MIB200A at UCDavis Module: Microbial Phylogeny; Class 1

Class 1:
MIB200
Biology of Prokaryotes
Class #1:
Introduction
UC Davis, Fall 2019
Instructor: Jonathan Eisen
1

Questions?
• Experience level reading scientific papers?
• Experience level writing scientific papers?
• Experience level discussing scientific papers?

Raff J. How to Read and Understand a Scientific Article
1. Begin by reading the introduction, not the abstract.
The abstract is that dense first paragraph at the very
beginning of a paper. In fact, that's often the only part of a
paper that many non-scientists read when they're trying to
build a scientific argument. (This is a terrible practice.
Don't do it.) I always read the abstract last, because it
contains a succinct summary of the entire paper, and I'm
concerned about inadvertently becoming biased by the
authors' interpretation of the results.
https://violentmetaphors.files.wordpress.com/2018/01/how-to-read-and-understand-a-scientific-article.pdf

2. Identify the big question. 
Not "What is this paper about?" but "What problem is this
entire ﬁeld trying to solve?" This helps you focus on why
this research is being done. Look closely for evidence of
agenda-motivated research.

3. Summarize the background in ﬁve sentences or less.
What work has been done before in this ﬁeld to answer the
big question? What are the limitations of that work? What,
according to the authors, needs to be done next? You need
to be able to succinctly explain why this research has been
done in order to understand it.

4. Identify the speciﬁc question(s). 
What exactly are the authors trying to answer with their
research? There may be multiple questions, or just one.
Write them down. If it's the kind of research that tests one
or more null hypotheses, identify it/them.

5. Identify the approach.
What are the authors going to do to answer the speciﬁc
question(s)?

6. Read the methods section.
Draw a diagram for each experiment, showing exactly
what the authors did. Include as much detail as you need
to fully understand the work.

7. Read the results section.
Write one or more paragraphs to summarize the results for each experiment,
each figure, and each table. Don't yet try to decide what the results mean; just
write down what they are. You'll often find that results are summarized in the
figures and tables. Pay careful attention to them! You may also need to go to
supplementary online information files to find some of the results. Also pay
attention to:
• The words "significant" and "non-significant." These have precise
statistical meanings.
• Graphs. Do they have error bars on them? For certain types of studies, a
lack of confidence intervals is a major red flag.
• The sample size. Has the study been conducted on 10 people, or 10,000
people? For some research purposes a sample size of 10 is sufficient, but for
most studies larger is better.

8. Determine whether the results answer the speciﬁc
question(s).  
What do you think they mean? Don't move on until you
have thought about this. It's OK to change your mind in
light of the authors' interpretation -- in fact, you probably
will if you're still a beginner at this kind of analysis -- but
it's a really good habit to start forming your own
interpretations before you read those of others.  

9. Read the conclusion/discussion/interpretation
section.  
What do the authors think the results mean? Do you agree
with them? Can you come up with any alternative way of
interpreting them? Do the authors identify any weaknesses
in their own study? Do you see any that the authors
missed? (Don't assume they're infallible!) What do they
propose to do as a next step? Do you agree with that?  

10. Go back to the beginning and read the abstract.  
Does it match what the authors said in the paper? Does it
ﬁt with your interpretation of the paper?

11. Find out what other researchers say about the
paper.
Who are the (acknowledged or self-proclaimed) experts in
this particular ﬁeld? Do they have criticisms of the study
that you haven't thought of, or do they generally support
it? Don't neglect to do this! Here's a place where I do
recommend you use Google! But do it last, so you are
better prepared to think critically about what other people
say.

