The document provides information on review papers and metagenomics. It begins with defining a review paper as a critical analysis of previously published literature that summarizes, classifies, analyzes and compares existing works. It describes the different types of review papers. The document then discusses metagenomics, providing a history and overview of the field. It explains that metagenomics involves directly extracting and sequencing DNA from environmental samples without culturing to study microbial communities. Examples of applications in various fields like medicine, engineering and agriculture are provided. The concluding remarks summarize key points about the importance of review papers and references are listed.

1. REVIEW PAPER
: an insight
Bipasha Roy
3rd Sem, MSc Biotechnology
ASSAM UNIVERSITY
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1 What is a review article
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Review article:
insight
Method of
writing.
Topic of discussion:
using review article
example
Conclusion

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WHY ?
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WHAT ?
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• A critical, constructive
analysis of the literature in
a specific field through
summary, classification,
analysis & comparison.
• A scientific text relying on
previously published
literature or data.
• New data from the author’s
experiments are not
presented.
• It provides extensive review of
previously published literature and to
put them into perspective.
• It offers critical evaluation of the
published literature.
• It creates an understanding of the
topic.
• Identify gap in knowledge.
• It provides a new
approach/perspective that would
stimulate further research.
Review paper

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TYPES
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Review article
Narrative
Selected studies are
compared and summarized
on the basis of the author’s
experience, existing
theories and models.
Results are based on
qualitative, not
quantitative.
Best evidence
A focus on the selected
studies is combined with
systematic method of
study- selection and result
exploration.
Systematic
Findings from various
individual studies are
analyzed statistically by
strict procedures. Meta-
Analysis are used to pool
the results of individual
studies.

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ARTICLE LENGTH
 Review article vary considerably in length. Narrative reviews
may range between 8,000 and 40,000 words (references and
everything else included).
 Systematic reviews are usually shorter than 10,000 words.

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ARTICLE
ELEMENTS
 TITLE:
i. Between eight to
12 words
ii. Helping readers to
decide whether they
should read the text
or not.
 LIST OFAUTHORS:
i. Declare intellectual
ownership of the
work.
ii. Provide contact
information.
 ABSTRACT:
i. Informs about the
main objectives and
result of the review
article.
ii. Usually 200 to 250
words.
 INTRODUCTION:
i. Provides info about the
context, indicates the
motivation for the review,
defines the focus, the
research question &
explain the text
ii. Between 10% and 20% of
the core text
 BODY:
i. Methodological approach
ii. Models of theories.
iii. Extent of support for a
given thesis.
iv. Studies that agree with
another vs studies that
disagree
v. Chronological order
vi. Geographical location
vii. 70 to 90% of the core
text.
 CONCLUSION:
i. Answer the
research question
set in the
introduction.
ii. 5 to 10% of the core
text.
 REFERENCE:
i. Shows interested
readers how to find
the literature
mentioned in the
text.
ii. A range between
50-100 refences.

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BENEFITS OF WRITING
A REVIEW PAPER
To identify recent and significant advances and discoveries in a particular field of study.
To determine the main people working in a specific field.
To help identify essential gaps in research to find solutions
They are used in current debates for references
They are good for generating ideas about next field of research
They also help the learner to become an expert in a particular area of study.

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Steps
1. Narrow the topic, define a few research
questions or hypothesis
2. Search for literature sources, refine topic
and research questions during the research
3. Read, evaluate, classify and make notes.
4. Redefine the focus and the research
questions, define the take-home message.
5. Compose a preliminary title.
6. Find a structuring principle for the article.

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Steps
7. Prepare an outline, find headings for the
sections in the different section.
8. Plan the content of each paragraph in the
different sections.
9. Prepare tables, concept maps, figures.
10. Draft the methods section
11. Draft the body section
12. Draft the conclusions

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Steps
13. Draft the introduction
14. Draft the abstract.
15. Revise drafts of different sections, abstract
& title, tables, figures & legends.
16. Revise citations and references.
17. Correct grammar, spelling, punctuation
18. Adjust the layout.

