome (WS) is a chronic wasting disease affecting abalone species attributed to the ... more Withering syndrome (WS) is a chronic wasting disease affecting abalone species attributed to the pathogen Candidatus Xenohaliotis californiensis (CXc). Wild populations of blue (Haliotis fulgens) and yellow (H. corrugata) abalone have experienced unusual mortality rates since 2009 off the peninsula of Baja California and WS has been hypothesized as a possible cause. Currently, little information is available about the genetic diversity of CXc and particularly the possible existence of strains differing in pathogenicity. In a recent phylogenetic analysis, we characterized five coding genes from this rickettsial pathogen. Here, we analyze those genes and two additional intergenic non-coding regions following multi-locus sequence typing (MLST) and multi-spacer typing (MST) approaches to assess the genetic variability of CXc and its relationship with blue, yellow and red (H. rufescens) abalone. Moreover, we used 16S rRNA pyrosequencing reads from gut microbiomes of blue and yellow abalo...
International journal of systematic and evolutionary microbiology, Jan 11, 2016
Background: The withering syndrome (WS) is an infectious disease initially affecting the gastro-i... more Background: The withering syndrome (WS) is an infectious disease initially affecting the gastro-intestinal tract (GI) of wild abalone populations of the coasts of Baja California. In spite of its high incidence, structural and functional changes in abalone GI microbiotas under WS-stressed conditions remain poorly investigated. Moreover, it is equally uncertain if interspecific microbiota features, such as the presence or absence of certain bacterial species, their abundances, and their functional capabilities, may prevent or at least lead to different microbiota responses. Healthy Haliotis fulgens and Haliotis corrugata from Baja California Sur (Mexico) harbor species-specific structural and functional microbiota profiles; hence, we hypothesize a distinctive microbiota response under WS-stressed conditions. Here, we compared both the structural arrangements and functional capabilities of healthy and dysbiotic microbiotas using 454 pyrosequencing high throughput sequencing technologi...
PeerJ, 2021
The shrimp gut is a long digestive structure that includes the Foregut (stomach), Midgut (hepatop... more The shrimp gut is a long digestive structure that includes the Foregut (stomach), Midgut (hepatopancreas) and Hindgut (intestine). Each component has different structural, immunity and digestion roles. Given these three gut digestive tract components’ significance, we examined the bacterial compositions of the Foregut, Hindgut, and Midgut digestive fractions. Those bacterial communities’ structures were evaluated by sequencing the V3 hypervariable region of the 16S rRNA gene, while the functions were predicted by PICRUSt2 bioinformatics workflow. Also, to avoid contamination with environmental bacteria, shrimp were maintained under strictly controlled conditions. The pairwise differential abundance analysis revealed differences among digestive tract fractions. The families Rhodobacteraceae and Rubritalaceae registered higher abundances in the Foregut fraction, while in the Midgut, the families with a higher proportion were Aeromonadaceae, Beijerinckiaceae and Propionibacteriaceae. F...
Fish physiology and biochemistry, 2021
The aquaculture industry's rapid growth to meet commercial demand can trigger an outbreak of ... more The aquaculture industry's rapid growth to meet commercial demand can trigger an outbreak of infectious diseases due to high-density farming. Antibiotic overuse and misuse in fish farming and its global health consequences have led to searching for more natural alternatives such as medicinal plants. In this sense, garlic (Allium sativum) has different bioactive compounds with biological properties for animal health. Among them are the ajoene, alliin, and allicin, which confer biological properties such as growth promotion, antimicrobial, antiviral, antioxidant, and antiparasitic. Ways to use garlic in aquaculture include oil, fresh mash, aqueous extract, and garlic powder. The powder presentation is the most used in aquaculture; it is generally applied by oral administration, adding to the feed, and the dose used ranges from 0.05 to 40 g/kg of feed. Garlic has been used in the aquaculture of different species such as rainbow trout (Oncorhynchus mykiss), spotted grouper (Epinephe...