Two papers for today
Proc. Natl. Acad. Sci. USA
Vol. 74, No. 11, pp. 5088-5090, November 1977
Evolution
Phylogenetic structure of the prokaryotic domain: The primary
kingdoms
(archaebacteria/eubacteria/urkaryote/16S ribosomal RNA/molecular phylogeny)
CARL R. WOESE AND GEORGE E. Fox*
Department of Genetics and Development, University of Illinois, Urbana, Illinois 61801
Communicated by T. M. Sonneborn, August 18,1977
ABSTRACT A phylogenetic analysis based upon ribosomal
RNA sequence characterization reveals that living systems
represent one of three aboriginal lines of descent: (i) the eu-
bacteria, comprising all typical bacteria; (ii) the archaebacteria,
containing methanogenic bacteria; and (iii) the urkaryotes, now
represented in the cytoplasmic component of eukaryotic
cells.
The biologist has customarily structured his world in terms of
certain basic dichotomies. Classically, what was not plant was
animal. The discovery that bacteria, which initially had been
considered plants, resembled both plants and animals less than
plants and animals resembled one another led to a reformula-
tion of the issue in terms of a yet more basic dichotomy, that of
eukaryote versus prokaryote. The striking differences between
eukaryotic and prokaryotic cells have now been documented
to construct phylogenetic classifications between do
Prokaryotic kingdoms are not comparable toeukaryoti
This should be recognized by,an appropriate terminolog
highest phylogenetic unit in the prokaryotic domain we
should be called an "urkingdom"-or perhaps "pr
kingdom." This would recognize the qualitative dist
between prokaryotic and eukaryotic kingdoms and emp
that the former have primary evolutionary status.
The passage from one domain to a higher one then be
a central problem. Initially one would like to know wheth
is a frequent or a rare (unique) evolutionary event. It i
tionally assumed-without evidence-that the euka
domain has arisen but once; all extant eukaryotes stem
common ancestor, itself eukaryotic (2). A similar prejudic
for the prokaryotic domain (2). [We elsewhere argue (15

Evolution
kingdoms
ABSTRACT A phylogenetic analysis based upon ribosomal
RNA sequence characterization reveals that living systems
represent one of three aboriginal lines of descent: (i) the eu-
bacteria, comprising all typical bacteria; (ii) the archaebacteria,
containing methanogenic bacteria; and (iii) the urkaryotes, now
represented in the cytoplasmic component of eukaryotic
cells.
The biologist has customarily structured his world in terms of
certain basic dichotomies. Classically, what was not plant was
animal. The discovery that bacteria, which initially had been
considered plants, resembled both plants and animals less than
plants and animals resembled one another led to a reformula-
tion of the issue in terms of a yet more basic dichotomy, that of
eukaryote versus prokaryote. The striking differences between
eukaryotic and prokaryotic cells have now been documented
to construct phylogenetic classifications between do
Prokaryotic kingdoms are not comparable toeukaryoti
This should be recognized by,an appropriate terminolog
highest phylogenetic unit in the prokaryotic domain we
should be called an "urkingdom"-or perhaps "pr
kingdom." This would recognize the qualitative dist
between prokaryotic and eukaryotic kingdoms and emp
that the former have primary evolutionary status.
The passage from one domain to a higher one then be
a central problem. Initially one would like to know wheth
is a frequent or a rare (unique) evolutionary event. It i
tionally assumed-without evidence-that the euka
domain has arisen but once; all extant eukaryotes stem
common ancestor, itself eukaryotic (2). A similar prejudic
for the prokaryotic domain (2). [We elsewhere argue (16

1. Begin by reading the introduction, not the abstract
2. Identify the big question.
3. Summarize the background in ﬁve sentences or less.
4. Identify the speciﬁc question(s).
5. Identify the approach.

Woese and Fox Methods
What is ribosomal RNA?

Woese and Fox Methods
Why Use ribosomal RNA for this?

Methods Question: Why Use rRNA for this?
• Universal
• Highly conserved functionally
• Evolves slowly
• Easy to extract and sequence
• Can compare sequences between species and used
to infer relationships

Woese and Fox Results: SAB Table For 13 Species

Woese and Fox Results: Kingdom #1

Type to enter text

Woese and Fox Results: Kingdom 2

Woese and Fox Results: Kingdom 3

Woese and Fox Results: Three Kingdoms

Type to enter text
Is There Another Way to View This?

