The stomach content analysis of whales in Alorand Lamalera Islands, Savu Sea, Indonesia
1

Delianis Pringgenies, 2Agus Hartoko, 2,3Jahved F. Maro,
4
Takashi Matsuishi
1

Department of Marine Science, Faculty of Fisheries and Marine Science, Diponegoro
University, Semarang, Central Java, 50275 Indonesia; 2 Department of Fisheries, Facultyof Fisheries and Marine Science, Diponegoro University, Semarang, Central Java, 50275
Indonesia; 3 Department of Fisheries, Tribuana University, Kalabahi, Alor, Indonesia;
4
Faculty of Fisheries Sciences, Hokkaido University, Japan. Corresponding author:
D. Pringgenies, pringgenies@yahoo.com

Abstract. There has been little information and no comprehensive study made on whales (Cetacean) in
Indonesia, particularly in the region of the Savu sea. Alor Island and Lamalera Island are a part of the
Savu sea region. Savu sea is the main migratory route for cetaceans. The research aims to determine
the DNA makeup of whales in the Savu sea region, both stranded and caught, and to perform a DNA
analysis of their stomach content to determine their natural diet. The research was conducted from May
to September 2020. The results of the DNA analysis of stranded whales found the species of Mesoplodon
densirostris. In the stomach of the stranded whale, a parasitic worm of Ancylostoma ceylanicum wasfound. DNA analysis of the whales caught by fishermen in Lamalera Island was Physeter catodon. The
squid Sepioteuthis lessoniana is determined to be the natural diet of the whales in this region.
Sepioteuthis lessoniana was determined to be the natural diet of the whales.
Key Words: Alor, DNA amplification, Lamalera, squid, whale.