Molecular Ecology
Zooplankton plays a pivotal role in sustaining the majority of marine ecosystems. The distributio... more Zooplankton plays a pivotal role in sustaining the majority of marine ecosystems. The distribution patterns and diversity of zooplankton provide key information for understanding the functioning of these ecosystems. Nevertheless, due to the numerous cryptic and sibling species and the lack of diagnostic characteristics for early developmental stages, the identification of the global-to-local patterns of zooplankton biodiversity and biogeography remains challenging in different research fields. The spatial and temporal changes in the zooplankton community in the open waters of the southern Gulf of Mexico were assessed using metabarcoding analysis of the V9 region of 18S rRNA and mitochondrial cytochrome oxidase c subunit I (COI). Additionally, a multi-scale analysis was implemented to evaluate which environmental predictors may explain the variability in the structure of the zooplankton community. Our findings suggest that the synergistic effects of dissolved oxygen concentration, temperature, and longitude (intended as a proxy for still unidentified predictors) may explain both spatial and temporal zooplankton variability even with low contribution. Furthermore, the zooplankton distribution likely reflects the coexistence of three heterogeneous ecoregions and a bio-physical partitioning of the studied area. Finally, some taxa were either exclusive or predominant with either 18S or COI markers. This may suggest that comprehensive assessments of the zooplankton community may be more accurately met by the use of multi-locus approaches.
Aquaculture International
This study aimed to evaluate the structural changes in the microbiota of Penaeus monodon during i... more This study aimed to evaluate the structural changes in the microbiota of Penaeus monodon during its ontogenetic development and evaluate functional shifts in metabolic pathways. To address these questions, shrimp were maintained under isolated conditions to avoid cross-contamination with other environmental bacteria and reared in twelve 50 L plastic tanks connected to a recirculation system. The replicates of pooled intestine specimens from 15 shrimp were analyzed at postlarvae, juvenile, and adult phases for nucleic acid extraction. We tested the V3 region of the 16S rRNA gene from the postlarvae, juvenile, and adult stages. Resulting amplicon sequence variants (ASVs) were used to evaluate both structural and functional shifts during tiger shrimp development. Although the richness and diversity of microbiota were only slightly affected, the phylum Proteobacteria (genus Vibrio) was significantly predominant in the earliest stages of life, while Actinobacteria (genus Actinotalea) significantly increased in adult shrimp. Moreover, functional predictions by PICRUSt suggested that microbiota is primarily involved in metabolic activities during each developmental stage. Overall, these results suggest that each ontogenetic stage may provide specific conditions for the proliferation of certain bacterial taxa. Nerveless, alternative microbiota maintains similar ecological activities; thus, we posit that “stage-specific” changes in microbiota may be regulated to guarantee pivotal host functions.
The gastro-intestinal (GI) microbiota of abalone contains a highly complex bacterial assemblage p... more The gastro-intestinal (GI) microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA 454 pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings reveal...
PeerJ
The GI microbiota of abalone contains a highly complex bacterial assemblage playing an essential ... more The GI microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities of abalone species characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their abalone host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA gene pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our finding...
Journal of invertebrate pathology, Jan 23, 2018
Withering syndrome (WS) is a chronic wasting disease affecting abalone species attributed to the ... more Withering syndrome (WS) is a chronic wasting disease affecting abalone species attributed to the pathogen Candidatus Xenohaliotis californiensis (CXc). Wild populations of blue (Haliotis fulgens) and yellow (H. corrugata) abalone have experienced unusual mortality rates since 2009 off the peninsula of Baja California and WS has been hypothesized as a possible cause. Currently, little information is available about the genetic diversity of CXc and particularly the possible existence of strains differing in pathogenicity. In a recent phylogenetic analysis, we characterized five coding genes from this rickettsial pathogen. Here, we analyze those genes and two additional intergenic non-coding regions following multi-locus sequence typing (MLST) and multi-spacer typing (MST) approaches to assess the genetic variability of CXc and its relationship with blue, yellow and red (H. rufescens) abalone. Moreover, we used 16S rRNA pyrosequencing reads from gut microbiomes of blue and yellow abalo...
International journal of systematic and evolutionary microbiology, Jan 11, 2016
Background: The withering syndrome (WS) is an infectious disease initially affecting the gastro-i... more Background: The withering syndrome (WS) is an infectious disease initially affecting the gastro-intestinal tract (GI) of wild abalone populations of the coasts of Baja California. In spite of its high incidence, structural and functional changes in abalone GI microbiotas under WS-stressed conditions remain poorly investigated. Moreover, it is equally uncertain if interspecific microbiota features, such as the presence or absence of certain bacterial species, their abundances, and their functional capabilities, may prevent or at least lead to different microbiota responses. Healthy Haliotis fulgens and Haliotis corrugata from Baja California Sur (Mexico) harbor species-specific structural and functional microbiota profiles; hence, we hypothesize a distinctive microbiota response under WS-stressed conditions. Here, we compared both the structural arrangements and functional capabilities of healthy and dysbiotic microbiotas using 454 pyrosequencing high throughput sequencing technologi...