Class 1:
MIB200
Biology of Prokaryotes
Organisms without Nuclei
Class #1:
Introduction
UC Davis, Fall 2019
Instructor: Jonathan Eisen
61

Evolution
kingdoms
ABSTRACT A phylogenetic analysis based upon ribosomal to construct phylogenetic classifications between do
67

• Although we have yet to determine even the outlines of the
bacterial tree, common threads are beginning to emerge that
revise our current views of bacterial diversity and distribution in
the environment.
Hugenholtz et al

• These relatedness groups have variously been called
“kingdoms,” “phyla,” and “divisions”; we use the latter term.
• For the purposes of this review we define a bacterial division
purely on phylogenetic grounds as a lineage consisting of two
or more 16S rRNA sequences that are reproducibly
monophyletic and unaffiliated with all other division-level
relatedness groups that constitute the bacterial domain
• We judge reproducibility by the use of multiple tree-building
algorithms, bootstrap analysis, and varying the composition
and size of data sets used for phylogenetic analyses.
Hugenholtz et al

• Division-level nomenclature has not even been consistent
between studies, so some divisions are identified by more
than one name. For instance, green sulfur bacteria is
synonymous with Chlorobiaceae; high- G C gram-positive
bacteria is synonymous with Actinobacteria and
Actinomycetales. Indeed, it probably is premature to
standardize taxonomic rankings for bacterial divisions at this
point when our picture of microbial diversity is likely still
incomplete and the topology of the bacterial tree is still
unresolved.

• Figure 1 represents the division-level diversity of the bacterial
domain as inferred from representatives of the approximately
8,000 bacterial 16S rRNA gene sequences currently available.
Although 36 divisions are shown in Fig. 1, several other
division-level lineages are indicated by single environmental
sequences (9, 21, 37), suggesting that the number of bacterial
divisions may be well over 40.

FIG. 1.
Evolutionary distance tree of the
bacterial domain showing currently
recognized divisions and putative
(candidate) divisions. The tree was
constructed using the ARB
software package (with the Lane
mask and Olsen rate-corrected
neighbor-joining options) and a
sequence database modified from
the March 1997 ARB database
release (43). Division-level
groupings of two or more
sequences are depicted as
wedges. The depth of the wedge
reflects the branching depth of the
representatives selected for a
particular division. Divisions which
have cultivated representatives
are shown in black; divisions
represented only by environmental
sequences are shown in outline.
The scale bar indicates 0.1
change per nucleotide. The
aligned, unmasked data sets used
for this figure and Fig. 3 through
6are available from http://
crab2.berkeley.edu/pacelab/
176.htm.
74

• Indeed, 13 of the 36 divisions shown in Fig. 1 are characterized
only by environmental sequences (shown outlined) and so are
termed “candidate divisions” new bacterial divisions
• One of these candidate divisions, OP11, is now sufficiently well
represented by environmental sequences to conclude that it
constitutes a major bacterial group (see below).
• Phylogenetic studies so far have not resolved branching
orders of the divisions; bacterial diversity is seen as a fan-like
radiation of division-level groups (Fig. 1). The exception to this,
however, is the Aquificales division, which branches most
deeply in the bacterial tree in most analyses.
•

FIG. 2.
Relative representation in
selected cosmopolitan
bacterial divisions of 16S
rRNA sequences from
cultivated and uncultivated
organisms. Results were
compiled from 5,224 and
2,918 sequences from
cultivated and uncultivated
organisms, respectively.
79