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• As an example to the topic that is being discussed, the following
review article is attached by the name ‘Metagenomics’.
METAGENOMICS :
INTRODUCTION:
The term metagenomics was first used by Jo Handelsman, Jon Clarly, Robert M. Goodman and first
appeared in publication in 1998. Metagenomics defined as “the genomics of analysis of microorganism by
direct extraction and cloning DNA from an assemblage of microorganism”.
It is the study of genetic material recovered directly from environmental samples. (Soil, sea water, human gut).
Metagenomics approaches are becoming increasingly popular in large-scale genomics applications as a way to
study the taxonomic and functional composition of microbial communities from environmental, agricultural, and
clinical settings. Unlike traditional single-genomics approaches, Metagenomics does not rely on having to
singularize individual bacterial clones from complex microbial mixtures, but catalogs by sequencing all genes
and genomes from a mixed community at once (36). The single-isolate approach has been proven successful in
the identification and analysis of diseases caused by essentially a single genotype. However, as practiced in
epidemiological studies, selecting a single colony for sequencing might mask the possibility that a population of
highly similar but still distinguishable individual genotypes may be responsible for the disease phenotype or
outbreak. Moreover, if a sample such as human stool, consisting of genotypes from different bacterial, archaeal,
and eukaryotic species, is to be analyzed, the one-genome-at-a-time approach would not be possible because not
all microbial cells are cultivable. In metagenomics, whole genomic DNA is prepared from samples, regardless of
its microbial composition and is characterized by whole genome sequencing. The assignment of resulting DNA
fragments, individual reads or assembled sequence contigs, to individual taxonomic groups or known genome
sequences is carried out by sophisticated bioinformatics tools.

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For example, a number of tools exist that provide an overview of the species composition of metagenomics samples based on
direct nucleotide sequence compositions (37,38), comparisons of conserved protein domain-coding sequences (38),
identification of 16S rRNA sequences within the sample (39), or oligonucleotide frequencies (40). Other common types of WGS
metagenomics sequence analyses include determination of the functional composition of a microbial community based on the
assignment of protein-coding open reading frames to functional categories, such as protein domain families [Pfam (41)] or Gene
Ontologies [GO (42)]. Consequently, analysis of WGS metagenomics data sets involves a large statistical component, as
sequence data must be evaluated based on relative abundances rather than on absolute presence/absence data. It should be noted
that the metagenomics field is still under active development, and the application of next-generation sequencing technologies is
further changing the metagenomics landscape, increasing the amount of available sequence data to a point where it is now
possible to fully characterize low complexity microbial communities. New types of bioinformatics sequence analyses are
therefore to be expected.
HISTORY :
early metagenomics studies revealed that there are probably large groups of microorganisms in many
environments that cannot be cultured and thus cannot be sequenced. These early studies focused on
16S ribosomal RNA (rRNA) sequences which are relatively short, often conserved within a species, and
generally different between species. Many 16S rRNA sequences have been found which do not belong to any
known cultured species, indicating that there are numerous non-isolated organisms. These surveys of
ribosomal RNA genes taken directly from the environment revealed that cultivation based methods find less
than 1% of the bacterial and archaeal species in a sample. Much of the interest in metagenomics comes from
these discoveries that showed that the vast majority of microorganisms had previously gone unnoticed.
Early molecular work in the field was conducted by Norman R. Pace and colleagues, who used PCR to
explore the diversity of ribosomal RNA sequences. The insights gained from these breakthrough studies led
Pace to propose the idea of cloning DNA directly from environmental samples as early as 1985.] This led to
the first report of isolating and cloning bulk DNA from an environmental sample, published by Pace and
colleagues in 1991 while Pace was in the Department of Biology at Indiana University. Considerable efforts
ensured that these were not PCR false positives and supported the existence of a complex community of
unexplored species. Although this methodology was limited to exploring highly conserved, non-protein
coding genes, it did support early microbial morphology-based observations that diversity was far more
complex than was known by culturing methods. Soon after that, Healy reported the metagenomics isolation of
functional genes from "zoo libraries" constructed from a complex culture of environmental organisms grown
in the laboratory on dried grasses in 1995.

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HISTORICAL EVENTS IN METAGENOMICS:
 In 1985, Pace and coworker introduced the idea of directly from environmental samples.
 In 1991 Schmidt and coworker cloning of DNA from Picoplankton in a phase vector subsequent 16S
rRNA gene sequence analyses.
 In 1995, Healy reported first successful function driven metagenomics library was screened and termed
that Zoolibraies.
 In, 2002, Mya Breitbart and Forest Rohwer, used shotgun sequencing to show that 200 liters of seawater
contain over 5000 different viruses.
TYPES OF METAGENOMICS
There are two basic types of Metagenomics studies:
I. Sequence-based Metagenomics- involves sequencing and analysis of DNA from environmental samples.
II. Function-based Metagenomics involves screening for a particular function or activity.
APPLICATIONS OF METAGENOMICS:
Metagenomics has the potential to advance knowledge
in a wide variety of field.
I. Medicine
II. Engineering
III. Agriculture
IV. Ecology
V. Biotechnology
APPLICATIONS:
Metagenomics is the culture-independent genomic research of microbial communities. Metagenomics
presents a powerful tool to study prokaryotes and viruses in the environment via the analysis of their DNA
obtained directly from environmental samples. This technology considers the DNA of microbes in a

