This pattern makes an oval-shaped bacterium about 4 inches long (that's about 50,000 times actual size).
Row 1: Cast on 3 sts, and push these sts to the other end of the needle as if making I-cord.
Row 2: Kfb in each stitch with a new needle. At the end you should have 2 stitches on each of 3 needles. That was the hard part; the rest is easy.
Row 3: Kfb across - now you have 4 sts/needle
Row 4: (K1, M1, K3) across - 5 sts/needle
Row 5: K across
Row 6: (K1, M1, K4) across - 6 sts/needle
Row 7: K across
Row 8: (K1, M1, K5) across - 7 sts/needle
Row 9: K across
Row 10: (K1, M1, K6) across - 8 sts/needle
K plain for 15-20 rows, or as long as you like.
Now is a good time to add the face (insert eyes, embroider mouth, etc). The "head" is the end of the bacterium you have already made. When you're done, add some stuffing and continue knitting.
The decreases mirror the increases, so the bacterium is roughly symmetrical.
Row 21: (K1, K2tog, K5) across - 7 sts/needle
Row 22: K
Row 23: (K1, K2tog, K4) across - 6 sts/needle
Row 24: K
Row 25: (K1, K2tog, K3) across - 5 sts/needle
Don't forget to finish adding stuffing before the opening gets too small!Row 26: (K1, K2tog, K2) across - 4 sts/needle
Cut off yarn leaving a longish tail. Use a yarn needle to draw tail through remaining stitches like a drawstring. Secure the tail with a knot, if desired, and hide the end inside the bacterium body.
Cilia or small flagella: cut lengths of yarn about 4" long. Fold a piece of yarn in half. Use a crochet hook to pull the folded yarn halfway through a loop of knitting. Pull the ends of the folded yarn through the folded end (this is a knot known as a "ring knot").
Large flagella: pick up 3 sts in the desired place (probably the bottom end of the bacterium's body). Work these in I-cord until flagellum is desired length. Bind off and hide the tail of yarn inside the I-cord.
I typically use a worsted-weight soft acrylic yarn, since it's cheap, soft, and washable. Cotton or machine-washable wool substitutes well. If the label suggests using a size 8 needle, for example, use a set of size 4 or size 6 needles instead. This produces a tight fabric that holds the stuffing in well.
Some people like to felt their stuffed animals. To do this, use wool that is NOT labeled as machine-washable. Knit the bacterium's body on regular size needles (the same size the label recommends - about a size 8 for worsted weight). Put the eyes in if they're plastic but don't add any embroidery or other details. Throw the bacterium in the washing machine! It will come out slightly smaller, and with its wool fibers all matted into a solid fabric. Look up "fulling" and "felting" for more information on this process. Once the bacterium is rinsed and dry, continue with your embroidery and embellishment.
If you're looking for an acrylic, try Red Heart Soft Yarn. If you're looking for a feltable wool, try Patons Classic Merino.