• The database of environmental rRNA sequences is compromised in resolving
some phylogenetic issues by a large number of relatively short sequences.
More than half of the sequences collated in Table 1 are less than 500
nucleotides (nt) long, which represents only one-third of the total length of
16S rRNA. This is due to an unfortunate trend in many environmental studies
of sequencing only a portion of the gene in the belief that a few hundred
bases of sequence data is sufficient for phylogenetic purposes. Indeed, 500
nt is sufficient for placement if some longer sequence is closely related ( 90%
identity in homologous nucleotides) to the query sequence. In the case of
novel sequences, 85% identical to known sequences, however, 500 nt is
usually insufficient comparative information to place the sequence accurately
in a phylogenetic tree and can even be misleading

Acidobacterium
FIG. 3.
Phylogenetic dendrogram of the Acidobacterium division.
Names of cultivated organisms are shown in bold. The
habitat source of each environmental sequence is indicated
before the clone name. GenBank accession numbers are
listed parenthetically. Subdivisions (see the text) are
indicated by brackets at the right of the tree. Construction
of the tree was as described for Fig. 1. The robustness of
the topology presented was estimated by bootstrap
resampling of independent distance, parsimony, and rate-
corrected maximum-likelihood analyses as previously
described (2). Distance and parsimony analyses were
conducted using test version 4.0d61 of PAUP*, written by
David L. Swofford. Branch points supported (bootstrap
values of >75%) by most or all phylogenetic analyses are
indicated by filled circles; open circles indicate branch
points marginally supported (bootstrap values of 50 to
74%) by most or all analyses. Branch points without circles
are not resolved (bootstrap values of <50%) as specific
groups in different analyses. The scale bar indicates 0.1
change per nucleotide.
81

Verrucomicrobia
FIG. 4.
Phylogenetic dendrogram of the
Verrucomicrobia division. Names of
cultivated organisms are shown in
bold. The habitat source of each
environmental sequence is indicated
before the clone name. GenBank
accession numbers are listed
parenthetically. Subdivisions (see the
text) are indicated by brackets at the
right of the tree. Tree construction
and support for branch points was as
described for Fig. 1 and 3,
respectively. The scale bar indicates
0.1 change per nucleotide.
82

Green non sulfur
FIG. 5.
GNS division. Names of cultivated
organisms are shown in bold. The
habitat source of each environmental
sequence is indicated before the
clone name. GenBank accession
numbers are listed parenthetically.
Subdivisions (see the text) are
indicated by brackets at the right of
the tree. Tree construction and
support for branch points was as
d e s c r i b e d f o r F i g . 1 a n d 3 ,
respectively. The scale bar indicates
0.1 change per nucleotide.
83

OP11
FIG. 6.
OP11 division. The habitat source
of each environmental sequence
is indicated before the clone
name. GenBank accession
n u m b e r s a r e l i s t e d
parenthetically. Subdivisions (see
the text) are indicated by brackets
at the right of the tree. Tree
construction and support for
branch points was as described
for Fig. 1 and 3, respectively. The
four MIM clones and F78 clone
are unreleased sequences
generously made available to us
by Pascale Durand (10) and
Floyd Dewhirst (8). The scale bar
indicates 0.1 change per
nucleotide.
84

Conclusions
• novelties are known as well, for instance, endospore formation by the
low-G C gram-positive bacteria or axial filaments (endoflagella) in the
spirochetes. Some biochemical properties evidently have transferred
laterally among the divisions. For example, the two types of
photosynthetic complexes, photosystem I (PSI) and PSII, are each
distributed sporadically among the divisions, consistent with lateral
transfer (3). Lateral transfer may also have resulted in combinatorial
novelty among the divisions; PSI and PSII, for instance, apparently
came together in the cyanobacteria to create oxygenic
photosynthesis, with profound consequences to the biosphere (3).
• Many more such division-specific qualities and cooperations should
become evident at the molecular level as comparative genomics
gives us a sharper phylogenetic picture of bacterial diversity.

• PCR and microbial community surveys possible issues
• Where could this go “wrong”?
•

MIB200A at UCDavis Module: Microbial Phylogeny; Class 1

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