Introduction. Alor and Lamalera are islands located in the Savu sea region, at the eastend of Nusa Tenggara Islands, Indonesia. These islands are bordered by the Sea ofFlores and Banda Sea to the north, Ombai strait to the south (separating it from Timor
Islands), and Strait of Pantar to the west (separating it from Pantar Island). Pods ofwhales can be found in the waters of Alor, Lamalera, and their surrounding regions.
Every year, cases of stranded whales are reported. Whales are marine mammals that live
in seas worldwide and are sought after for their economic value. Two parvorders ofwhales are currently known: the toothed whale (Odontoceti) and Baleen whales(Mysticeti). Odontoceti is carnivorous, and its diet consists of fish, squids, and cuttlefish.
They are closely related to dolphins and snub fin dolphins. Members of Mysticeti
parvorder are generally ampler in size than those of Odontoceti. They possess distinct,
brush-like organs called baleens. This unique structure is used to catch their natural diet,planktons (Bergman 2012; Berta et al 2016).
There are 31 species of cetaceans of whales, dolphins, dugong in the Indonesianseawaters (Rosas et al 2012). These animals are spread all over the coast to the deepsea and have both residential and migratory behavior. Several species of cetaceans with
migratory behavior occupy the Eastern Indonesia waters as a migratory pathway fromthe Indian to Pacific ocean through the straits of Komodo island, Solor - Lembata, Alor,
Banda Sea, southeast Sulawesi, east Sulawesi, and Sorong – Fakfak of Papua island at
the north (Mujiyanto et al 2017). Bottlenose dolphins (Tursiops truncatus) were recorded
and exhibited bow-riding behavior and feeding; Fraser's dolphin (Lagenodelphis hosei)
were recorded exhibiting the behavior of traveling and aerials driving arc; Pantropicalspinner dolphins (Stenella longirostris) were recorded showing traveling bows andaerials; and the Pantropical dolphins (Stenella attenuata) were recorded exhibiting aerial
avoidance and aerial behavior. Recorded whales were the dwarf killer whale (Feresa
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attenuate) and dwarf sperm whales (Kogia breviceps). The coastal fishing communities ofAlor and Lamalera are very familiar with whales, because these animals are one of themarine products that are considered delicacies and precious materials in ethnic crafts.
However, the causes of frequent stranding of whales in the region, both individually anden masse, have yet to be determined.
More information regarding the Cetacean species based on DNA analysis in Alorand Lamalera is necessary to be obtained because it can contribute to marine wildlife
conservation efforts. Effective and appropriate conservation efforts must be based on
precise data, as the authors provide in this paper. Therefore, it is necessary to study
whales in the Strait of Alor and Lamalera, East Nusa Tenggara, Indonesia. So far, theactual cause of the population decline is unknown. Traditional whaling (through whale
capturing) has a minimum destructive impact on fish. The research had two objectives.
Firstly, to determine the types of whales stranded in the Alor Strait and those caught on
the Lamalera coast as part of the Savu Sea, East Nusa Tenggara, Indonesia. Secondly, toprovide DNA analysis of whale guts. The purpose of this research is to determine the DNA
analysis of the captured whale, stranded whale, whale guts content to confirm theirpresence in the Savu sea. The analysis of the whale stomach content reveals the whale
natural feed, based on DNA analysis.
Material and Method
Sample collection. The meat samples of stranded whales were collected from coastal
areas of Alor Strait, and the samples of caught whales were collected from fishermen
operating in the vicinity of Lamalera. The samples collected were slices of the whale meatand the stomach content of whales. After collection, the samples were stored in a cooler
box and transported to Genetica Science Indonesia laboratory, Jakarta, for analysis. To
analyze the identification of whales with molecular methods, it is enough to collect any
fish body parts weighing 100 g.
DNA extraction, DNA amplification, and sequencing. DNA extraction of all samples
was performed using two commercial kits, ZR Tissue and Insect DNA MiniPrep genomic
DNA. The sample was directly placed into a ZR BashingBead ™ Lysis Tube and wasprocessed.
The DNA from the samples was isolated and purified with Fast-Spintechnology.
Genomic DNA extraction was carried out using ZR Tissue and Insect DNA
MiniPrep. The amplification PCR utilized MyTaq Red Mix (Bioline) BIO-25047. PCR MasterMix consisted of several components (25µl), namley: dd H2O reagent, MyTaq Red Mix(Bioline)
BIO-25047,
VF2_t1:TGTAAAACGACGGCCAGTCAACCAACCACAAAGACATTGGCAC,
FishF2_t1:
TGTAAAACGACGGCCAGTCGACTAATCATAAAGATATCGGCAC,
FishR2_t1:
CAGGAAACAGCTATGACACTTCAGGGTGACCGAAGAATCAGAA,
FR1d_t1:
CAGGAAACAGCTATGACACCTCAGGGTGTCCGAARAAYCARAA dan template DNA. The
sequencing process was carried out using ABI PRISM 3730xl Genetic Analyzer developedby Applied Biosystems, USA. The kit used for the sequencing purpose is BigDye®
Terminator v3.1 Cycle Sequencing.
Homology Using BLAST. Analysis of the sample DNA sequence was compared with thesequence in the DNA database. The search was carried out using the Basic Local
Alignment Search Tool (BLAST) database in National Center for Biotechnology
Information, National Institute for Health, USA (Pearson 2013) to determine thepercentage match of species based on the level of homology of the nucleotide basesequence. The sequence of nucleotide bases is then compared with a database available
on GenBank. Visual qualitative data, DNA isolation and amplification profiles, andelectropherograms are presented descriptively.

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Results and Discussion
Stranded whales in Alor coast and caught whales in Lamalera coast. There arereports of whales stranded in Alor waters almost every year. They mention up to 7
whales between 5 and 7 meters long. However, the authors got information from theresearch site that the longest stranded whale recorded in the area exceeded 10 meters.
April to November is when it is common to find beaching whales on the coast of Alor
Island. Stranded whales are commonly dark blue/gray on top, and lighter gray on theunderside, and their heads are usually in the shades of brown. Almost all of them have
injuries on their bodies. These whales are generally found in physical decomposition(Figure 1a). They are then buried on the beach using heavy equipment. Whales caught inthe coastal area of Lamalera and its surroundings are usually cut and distributed tocoastal village communities to be consumed. Each family processes them into various
products. One processed product made from whale meat is the sun-dried marinated fishjerky (Figure 1b). The stomach content of the stranded or captured whales and thedigestive material found in their stomachs are presented in Figures 1c and 1d. Squid(Sepioteuthis lessoniana) is the whale's natural feed and a species abundant in Alor and
Lamalera seawater.