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population as a whole. It can not only identify the microbial of microbial species present but also provide insight into the
functional roles and metabolic activities of the microorganisms. The coupling of this method with function-based activity is a
powerful technique for the discovery of new functional genes from uncultured microbes. It has the potential to advance
knowledge in a wide variety of field.
- Medicine
- Engineering
- Agriculture
- Ecology
- biotechnology

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Biotechnological applications
Currently, there is a global political drive to promote white biotechnology as a key feature of modern
industrialized society. Metagenomics has the potential to substantially impact industrial production.
Bioactive compounds:
Unique bioactive compounds have been identified through metagenomics studies, including terragines,
violacein, and indirubin. Drugs originated from marine microorganisms, such as cytarabine (anti-cancer),
cephalosporins (anti-microbial), and vidarabine (anti-virus), have been established on the pharmaceutical
market.
Antibiotics:
Novel antibiotics and enzymes are among the early discoveries from metagenomics. The discovery of
streptomycin, turbomycin, and other antibiotics sprang from basic studies of the soil microbiome. Functional
metagenomics serves to find novel antibiotics or novel antibiotic resistance genes, and descriptive
metagenomics serves to analyze changes in the composition of the microbiome and to track the presence and
abundance of known antibiotic resistance genes in different environments.
Enzymes:
New genetic information on industrial enzymes, such as lipases, proteases, lyases, amylases, nitrilases, has
been produced by metagenomics approaches. Enzymes have a wide range of applications, including the
production of highly active pharmaceuticals and active ingredients (such as high-performance laundry
detergents). The versatility of industrial enzymes allows their use in the processes to degrade natural polymers
such as cellulose, proteins and starch, as well as for the synthesis of asymmetric chemicals.
LATEST RESEARCH & REVIEWS:
1] Application of metagenomics in the human gut microbiome.
Wang WL, Xu SY, Ren ZG, Tao L, Jiang JW, Zheng SS
2] Bioinformatics for NGS-based metagenomics and the application to biogas research
Sebastian Jünemann, Nils Kleinbölting, Sebastian Jaenicke, Christian Henke, Julia Hassa, Johanna
Nelkner, Yvonne Stolze, Stefan P Albaum, Andreas Schlüter, Alexander Goesmann, Alexander Sczyrba, Jens
Stoye
3] Metagenomics as a Tool To Monitor Reclaimed-Water Quality
Pei-Ying Hong, David Mantilla-Calderon, Changzhi Wang

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LIMITATIONS:
• Too much data.
• Most gene are not identifiable
• Contamination, chimeric clone sequences
• Extraction problem
• Requires proteomics or expression studies to demonstrate phenotypic characteristics
• Need a standard method for annotating genomes
• Can only progress as library technology progresses, including sequencing technology.
• Requires high throughput instrumentation not readily available to most institutions.
REFERENCES:
1. Review on Metagenomics and its Applications
-Asiya Nazir, Department of College of Arts and Sciences, Abu Dhabi University, Abu Dhabi 59911,
UAE
2. Metagenomics and its application
- Pradeep Kumar, Sardar Vallabhbhai Patel University of Agriculture and Technology
3. Applications of Metagenomics in Biotechnology and Health Care
- https://www.cd-genomics.com/
4. Genomics
-Microbial Forensics (Second Edition) 2011 : W. Florian Fricke, Jacques Ravel

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 Review articles Establishes the validity of research based
upon the expert knowledge of other researchers in the
discipline, therefore preventing falsified work from being
accepted within an area of study. It Provides valuable
feedback so that researchers can revise and improve their
papers before publication.
 Enables journal editors to select the most important research
findings for publication in their journals, based upon the
objective, independent reviews of an expert group.
 Review articles helps the researchers to establish a link
between the topic of discussion and the research work.
So, importance of review articles can’t be nullified.
CONCLUDING REMARKS

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 How-to-write-review-article:
-authorservices.taylorandfrancis.com
 How to write a review article?:
- Ömer Gülpınar and Adil Güçal Güçlü, Turkish Journal of Urology,
2013 Sep; 39(Suppl 1): 44–48
 Review on Metagenomics and its Applications
-Asiya Nazir, Department of College of Arts and Sciences, Abu Dhabi
University, Abu Dhabi 59911, UAE
 Metagenomics and its application
- Pradeep Kumar, Sardar Vallabhbhai Patel University of Agriculture
and Technology
 Applications of Metagenomics in Biotechnology and
Health Care
- https://www.cd-genomics.com/
 Genomics
-Microbial Forensics (Second Edition) 2011 : W. Florian Fricke,
Jacques Ravel
REFERENCES

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THANK YOU