(a1)

(a2)

(c)

(b)

(d)

Figure 1. (a1) stranded whale in Alor beach; (a2) caught whale in Lamalera beach, (b)dried whale meat for consumption, (c) stomach content of a stranded whale, (d) squid(Sepioteuthis lessoniana) found in the stomach of caught whale (Source: authors’personal archive).
Identification of whale, their stomach content and diet, and DNA amplification.
The stomach content of a stranded whale was extricated from its intestines. Cuts of thestomach content were collected and were analyzed using the molecular DNA method.
Amplified COI gene was measured at 700 bp of length using the 10,000 bp DNA ladderfor comparison. Amplified COI gene was measured at 700 bp of length using the 10,000
bp DNA ladder for comparison. The results of DNA amplification of stranded whale
isolates, caught whales, and their stomach content are presented in Figure 2. It can beseen that the isolates produce a single band with a size of 700 bp (base pair) according
to the comparison using DNA markers. The measured isolates had base lengths of, inincreasing order, 100, 200, 300, 400, 500 600, 700, 800, 900, 900, 1000, 1500, and3000 base pairs, respectively.

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Marker

Stomach Content ofStranded Whale

Stranded Whale

Caught Whale

Natural feed

M

3000
1500
1000
900
800
700
600
500
400
300
200
100

Figure 2. DNA amplification of the stomach content of stranded and caught whales(source: photo taken by authors).
Material identification using BLAST analysis indicates that the stranded whale stomach
content isolate (spesific amino acid compound that is separated chemically indicating theDNA) with access number KY640299.1 has the value of 98% homology with the parasite
Ancylostoma ceylanicum. It also indicated that the stranded whale isolate with accessnumber KF032875.2 has 97% homology with the whale species Mesoplodon densirostris.
Meanwhile, caught whale gut isolate with access number KJ168062.1 has the value of
98% homology with squid from the species of Sepioteuthis lessonianai. Whale isolatewith access number KU891394.1 has the value of 100% homology with Physeter catodon
whale species (Table 1 and Figure 2).
Table 1
The identity of stranded whales, caught whales and the contents of their stomachs by
BLAST analysis
No

IsolateRelative match

1

Stranded whale

2
3

Stomach content of
stranded whale
Caught whale

M. densirostris isolate SWFSC ID
z0079838 mitochondrion, partial
genomeA. ceylanicum

4

Natural feed, squid

P. catodon isolate mtGen81
mitochondrion, complete genome
S. lessoniana

Homology(%)
97%

KF032875.2

98%

KY640299.1

100%

KU891394.1

98%

KJ168062.1

Access No.

The results of phylogenetic tree processing indicate the clustering of isolates with otherorganisms in the closest to the furthest levels. The intestinal contents of the stranded
whales were related to the parasitic roundworm A. ceylanicum, with U. sanguinis
haplotype, Rhabditida sp, and Nematode sp as the outer group. The phylogenetic tree of
stranded whales indicates that the isolates are related to whale species of M. densirostris.
The phylogenetic tree of stomach content isolates of caught whales shows clustering withthe genus Teuthida and the species S. lessoniana. The phylogenetic tree of caught whales
clustering with whales of the species Physeter catodon. Morphologically, P. catodon whale

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has a distinguishably large and blunt cranium. The size of its head can take up to onethird of its total body length. The tip of its lower mandible is located precisely at the rearend of its frontal cranium.
There are also reports that smaller whales, such as members of the genus
Berardius, washed ashore of Lamalera island. Whales of the species B. minimus, a newly
named species, can also be found in the local waters of Hokkaido, Japan (Yamada et al2019). Information on the distribution and ecology of whales is still limited, especially forregions in Indonesia, because the distribution of species and their behavior is unknown.
This research focuses on two types of whales, stranded whales and caught whales. DNA
analysis indicated that the strand whale sample type was M. densirostris, while the DNA
sample of the caught whale was P. catodon. According to information from people aroundthe coast of Alor and Lamalera, Mesplodon (beaked whale) is often stranded around thecoast of Alor, and P. catodon is the primary source of livelihood for whale hunters in
Lamalera.
P. catodon with box-like head morphology is one the most common in temperate
and tropical latitudes and most likely to be found in waters inhabited by squid because it
is a carnivore feeding on squid or molluscivore. It has a swimming depth from 1,000 m tothe sea's surface and is adapted to cold-water upwellings. Because they are so welladapted for deep-water swimming, they are in real danger of stranding when they moveinshore. This study found a parasitic worm of the species A. ceylanicum in the stomach
content of the stranded whales. The presence of these pathogenic organisms may explain
why the whales can become unhealthy, which may eventually lead to stranding. As
happened to other types of mammals (seals) these hookworms are also the cause ofdeath (Seguel et al 2018). A.ceylanicum is a hookworm commonly found in domestic
dogs and cats throughout Asia and Australia. Studies in Australia inform intervention andprevention strategies to control hookworm parasites such as A. ceylanicum in dogs andhumans. A "One Health" approach is essential for preventing these diseases(Beknazarova et al 2020).
A. ceylanicum is more common in tropical soils and areas, and its presence canpose a health and environmental threat (Smout et al 2017). The results of this study arealso supported by Papaiakovou (Papaiakovou et al 2017), which explains that A.
ceylanicum is a zoonotic hookworm, which is most likely the second most common
hookworm species infecting humans in Asia. WHO also reports that A. ceylanicum is thecause of 'neglected diseases' which are zoonotic, and this parasite can harm generalpublic health (Thompson 2015).
The discovery of this parasite in the whale's stomach can be an indicator of thepoor health of the whales so that they cannot navigate properly and eventually die frombeing stranded on the beach. This finding is related to the research findings reported by(García-Grajales et al 2017). A survey was conducted along the central coast of Oaxaca,
Mexico. The results of the study reported the condition of several M. peruvianus whale
carcasses that were washed ashore. The main pathological research findings refer to therespiratory and digestive systems of whales. They describe air that appeared from thechest cavity, indicating pneumothorax, collapsed lungs, and showed consistency ofatelectasis if touched. A collapsed lung of a stranded individual may be the result of
apnea, which is associated with dysbarism (García-Grajales et al 2017).
Tracing the natural diet of whales in the Strait of Alor and Lamalera using DNA
analysis of stomach content indicated that their food in the area predominantly consistsof squid from the species S. lessoniana. A study by Clarke & Pascoe (1997) on theanalysis of stomach content of stranded, male P. catodori whales in Penzance, Cornwall
reported a diet consisting of four families of cephalopods, namely Histioteuthis spp.,
Architeuthis spp., T. sagittatus, and Galiteuthis sp. This diet is enriched with the intake of
Oceanic Octopod, Haliphron atlanticus, and only one neritic species: Loligoforbesi. The
results of this study indicated that most of the squid consumed were oceanic species,
namely Histioteuthis spp., Architeuthis spp., T. sagittatus, and Galiteuthis sp. This finding
is similar to what was reported in a study by Santos et al (2001), who discovered thatthe whale's diet consisted of oceanic squid, oceanic fish remains, and crustaceans. The
squid found in the stomach of P. catodori from the coast of Alor, Indonesia, is S.

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lessoniana, a neritic species. This finding could indicate that the coasts of Alor and
Lamalera are the feeding grounds for these two whale species because of theconcentration of the number of the squid species and the suitability of the currents in thetwo regions. Whale migration and residence patterns are closely related to currents,
which in turn affects the potential abundance of food sources in the waters (Aulich et al2019). This condition makes the straits of Alor and Lamalera as ideal stopping points inthe migration routes of these two whale species. S. lessoniana is a squid species with avery short life cycle, only four months, with more than 1000 spawns being hatched per
cycle. After they lay eggs, they still have a chance to spawn again. This fertility is thesource of abundance and the speed of population recovery for this species (Pringgenies
et al 2000; Arkhipkin et al 2015; Pringgenies & Ariyanto 2021). In comparison, the squidof the L. duvaucelii species has a life cycle of 12 months. Mature individuals of thisspecies can spawn eggs only once because afterward, the parent will die (Lipiński et al2016). Visual and field observations at the coastal fish markets of Alor and Lamalera
indicate abundant populations of squid and fish species from deep waters in these twoareas. Jefferson et al (1993) estimated that M. densirostris had various species of deepsea fish and squids as its natural diet. Furthermore, the paper also reported that
Blainville's beaked whale was found in the temperate and tropical waters. The species iscommonly found off the shores of Hawaii, where they have been observed both in thewater and stranded on the coast. They are found in deep water, either individually or insmall pods, where the depth of the oceans reaches 1000 fathoms (about 660 m). Due totheir deep-water habitat, Blainville's beaked whale has rarely been seen swimming freely
over the years, and it was identified as a species only by its skeletal remains.
The molecular DNA analysis of this study revealed that the caught whale in
Lamalera was Physeter catodon and the species of the stranded whale was Mesoplodon
densirostris. The Baleen whale, its common name, was seen in the waters around
Denmark with a length of almost 9 meters, possessing a very large head covering nearly
the entirety of its body (Friel & Sleeman 2003), similar to those seen in the waters ofAlor and Lamalera, Indonesia. An increase in P. catodon population was reported amongwaters in England and Ireland (Cabot 1967). The information is exciting because this
could mean that the whales of the species P. catodon may thrive due to their low
mortality rate. Another interesting finding regarding this species is the commensal
bacteria that exist in its body. Commensal bacteria live in symbiosis in the body ofwhales, are not harmful, and can even be beneficial in some cases. Like bacteria from thestomach contents of sea cucumbers, they have the potential to act as an anti-bacterial(Pringgenies et al 2019). Bacterial symbionts in gastropods can be anti-bacterial multidrug resistant (Bahry et al 2017). However, in certain conditions, for example, in
immuno-suppressants, these bacteria can be a health risk to the host. Commensal
microbes of mammals play an essential role in the health of their host. The research
results on tissue samples of whale blood, feces, and muscle microbiome showed
differences in symbiotic microorganisms among the three tissues. Pathogenic bacteria
detected in blood, muscle, and fecal samples can cause several health problems inwhales (Li et al 2019). The findings of this research on whales in the waters of Alor and
Lamalera contribute to the new knowledge regarding the health problems as a cause ofwhale mortality. They can be used as a benchmark for monitoring the health of marine
mammals. This very first study of whale (Cetacean) species identification using molecularmethod of DNA analysis will give the high accuracy and universal result, but may havesome difficulties in whale meat sample collection in remote areas. This is because theAlor Island and Lamalera areas are beautiful small islands but with limited accesspossibilities.
Conclusions. DNA analysis found that the species of the stranded whale was
Mesoplodon densirostris, whereas the caught whale species was P. catodon. The resultsof the DNA analysis showed that the parasitic worm A. ceylanicum was present in thestomach content of the stranded whale. They also revealed that the squid S. lessoniana
was the natural diet of the whales in this region.

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Acknowledgements. The authors would like to thanks to the Research Institute of
Diponegoro University for the research funding no. 233-39/UN7.6.1/PP/2021. Special
thanks also to the local fisherman and traditional elder for their support andcollaborations during the field whale meat sample collections in Alor and Lamalera.
Conflict of interest. The authors declare that there is no conflict of interest.
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Received: 02 September 2021. Accepted: 12 October 2021. Published online: 30 October 2021
Authors:
Delianis Pringgenies, Department of Marine Sciences, Faculty of Fisheries and Marine Sciences, Diponegoro
University, 50275 Semarang, Indonesia, e-mail: pringgenies@yahoo.com;
delianispringgenies@lecturer.undip.ac.id
Agus Hartoko, Department of Fisheries, Faculty of Fisheries and Marine Sciences, Diponegoro University, 50275
Semarang, Indonesia, e-mail: agushartoko@lecturer.undip.ac.id
Jahved Ferianto Maro, Doctoral Program, Department of Fisheries, Faculty of Fisheries and Marine Sciences,
Diponegoro University, 50275 Semarang, Indonesia, e-mail: yantugisuntrib@gmail.com
Takashi Matsuishi, Faculty of Fisheries Sciences, Hokkaido University, Japan, e-mail: catm@fish.hokudai.ac.jp
This is an open-access article distributed under the terms of the Creative Commons Attribution License, which
permits unrestricted use, distribution and reproduction in any medium, provided the original author and source
are credited.
How to cite this article:
Pringgenies D., Hartoko A., Maro J. F., Matsuishi T., 2021 The stomach content analysis of whales in Alor and
Lamalera Islands, Savu Sea, Indonesia. AACL Bioflux 14(5):3119-3126.

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